https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&feedformat=atom&user=Zm714ChemWiki - User contributions [en]2026-05-18T19:54:45ZUser contributionsMediaWiki 1.43.0https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734544Rep:Mod:1SC2018-10-05T14:53:15Z<p>Zm714: /* Part 2: Epoxides and their reactions */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian <ref name=G>M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview <ref name=G /> to conduct calculations. Some of your calculations may take several hours to run, even on the HPC! As such, we advise that you use your time wisely. For example, you could run your calculations overnight (but make sure that you know that they won't fail within one second of running!) and write up your wiki and conduct research and run smaller calculations during the day. It is completely up to you where you work or when you run your simulations.<br />
<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this as you progress through this lab. You will need to conduct research and consult experimental results/ other published computational simulations at various points in order to verify the validity of your results - this is what happens in computational research!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. You can run these calculations either on the College Desktop computers or the HPC. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by Kureshy <i>et al</i> who used Jacobson like catalysts to do the above. <ref>R. Kureshy, S. Singh, N. H. Khan, H. R. Abdi, S. Agrawal, R. V. Jasra; <i>Tetrahedron Asymmetry</i>; <b>17</b>; 11; 2006; DOI: https://doi.org/10.1016/j.tetasy.2006.05.029 </ref> <br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734543Rep:Mod:1SC2018-10-05T14:45:09Z<p>Zm714: /* Introduction */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian <ref name=G>M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview <ref name=G /> to conduct calculations. Some of your calculations may take several hours to run, even on the HPC! As such, we advise that you use your time wisely. For example, you could run your calculations overnight (but make sure that you know that they won't fail within one second of running!) and write up your wiki and conduct research and run smaller calculations during the day. It is completely up to you where you work or when you run your simulations.<br />
<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this as you progress through this lab. You will need to conduct research and consult experimental results/ other published computational simulations at various points in order to verify the validity of your results - this is what happens in computational research!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. You can run these calculations either on the College Desktop computers or the HPC. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734542Mod:Lab Toolbox2018-10-05T14:44:01Z<p>Zm714: </p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian <ref name=G> M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview <ref name=G/> window. A calculation was set up with the following: <ref name=HRL>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview <ref name=G /> or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. What could be the differences for these values, both computational and experimental?<br />
<br />
==Enantiomeric excess <ref name=HRL/>==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. Methods to develop chiral catalysts which synthesise one enantiomer over another are therefore highly valued. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734541Mod:Lab Toolbox2018-10-05T14:42:47Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian <ref name=G> M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview <ref name=G/> window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview <ref name=G /> or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. What could be the differences for these values, both computational and experimental?<br />
<br />
==Enantiomeric excess <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref>==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. Methods to develop chiral catalysts which synthesise one enantiomer over another are therefore highly valued. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734540Mod:Lab Toolbox2018-10-05T14:38:15Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian <ref>M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview <ref>M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview <ref>M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. What could be the differences for these values, both computational and experimental?<br />
<br />
==Enantiomeric excess <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref>==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. Methods to develop chiral catalysts which synthesise one enantiomer over another are therefore highly valued. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734539Rep:Mod:1SC2018-10-05T14:36:46Z<p>Zm714: /* Introduction */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview <ref>M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. J. Montgomery, J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian 09, Revision D.01, Wallingford CT, 2013.</ref> to conduct calculations. Some of your calculations may take several hours to run, even on the HPC! As such, we advise that you use your time wisely. For example, you could run your calculations overnight (but make sure that you know that they won't fail within one second of running!) and write up your wiki and conduct research and run smaller calculations during the day. It is completely up to you where you work or when you run your simulations.<br />
<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this as you progress through this lab. You will need to conduct research and consult experimental results/ other published computational simulations at various points in order to verify the validity of your results - this is what happens in computational research!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. You can run these calculations either on the College Desktop computers or the HPC. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734538Mod:Lab Toolbox2018-10-05T14:34:58Z<p>Zm714: /* Enantiomeric excess https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. What could be the differences for these values, both computational and experimental?<br />
<br />
==Enantiomeric excess <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref>==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. Methods to develop chiral catalysts which synthesise one enantiomer over another are therefore highly valued. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734537Mod:Lab Toolbox2018-10-05T14:33:48Z<p>Zm714: /* Enantiomeric excess */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. What could be the differences for these values, both computational and experimental?<br />
<br />
==Enantiomeric excess <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref>==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734536Mod:Lab Toolbox2018-10-05T14:33:07Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. What could be the differences for these values, both computational and experimental?<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734535Mod:Lab Toolbox2018-10-05T14:30:29Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. Differences can arise in this case because of the several different forms fructose can exist in.<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734534Mod:Lab Toolbox2018-10-05T14:30:09Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
<i><b>Insert energy chemdraw here of fructose.</b></i><br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. Differences can arise in this case because of the several different forms fructose can exist in.<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734533Mod:Lab Toolbox2018-10-05T14:26:59Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <ref>https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic</ref><br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. Differences can arise in this case because of the several different forms fructose can exist in.<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734532Mod:Lab Toolbox2018-10-05T14:25:28Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = + 131° and the literature value reported is + 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. Differences can arise in this case because of the several different forms fructose can exist in.<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734531Mod:Lab Toolbox2018-10-05T14:15:01Z<p>Zm714: /* Basis Sets */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding of what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = 131° and the literature value reported is 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. Differences can arise in this case because of the several different forms fructose can exist in.<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734530Mod:Lab Toolbox2018-10-05T14:14:19Z<p>Zm714: /* Basis Sets */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = 131° and the literature value reported is 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. Differences can arise in this case because of the several different forms fructose can exist in.<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734432Mod:Lab Toolbox2018-09-24T17:17:30Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a Grimme dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = 131° and the literature value reported is 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref>. Differences can arise in this case because of the several different forms fructose can exist in.<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734431Mod:Lab Toolbox2018-09-24T17:16:45Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a Grimme dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussian09/Gaussview or on the Imperial HPC.<br />
<br />
We find our calculated result gives [α]<sub>589 nm</sub> = 131° and the literature value reported is 95° <ref>Hricoviniova-Bilikova, Zuzana; Hricovini, Milos; Petrusova, Maria; Serianni, Anthony S.; Petrus, Ladislav; Carbohydrate Research, 1999, vol. 319, 1-4, p. 38 - 46</ref><br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734430Mod:Lab Toolbox2018-09-24T17:08:44Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a Grimme dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (+) and (-)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab. Here, we have conducted an optical rotation on L-Fructose.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find our calculated result gives [α]<sub>589 nm</sub> = 131°<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734429Mod:Lab Toolbox2018-09-24T17:05:13Z<p>Zm714: /* Basis Sets */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a Grimme dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. For this work, we are not looking at the effects of dispersion however they are important in many systems. <ref>S. Grimme, J. Antony, S. Ehrlich and H. Krieg, J. Chem. Phys.,2010, 132, 1-19 DOI:10.1063/1.3382344.</ref><ref>S. Grimme, S. Ehrlich and L. Goerigk, J. Comput. Chem., 2011, 32, 1456–1465.</ref><ref>S. Grimme, A. Hansen, J. G. Brandenburg and C. Bannwarth, Chem. Rev., 2016, 116, 5105–5154.</ref><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734428Mod:Lab Toolbox2018-09-24T16:55:11Z<p>Zm714: /* Basis Sets */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a Grimme dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. <b>Grimme reference required</b><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
Use the keyword below in all calculations:<br />
<br />
<pre><br />
integral=grid=ultrafine<br />
</pre><br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734427Mod:Lab Toolbox2018-09-24T16:49:25Z<p>Zm714: /* Basis Sets */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). <br />
<br />
The B3LYP functional has been selected since due to its hybrid nature and therefore potential for more accurate results. This functional is, however, not good alone for modelling dispersion interactions and therefore either a Grimme dispersion term must be added to the end e.g. B3LYP-D3 or a new functional must be selected. <b>Grimme reference required</b><br />
<br />
There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report. The same logic applies to selecting a functional.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734426Rep:Mod:1SC2018-09-24T16:43:50Z<p>Zm714: /* Part 2: Epoxides and their reactions */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview to conduct calculations. Some of your calculations may take several hours to run, even on the HPC! As such, we advise that you use your time wisely. For example, you could run your calculations overnight (but make sure that you know that they won't fail within one second of running!) and write up your wiki and conduct research and run smaller calculations during the day. It is completely up to you where you work or when you run your simulations.<br />
<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this as you progress through this lab. You will need to conduct research and consult experimental results/ other published computational simulations at various points in order to verify the validity of your results - this is what happens in computational research!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. You can run these calculations either on the College Desktop computers or the HPC. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734425Mod:Lab Toolbox2018-09-24T14:59:38Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1d)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734424Mod:Lab Toolbox2018-09-24T14:30:14Z<p>Zm714: /* Basis Sets */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer or in good time on the HPC. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and what a basis set is. Does the functional or basis set determine the Hamiltonian used for calculations?<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734423Mod:Lab Toolbox2018-09-20T13:05:01Z<p>Zm714: /* Basis Sets */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. You are also advised to research the size of the basis sets and report and discuss any relevant findings.<br />
<br />
It is best to watch the video on DFT at this point to get a better understanding od what is going on in a chemical simulation with DFT, and which part of the Hamiltonian is important in basis set selection.<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734422Mod:Lab Toolbox2018-09-19T17:23:45Z<p>Zm714: /* Enantiomeric excess */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers have different effects on the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734419Mod:Lab Toolbox2018-09-13T16:12:30Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
Other information<br />
...blank line...<br />
589nm<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers are not processed by the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734418Mod:Lab Toolbox2018-09-13T15:06:15Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
<br />
%chk=\\icnas4.cc.ic.ac.uk\...<br />
# b3lyp/6-31++g(d,p) scrf=(cpcm,solvent=water) geom=connectivity<br />
integral=grid=ultrafine polar(optrot) CPHF=RdFreq<br />
<br />
Title Card Required<br />
<br />
0 1<br />
x,y,z co-ordinates and atoms<br />
...<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
589nm<br />
...blank line...<br />
Other<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers are not processed by the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734417Mod:Lab Toolbox2018-09-13T15:05:07Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 and 2 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
---insert input line here-----------------------<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
589nm<br />
...blank line...<br />
Other<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers are not processed by the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734416Mod:Lab Toolbox2018-09-13T15:04:30Z<p>Zm714: /* Enantiomeric excess */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
---insert input line here-----------------------<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
589nm<br />
...blank line...<br />
Other<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in the pharmaceutical industry for medicines, as some enantiomers are not processed by the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above. Refer to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction this page] for additional information.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734415Mod:Lab Toolbox2018-09-13T15:02:49Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
---insert input line here-----------------------<br />
</pre><br />
<b>3)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
589nm<br />
...blank line...<br />
Other<br />
</pre><br />
<br />
<b>4)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in teh pharmaceutical industry for medicines, as some enantiomers are not processed by the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734414Mod:Lab Toolbox2018-09-13T15:02:09Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is found naturally in foods such as honey and various fruits. It is one of the sweetest sugars and is produced from starch or sucrose, amongst other methods. <ref>W. Wach; Ullmanm's encyclopedia of Industrial Chemistry; <i>Wiley-VCH</i>; 2012; DOI: 10.1002/14356007.a12_047.pub2</ref> The Shi catalyst is also is derived from fructose. <br />
<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<b>3)</b> The input line containing the keywords (usually the second line was edited to contain the additional: <b>polar(optrot) cphf=rdfreq</b>.<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
---insert input line here-----------------------<br />
</pre><br />
<b>4)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
589nm<br />
...blank line...<br />
Other<br />
</pre><br />
<br />
<b>5)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in teh pharmaceutical industry for medicines, as some enantiomers are not processed by the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Mod:Lab_Toolbox&diff=734413Mod:Lab Toolbox2018-09-13T14:14:21Z<p>Zm714: /* Fructose */</p>
<hr />
<div>==Basis Sets==<br />
<br />
In this lab, a functional has been provided for you (B3LYP) and you much select which basis set to use (3-21+G, 6-31++G(d,p), 6-311++G(d,p)). There are various factors which need to be considered when selecting a basis set for calculations. Ideally, you will read various literature surrounding the subject, evaluating the suitability of the basis set for your computational investigations.<br />
Several different basis sets exist and you must determine what differentiates each basis set from another and make a judgement on which is best to use for the particular task. Bond lengths, angles etc are a potential method for this, but there are drawbacks - some of which you should discuss in your report.<br />
<br />
In this case, in addition, you will need to to consider the time it takes to run calculations using the different basis sets and whether they can be successfully completed in the time allocated on your desktop computer. <br />
<br />
It is best to watch the video on DFT and basis sets at this point to get a better understanding od what is going on in a chemical simulation with DFT and what a basis set actually is<br />
<br />
==Fructose==<br />
<br />
Fructose is a sugar which is used in ......<br />
<br />
It is well established that Fructose can exist in five different forms in solution: the open ring, α-D-fructopyranse, β-D-fructopyranose, α-D-fructofuranose and β-D-fructofuranose.<br />
Experiments determined that two of these forms dominate the equilibrium between the five forms in water. These are the β-D-fructopyranose (~68%) and β-D-fructofuranose (~32%). Dissolved in other solvents, different ratios of each of the forms dominates. <ref>R. S. Shallenberger; Pure & Appi. Chem. Vol. 50, pp. 1409—1420 </ref>.<br />
Assuming, however, that each of these forms exists in equilibrium in a vacuum, it is possible to determine which forms of fructose are the most stable at 25 °C. It can be seen from the figure below that the most stable are the pyranose forms, then the furanose and then the open chain. This allows us to determine the relative stability of the structures. It is also important to note at this point that energies can be compared because there are same number and type of atoms on each isomer, and the same level of theory (i.e. basis set and functional) has been used for all calculations. Running frequency calculations allows one to find out the energy of the molecule at 25 °C.<br />
<br />
<center>[[File:Diagram_of_eq_zm714.png|300px|center|thumb|left|<b>Fig. 1</b> Equilibrium of fructose. Adapted from 1 ]]</center><br />
<br />
Fructose can exist as a pair of enantiomers, L and D-Fructose. It is often more common to see these as (-) and (+)-Fructose, which is indicative of the rotation of the plane of polarised light. Whilst there are several other methods (which can also be calculated using G09) to determining whether two molecules are enantiomers, such as ECD and VCD, optical rotation is the one which can easily be carried out in the lab.<br />
<br />
In order to determine the optical rotation of fructose, it is necessary to add some additional keywords to the Gaussian .gif file after it has been generated and saved, but not run.<br />
<br />
<b>1)</b> The output from any prior optimisation and frequency analysis of the open chain of fructose was copied into a new Gaussview window. A calculation was set up with the following: <br />
<br />
<b>1a)</b> An Energy calculation was conducted<br />
<br />
<b>1b)</b> The solvation of the system was set to CPCM, and water as a solvent.<br />
<br />
<b>1c)</b> The additional keywords <b>polar(optrot) cphf=rdfreq</b> were added to the input line.<br />
<br />
<b>1c)</b> The job was saved but not run.<br />
<br />
<b>2)</b> The corresponding .gif file for that molecule was opened using Notepad++<br />
<br />
<b>3)</b> The input line containing the keywords (usually the second line was edited to contain the additional: <b>polar(optrot) cphf=rdfreq</b>.<br />
<br />
For example, the input line should be:<br />
<br />
<pre><br />
---insert input line here-----------------------<br />
</pre><br />
<b>4)</b> The wavelengths at which the optical rotation was taken was added at the end of the document.<br />
<br />
<pre><br />
end x,y,z co-ordinates<br />
...blank line...<br />
589nm<br />
...blank line...<br />
Other<br />
</pre><br />
<br />
<b>5)</b> This job was then saved and then run on either Gaussview or on the Imperial HPC.<br />
<br />
Comparing this with literature, we find ...<br />
<br />
==Enantiomeric excess==<br />
<br />
Enantiomeric excess (ee) allows chemists to determine the percentage of which enantiomer is favourably produced in a chemical reaction. This is particularly important in teh pharmaceutical industry for medicines, as some enantiomers are not processed by the body. <b>Reference required here</b> As such, methods to develop chiral catalysts which synthesise one enantiomer over another are favoured. <br />
<br />
The ee of a reaction can also be calculated from the Gibbs Free Energy of the transition state of the reaction.<br />
<br />
<b>1)</b> This can be done by calculating the difference in the transition state energies for the two diasteromeric transition states<br />
<br />
<b>2)</b> Then calculating the rate constant <i>k</i>, and relating the result above to the rate constant.<br />
<br />
<b>3)</b> Then calculating the enantiomeric excess.<br />
<br />
Conduct research on this topic in order to find a paper which yields additional information and equations from the above.<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734412Rep:Mod:1SC2018-09-13T13:50:15Z<p>Zm714: /* Introduction */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview to conduct calculations. Some of your calculations may take several hours to run, even on the HPC! As such, we advise that you use your time wisely. For example, you could run your calculations overnight (but make sure that you know that they won't fail within one second of running!) and write up your wiki and conduct research and run smaller calculations during the day. It is completely up to you where you work or when you run your simulations.<br />
<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this as you progress through this lab. You will need to conduct research and consult experimental results/ other published computational simulations at various points in order to verify the validity of your results - this is what happens in computational research!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734411Rep:Mod:1SC2018-09-13T13:50:00Z<p>Zm714: /* Introduction */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview to conduct calculations. Some of your calculations may take several hours to run, even on the HPC! As such, we advise that you use your time wisely. For example, you could run your calculations overnight (but make sure that you know that they won't fail within one second of running!) and write up your wiki and conduct research and run smaller calculations during the day. It is completely up to you where you work or when you run your simulations.<br />
<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_ToolboxLab Toolbox] is provided and you should consult this as you progress through this lab. You will need to conduct research and consult experimental results/ other published computational simulations at various points in order to verify the validity of your results - this is what happens in computational research!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734410Rep:Mod:1SC2018-09-13T13:45:34Z<p>Zm714: /* Introduction */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview to conduct calculations. Some of your calculations may take several hours to run, even on the HPC! As such, we advise that you use your time wisely. For example, you could run your calculations overnight (but make sure that you know that they won't fail within one second of running!) and write up your wiki and conduct research and run smaller calculations during the day. It is completely up to you where you work or when you run your simulations.<br />
<br />
A [Lab Toolbox] is provided and you should consult this as you progress through this lab. You will need to conduct research and consult experimental results/ other published computational simulations at various points in order to verify the validity of your results - this is what happens in computational research!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734409Rep:Mod:1SC2018-09-13T13:39:03Z<p>Zm714: /* Part 2: Epoxides and their reactions */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview to conduct calculations.<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:1SC#Part_3:_Enantiomeric_Excess Part 3: Enantiomeric Excess] (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734408Rep:Mod:1SC2018-09-13T13:38:06Z<p>Zm714: /* Part 2: Epoxides and their reactions */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview to conduct calculations.<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
Whilst your calculations are running for this part of the lab, we recommend that you continue to <i>Part 3: Enantiomeric Excess</i> (below) of the lab. Calculations on the HPC may take a while to run!<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734407Rep:Mod:1SC2018-09-12T18:04:12Z<p>Zm714: /* Introduction */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
You should use Gaussian 09/ Gaussview to conduct calculations.<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734406Rep:Mod:1SC2018-09-12T18:00:55Z<p>Zm714: /* Part 3: Enantiomeric Excess */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
For this part of the lab, you will need to click [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] for the script. Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734405Rep:Mod:1SC2018-09-12T18:00:03Z<p>Zm714: /* Objectives */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers. This can help you understand which one may be formed in excess in a reaction.<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides. In the lab, this can be used to determine which enantiomer you have an excess of. Computational Simulations also allow you to calculate such properties.<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations.<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734404Rep:Mod:1SC2018-09-12T17:44:40Z<p>Zm714: /* Part 3: Enantiomeric Excess */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>"Investigating the non-covalent interactions in the active-site of the reaction transition state"</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734403Rep:Mod:1SC2018-09-12T17:44:18Z<p>Zm714: /* Part 3: Enantiomeric Excess */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here] Do not complete any sections other than those under <b><i>"Using the (calculated) properties of transition state for the reaction"</i></b> and do not complete the sections thereafter beginning <b><i>Investigating the non-covalent interactions in the active-site of the reaction transition state</i></b><br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734402Rep:Mod:1SC2018-09-12T17:40:17Z<p>Zm714: /* Part 3: Enantiomeric Excess */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:organic#Using_the_.28calculated.29_properties_of_transition_state_for_the_reaction here]<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734401Rep:Mod:1SC2018-09-12T17:26:12Z<p>Zm714: /* Objectives */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Determine the stability of isomers<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab here<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734400Rep:Mod:1SC2018-09-12T17:24:53Z<p>Zm714: /* Part 1: Basis sets */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Be able to determine the stability of isomers<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub)]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab here<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734399Rep:Mod:1SC2018-09-12T17:24:27Z<p>Zm714: /* Part 1: Basis sets */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Be able to determine the stability of isomers<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers (via the [https://www.imperial.ac.uk/admin-services/ict/self-service/computers-printing/software-hub/ Software Hub]or the [https://portal.hpc.imperial.ac.uk/ HPC].<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab here<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734398Rep:Mod:1SC2018-09-12T17:23:01Z<p>Zm714: /* Intended Learning Outcomes */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Conduct complex computational calculations<br />
<br />
<b>3)</b> Analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<br />
<b>1)</b> Be able to determine the stability of isomers<br />
<br />
<b>2)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>3)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers or the HPC.<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab here<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734397Rep:Mod:1SC2018-09-12T17:09:05Z<p>Zm714: /* Aims and Objectives */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Intended Learning Outcomes==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Introduce you to methods for basis set selection<br />
<br />
<b>2)</b> Learn how to conduct complex computational calculations<br />
<br />
<b>3)</b> Be able to analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Be able to determine the stability of isomers<br />
<br />
<b>3)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>4)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers or the HPC.<br />
<br />
==Part 2: Epoxides and their reactions<br> ==<br />
<br />
Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
<br />
Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
<br />
Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
<br />
Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
<br />
==Part 3: Enantiomeric Excess==<br />
<br />
Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
<br />
H.R. Computational lab here<br />
<br />
==References==</div>Zm714https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:1SC&diff=734393Rep:Mod:1SC2018-09-11T18:05:32Z<p>Zm714: /* Part 2: Epoxides and their reactions */</p>
<hr />
<div>==Introduction==<br />
<br />
<br />
This lab assumes that you are already familiar with the [http://www.huntresearchgroup.org.uk/teaching/year1_lab_start.html first] and [http://www.huntresearchgroup.org.uk/teaching/year2a_lab_start.html second] year Gaussian labs. Please revise these before beginning work here.<br />
A [https://wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:Lab_Toolbox Lab Toolbox] is provided and you should consult this before beginning the lab.<br />
<br />
In this lab, if you have already conducted the synthetic experiment, are encouraged to cite your findings and compare results from computational simulations with your results. This is what happens in projects!<br />
<br />
==Aims and Objectives==<br />
<br />
This lab follows on from the 1S Synthesis Lab of the Jacobson and Shi catalysts which you conducted/will conduct this year.<br />
By the end of this lab, you should be able to:<br />
<br />
===Aims===<br />
<b>1)</b> Introduce you to methods for basis set selection<br />
<br />
<b>2)</b> Learn how to conduct complex computational calculations<br />
<br />
<b>3)</b> Be able to analyse data effectively and efficiently from the outputs of computational simulations<br />
<br />
===Objectives===<br />
<b>1)</b> Understand and appreciate how to select a basis set for computational calculations.<br />
<br />
<b>2)</b> Be able to determine the stability of isomers<br />
<br />
<b>3)</b> Calculate the Optical Rotations of your epoxides<br />
<br />
<b>4)</b> Determine the enantiomeric excess of your products via transition state calculations<br />
<br />
==Part 1: Basis sets==<br />
<br />
Basis sets are used in computational chemistry (those programs which use Gaussian Type Orbtials) as a method to approximate the atomic orbitals in a chemical system. Fructose is a precursor to the Shi catalyst (<b>Fig. 1</b>) and you should use fructose as a base molecule to determine which basis set you will use to run any further calculations. You will need to use the <b>B3LYP</b> functional at all times during this work. <br />
<br />
[[File:Shi_reaction_zm714.png|600px|thumb|center|<b>Fig. 1</b> Shi Catalyst Synthesis from 1S lab]]<br />
<br />
Basis sets for selection are: <b>3-21G</b>, <b>6-31++G(d,p)</b> and <b>6-311++G(d,p)</b><br />
<br />
Determine which of these basis sets will provide a good degree of accuracy to your calculations. Discuss the difference between the basis sets and justify your selection, making a critical evalutation. You may use the desktop computers or the HPC.<br />
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==Part 2: Epoxides and their reactions<br> ==<br />
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Four different alkenes are investigated with in the 1S lab: '''styrene''', '''trans-β-methylstyrene''', '''trans-Stilbene '''and '''1,2-Dihydronaphthalene'''. <br />
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Upon oxidation, these alkenes all form the corresponding epoxide, where the oxygen can either be distinguished as being face up or down for some alkenes. This leads to a pair of enantiomers for each of the epoxides. Determine a method to distinguish between the two enantiomers of the epoxide produced; run a calculation to verify they are enantiomers and discuss your results. Are the results reliable? What other methods could you use?<br />
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Trans-β-methylstyrene, forms trans-β-methylstyrene oxide after oxidation with the Jacobson and Shi catalysts. Reaction of an epoxide with a nuclophile, NH<sub>2</sub>Ph, yields new products. In fact, research was conducted by ____ who used Jacobson like catalysts to synthesise one of the products over all the others. <b>Reference Required</b><br />
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Determine the different products which could be formed and discuss their relative energies. Which is the most stable; can the kinetic and thermodynamic product be determined from this information?<br />
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==Part 3: Enantiomeric Excess==<br />
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Computational methods can also be used to calculate the enantiomeric excess of epoxides produced by either the Jacobson or Shi catalyst from a reaction. Determination depends on being able to distinguish between the various transition states.<br />
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H.R. Computational lab here<br />
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==References==</div>Zm714