https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&feedformat=atom&user=Se506 2026-05-16T05:30:05Z User contributions MediaWiki 1.43.0 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42114 2009-02-06T12:51:54Z

<p>Se506: /* Introduction */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> NB - The numbers used to refer to the various compounds studied here come from the course guide.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of ChemBio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers, which interconvert. Such isomers arise because of atropisomerism, a type of isomerism, which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group; it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vicinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature, which can achieve the hydrolysis in a very much shorter period that it would occur unaided, often this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method, which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intramolecular nucleophilic substitution to occur, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemistry of the hydroxyl group yet there is a significant difference in the half-life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> The stabilities of 13 and 14 have been analysed in ChemBio 3D, the chair-chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the N-substituent have been obtained.<br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42111 2009-02-06T12:51:20Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> NB - The number used to refer to the various compounds studied here come from the course guide.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of ChemBio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers, which interconvert. Such isomers arise because of atropisomerism, a type of isomerism, which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group; it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vicinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature, which can achieve the hydrolysis in a very much shorter period that it would occur unaided, often this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method, which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intramolecular nucleophilic substitution to occur, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemistry of the hydroxyl group yet there is a significant difference in the half-life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> The stabilities of 13 and 14 have been analysed in ChemBio 3D, the chair-chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the N-substituent have been obtained.<br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42104 2009-02-06T12:49:43Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of ChemBio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers, which interconvert. Such isomers arise because of atropisomerism, a type of isomerism, which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group; it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vicinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature, which can achieve the hydrolysis in a very much shorter period that it would occur unaided, often this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method, which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intramolecular nucleophilic substitution to occur, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemistry of the hydroxyl group yet there is a significant difference in the half-life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> The stabilities of 13 and 14 have been analysed in ChemBio 3D, the chair-chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the N-substituent have been obtained.<br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42102 2009-02-06T12:48:48Z

<p>Se506: /* Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue) */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of ChemBio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers, which interconvert. Such isomers arise because of atropisomerism, a type of isomerism, which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group; it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vicinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature, which can achieve the hydrolysis in a very much shorter period that it would occur unaided, often this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method, which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intramolecular nucleophilic substitution to occur, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemistry of the hydroxyl group yet there is a significant difference in the half-life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> The stabilities of 13 and 14 have been analysed in ChemBio 3D, the chair-chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the N-substituent have been obtained.<br /> <br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42099 2009-02-06T12:47:42Z

<p>Se506: /* How one might induce room temperature hydrolysis of a peptide */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers, which interconvert. Such isomers arise because of atropisomerism, a type of isomerism, which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group; it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vicinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature, which can achieve the hydrolysis in a very much shorter period that it would occur unaided, often this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method, which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intramolecular nucleophilic substitution to occur, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemistry of the hydroxyl group yet there is a significant difference in the half-life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> The stabilities of 13 and 14 have been analysed in ChemBio 3D, the chair-chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the N-substituent have been obtained.<br /> <br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42096 2009-02-06T12:47:24Z

<p>Se506: /* Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers, which interconvert. Such isomers arise because of atropisomerism, a type of isomerism, which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group; it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vicinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature, which can achieve the hydrolysis in a very much shorter period that it would occur unaided, often this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method, which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intramolecular nucleophilic substitution to occur, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemistry of the hydroxyl group yet there is a significant difference in the half-life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> The stabilities of 13 and 14 have been analysed in ChemBio 3D, the chair-chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the N-substituent have been obtained.<br /> <br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42093 2009-02-06T12:45:27Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature, which can achieve the hydrolysis in a very much shorter period that it would occur unaided, often this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method, which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intramolecular nucleophilic substitution to occur, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemistry of the hydroxyl group yet there is a significant difference in the half-life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> The stabilities of 13 and 14 have been analysed in ChemBio 3D, the chair-chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the N-substituent have been obtained.<br /> <br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42089 2009-02-06T12:43:36Z

<p>Se506: /* How one might induce room temperature hydrolysis of a peptide */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature which can achieve the hydrolysis in a very much shorter period that it would occur unaided, oftern this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intrmolecular nucleophilic substitution to ocurr, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemisrty of the hydroxyl group yet there is a significant difference in the half life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> Thye stabilities of 13 and 14 have been analised in ChemBio 3D, the chair chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the the N-substituent have been obtained.<br /> <br /> {| border=&quot;1&quot;<br /> |+ Energy Values (kcal/mol)<br /> ! Compound !! Axial !! Equatorial <br /> |-<br /> ! 13<br /> | 17.93 || 21.13<br /> |-<br /> ! 14<br /> |10.04<br /> |11.00<br /> |}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42083 2009-02-06T12:38:50Z

<p>Se506: /* How one might induce room temperature hydrolysis of a peptide */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature which can achieve the hydrolysis in a very much shorter period that it would occur unaided, oftern this will be in under a second. In the lab, the hydrolysis can be accelerated too, by using an esterification method which can be achieved in the order of minutes.<br /> <br /> Two molecules (13 and 14) were designed to allow an intrmolecular nucleophilic substitution to ocurr, involving nucleophilic attack by the hydroxyl group on the carbonyl carbon and the associated loss of a leaving group, gaseous ammonia. By considering entropic arguments it is the loss of ammonia that is undoubtedly the thermodynamic driving force behind the reaction.<br /> <br /> Amazingly the compounds 13 and 14 differ only in the relative stereochemisrty of the hydroxyl group yet there is a significant difference in the half life of the reaction, 21 minutes for 13 cf. 840 minutes for 14.<br /> <br /> Thye stabilities of 13 and 14 have been analised in ChemBio 3D, the chair chair conformation as in decalin has been used. Additionally, values for both axial and equatorial conformations of the the N-substituent have been obtained.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42046 2009-02-06T11:51:42Z

<p>Se506: /* How one might induce room temperature hydrolysis of a peptide */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===<br /> <br /> At RTP and a neutral pH the hydrolysis of a peptide may take in the order of 500 years. Obviously many of the processes fundamental to life involve the hydrolysis of peptides and therefore enzymes do exist in nature which can achieve the hydrolysis in a very much shorter period that it would occur unaided, oftern this will be in under a second. In the lab, the hydrolysis can be accelerated too, not quite as well as in nature but it can be achieved in the order of minutes.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42037 2009-02-06T11:44:42Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> <br /> ===How one might induce room temperature hydrolysis of a peptide===</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42024 2009-02-06T11:34:36Z

<p>Se506: /* References */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42023 2009-02-06T11:34:22Z

<p>Se506: /* Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> &lt;references /&gt;<br /> <br /> ==References==<br /> <br /> {{reflist}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42012 2009-02-06T11:29:22Z

<p>Se506: /* Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.<br /> <br /> ==References==<br /> <br /> {{reflist}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=42011 2009-02-06T11:27:30Z

<p>Se506: /* Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.<br /> <br /> With Carbonyl group up = 50.01 kcal/mol<br /> <br /> With Carbonyl group down = 68.99 kcal/mol<br /> <br /> Therefore, on the basis of thermodynamic stability only, we may conclude that the more stable atropisomer, by quite a margin, is the one in which the carbonyl group is orientated 'up'<br /> <br /> Scheyler &lt;ref&gt;[Maier, W. F.; Schleyer, P. v. R., J. Am. Chem. Soc. 1981, 103, 1891-1900.]&lt;/ref&gt; et al first introduced the concept of alkene hyperstability in 1981. The term is used to describe cycloalkenes that shown a negative strain energy. It is believed that this phenomenom is due to an increase in the interaction between the vincinal and transanular hydrogens of the ring, as in the case of the Taxol intermediate under study here. These compounds are typically difficult to hydrogenate and functionalise.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=41991 2009-02-06T10:55:00Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.<br /> <br /> <br /> ===Stereochemistry and Reactivity of an Intermediate in the Synthesis of Taxol===<br /> <br /> In the Paquette synthesis of the anti cancer drug Taxol, a key intermediate was found to have two isomers which intercovert. Such isomers arise because of atropisomerism, a type of isomerism which leads to isomers through restricted rotation about a single bond. Specifically this involves the position of the carbonyl group, it may be 'up' or 'down'. Using ChemBio 3D the more thermodynamically stable atropisomer was determined.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=41972 2009-02-06T10:39:44Z

<p>Se506: /* Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue) */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)<br /> <br /> It can be seen from the data that the relative position of the carbonyl has very little impact on the thermodynamic stability of the two reagents.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=41969 2009-02-06T10:34:40Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol<br /> <br /> <br /> ===Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)===<br /> <br /> The nucleophilic additions to two pyridinium ring derivatives were investigated here. In the first, the ring (5) is alkylated in the 4-position using a methyl magnesium iodide reagent. In the second the pyridinium derivative (7) is reacted with aniline, which acts to transfer a NHphenyl group to the 4-position of the ring.<br /> Both reagents have been investigated as models in the mm2 force field of chembio 3D. In both cases the geometry of the carbonyl has been varied to see what effect this has on the energy.<br /> <br /> 5 = 26.33 kcal/mol (C=O up), 26.32 kcal/mol (C=O down)<br /> <br /> 7 = 15.41 kcl/mol (C=O up), 15.20 kcal/mol (C=O down)</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=41867 2009-02-06T01:07:28Z

<p>Se506: /* The Hydrogenation of the cyclopentadiene dimer */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsional strain element (endo = 9.5, exo = 7.6). However, we know the endo form to be the observed product and therefore a kinetic argument should be applied to the dimerisation.<br /> <br /> The two dihydro derivatives were also analysed in a mm2 force field in chemBio 3D and their energy values are as follows:<br /> 3 = 35.93 kcal/mol,<br /> 4 = 31.15 kcal/mol</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=41864 2009-02-06T01:02:43Z

<p>Se506: /* The Hydrogenation of the cyclopentadiene dimer */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.<br /> <br /> For the dimerisation, both endo and exo forms were inputted into ChemBio 3D and the following energy value were obtained:<br /> Exo = 31.88 kcal/mol,<br /> Endo = 34.02 kcal/mol<br /> <br /> Clearly, the relative energies do not differ significantly and it would therefore be unwise to attach too great a weight to these figures. Yet the figures show that in the thermodynamic sense the exo form is slighly more stable than the endo form. Comparing the individual energy components it can be seen that the small energy difference comes from the torsion element. However we know this not to be the case and therefore a kinetic argument should be applied in this case.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=41857 2009-02-06T00:55:52Z

<p>Se506: /* The Hydrogenation of the cyclopentadiene dimer */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===<br /> <br /> Cyclopentadiene may dimerise spontaneously at room temperature over the course of several hours via a pericyclic cycloaddition. It is known that dimerisation results in the exclusive formation of the endo form dimer rather than the exo form. Hydrogenation of the dimer will give a dihydro derivative, of which there are two possible regioisomers. Further hydrogenation will give the tetrahydro form. <br /> Here, molecular modelling has been implemented to rationalise some of the observed reactivity of the dimerisation and hydrogenation of cyclopentadiene. Why is only the endo product formed on dimerisation and which of the two regioisomers of hydrogenation is most likely to form. The mm2 force field of ChemBio 3D has been used to optimise the geometries of the various forms involved and study their relative thermodynamic stabilities.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38361 2009-01-27T20:42:36Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.<br /> <br /> === The Hydrogenation of the cyclopentadiene dimer ===</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38359 2009-01-27T20:40:22Z

<p>Se506: /* Introduction */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.<br /> <br /> A number of chemical reactions were analysed in this experiment using the MM approach.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38358 2009-01-27T20:36:48Z

<p>Se506: /* Introduction */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.<br /> <br /> Throughout this computational journey of discovery, several MM programmes will be used. Most prevalent amongst them is ChemBio 3D using the Allinger MM2 force field. In addition Ghemical and Avagadro will be used. <br /> It is worth noting that comparisons of energies of different molecules are only valid when the same force field has been employed.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38353 2009-01-27T20:20:49Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. <br /> <br /> Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles. The model (or rather the computer programme carrying out the modelling) aims to find the total energy minimum of the system through optimising its molecular geometry. In essence, the bonds lengths and angles are varied, within the 3N-6 framework of 'molecular movement' to achieve the lowest energy conformation. The individual components of this total energy can then be analysed. <br /> <br /> One must however, be careful when using the MM approach and be aware of its limitations. Essentially the estimations made using MM are based upon that of known systems. Therefore data for inputted systems will be obtained through interpolation of known data. As such, data given for new molecules may well be inaccurate and unreliable as no basis exists from which a model can be produced. Conversely, systems consisting of bonds primarily based upon simple diatomic bonding, for instance hydrocarbons, can be modelled very accurately. Additionally, problems may arise in systems where an intimate knowledge of the position of electron density is required. As such, systems containing aromaticity, hyperconjugation or interactions arising from secondary overlap, may be difficult or even impossible to model. In some cases, one must resort to quantum mechanics once more with a view to solving the wave equations associated with such systems.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38344 2009-01-27T18:46:22Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data. Enter Molecular Mechanics (MM), an extremely useful method for understanding an array of molecular properties without need to solve wave equations. At its core, the MM approach uses five easily computed terms, each one itself modelled from classical mathematics. Each term or group of terms accounts for a component of the system's (molecule's) total energy. The strain in the system is estimated from three terms, the sum of diatomic bond stretches (modelled from Hooke's law), the sum of tri-atomic bond deformation angles (also modelled from Hooke's law) and the sum of the tetra-atomic bond torsions (modelled on a cosine wave). The steric repulsion of a system may be estimated from the sum of non-bonded Van-der-Waals repulsions (modelled on a Lennard Jones 12,6 potential) Finally the extent of Hydrogen bonding in the system is extrapolated from the sum of all electrostatic attractions of bond dipoles.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38317 2009-01-27T17:44:01Z

<p>Se506: /* Introduction */</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===<br /> <br /> Since the dawn of the Quantum Mechanics revolution in the early part of the 20th century answers have been sought to many simple and complex problems in chemistry and physics. In chemistry, the quantum mechanical approach proved highly successful as a means to understanding simple molecules, in terms of their bonding, their structure and therefore reactivity. However quantum mechanics falls down with more complex systems, not because it doesn't work, but because the sheer complexity of the mathematics involved and hence the computing constraints become significant. Chemists therefore needed other methods to understand the chemical systems they were working with. Such methods need not be exact but estimates (using known and well understood systems as a basis) to provide good theoretical backing to the known experimental data.</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38314 2009-01-27T17:03:12Z

<p>Se506: </p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==<br /> <br /> === Introduction ===</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:se506-module1&diff=38313 2009-01-27T17:01:25Z

<p>Se506: New page: = Third Year Computational Chemistry Lab = == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==</p> <hr /> <div>= Third Year Computational Chemistry Lab =<br /> <br /> == Module 1 - Structure and Spectroscopy (molecular mechanics and the molecular orbital) ==</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=13837 2007-12-07T11:55:00Z

<p>Se506: </p> <hr /> <div>==Introduction==<br /> '''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> Domoic acid displays neuroexcitatory properties; it causes neuronal death, literally by exciting cells to death. The actual mechanism for this is similar to that which occurs in sufferers of dementia. Domoic acid and other kainoid derivatives are therefore currently being studied intensively in an effort to develop tools (drugs) to fight other debilitating diseases such as Huntington’s and epilepsy. These neurological properties are believed to derive from the kainoids' structural similarity to the neurotransmitter, glutamic acid.<br /> [[Image:Law speer.jpg|left|thumb|Glutamic Acid.]]<br /> Domoic acid is the causative agent behind a rare condition known as 'Amnesic shellfish poisoning' or ASP. The condition causes short term memory loss (hence 'amnesic'); dizziness, nausea, vomiting and can eventually result in serious brain damage or death. Domoic acid poisons in this fashion by mimicking the action of glutamic in the hippocampus region of the brain (the area of learning and memory). However when the so called molecular trojan horse (dormoic acid) binds to receptors in the hippocampus an excitotoxic event occurs which causes the continuous sending of impulses, eventually leading to 'burn out' resulting in brain lesions and the memory loss characteristic of the condition.<br /> <br /> ==Synthesis==<br /> <br /> The total synthesis of Domoic as has been reported just once by Ohfune and Tomita in 1982&lt;ref&gt;Ohfune, Y.; Tomita, M. J. Am. Chem. Soc. 1982, 104, 3511.&lt;/ref&gt;. The various steps in the synthesis are shown below:<br /> <br /> [[Image:Examp5e.jpg]]<br /> [[Image:Exa6ple.jpg]]<br /> [[Image:Exam7le.jpg]]<br /> <br /> == References ==<br /> <br /> &lt;references/&gt;<br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=13821 2007-12-07T11:42:52Z

<p>Se506: </p> <hr /> <div>&lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |- <br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}<br /> <br /> <br /> '''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> Domoic acid displays neuroexcitatory properties; it causes neuronal death, literally by exciting cells to death. The actual mechanism for this is similar to that which occurs in sufferers of dementia. Domoic acid and other kainoid derivatives are therefore currently being studied intensively in an effort to develop tools (drugs) to fight other debilitating diseases such as Huntington’s and epilepsy. These neurological properties are believed to derive from the kainoids' structural similarity to the neurotransmitter, glutamic acid.<br /> [[Image:Law speer.jpg|left|thumb|Glutamic Acid.]]<br /> Domoic acid is the causative agent behind a rare condition known as 'Amnesic shellfish poisoning' or ASP. The condition causes short term memory loss (hence 'amnesic'); dizziness, nausea, vomiting and can eventually result in serious brain damage or death. Domoic acid poisons in this fashion by mimicking the action of glutamic in the hippocampus region of the brain (the area of learning and memory). However when the so called molecular trojan horse (dormoic acid) binds to receptors in the hippocampus an excitotoxic event occurs which causes the continuous sending of impulses, eventually leading to 'burn out' resulting in brain lesions and the memory loss characteristic of the condition.<br /> <br /> ==Synthesis==<br /> <br /> The total synthesis of Domoic as has been reported just once by Ohfune and Tomita in 1982. The various steps in the synthesis are shown below:<br /> <br /> [[Image:Examp5e.jpg]]<br /> [[Image:Exa6ple.jpg]]<br /> [[Image:Exam7le.jpg]]</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=13817 2007-12-07T11:41:30Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> Domoic acid displays neuroexcitatory properties; it causes neuronal death, literally by exciting cells to death. The actual mechanism for this is similar to that which occurs in sufferers of dementia. Domoic acid and other kainoid derivatives are therefore currently being studied intensively in an effort to develop tools (drugs) to fight other debilitating diseases such as Huntington’s and epilepsy. These neurological properties are believed to derive from the kainoids' structural similarity to the neurotransmitter, glutamic acid.<br /> [[Image:Law speer.jpg|left|thumb|Glutamic Acid.]]<br /> Domoic acid is the causative agent behind a rare condition known as 'Amnesic shellfish poisoning' or ASP. The condition causes short term memory loss (hence 'amnesic'); dizziness, nausea, vomiting and can eventually result in serious brain damage or death. Domoic acid poisons in this fashion by mimicking the action of glutamic in the hippocampus region of the brain (the area of learning and memory). However when the so called molecular trojan horse (dormoic acid) binds to receptors in the hippocampus an excitotoxic event occurs which causes the continuous sending of impulses, eventually leading to 'burn out' resulting in brain lesions and the memory loss characteristic of the condition.<br /> <br /> ==Synthesis==<br /> <br /> The total synthesis of Domoic as has been reported just once by Ohfune and Tomita in 1982. The various steps in the synthesis are shown below:<br /> <br /> [[Image:Examp5e.jpg]]<br /> [[Image:Exa6ple.jpg]]<br /> [[Image:Exam7le.jpg]]<br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |- <br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=File:Exam7le.jpg&diff=13815 2007-12-07T11:38:47Z

<p>Se506: </p> <hr /> <div></div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=File:Exa6ple.jpg&diff=13814 2007-12-07T11:38:24Z

<p>Se506: </p> <hr /> <div></div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=File:Examp5e.jpg&diff=13810 2007-12-07T11:37:19Z

<p>Se506: </p> <hr /> <div></div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=13783 2007-12-07T11:24:04Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> Domoic acid displays neuroexcitatory properties; it causes neuronal death, literally by exciting cells to death. The actual mechanism for this is similar to that which occurs in sufferers of dementia. Domoic acid and other kainoid derivatives are therefore currently being studied intensively in an effort to develop tools (drugs) to fight other debilitating diseases such as Huntington’s and epilepsy. These neurological properties are believed to derive from the kainoids' structural similarity to the neurotransmitter, glutamic acid.<br /> [[Image:Law speer.jpg|left|thumb|Glutamic Acid.]]<br /> Domoic acid is the causative agent behind a rare condition known as 'Amnesic shellfish poisoning' or ASP. The condition causes short term memory loss (hence 'amnesic'); dizziness, nausea, vomiting and can eventually result in serious brain damage or death. Domoic acid poisons in this fashion by mimicking the action of glutamic in the hippocampus region of the brain (the area of learning and memory). However when the so called molecular trojan horse (dormoic acid) binds to receptors in the hippocampus an excitotoxic event occurs which causes the continuous sending of impulses, eventually leading to 'burn out' resulting in brain lesions and the memory loss characteristic of the condition.<br /> <br /> ==Synthesis==<br /> <br /> The total synthesis of Domoic as has been reported just once by Ohfune and Tomita in 1982. The various steps in the synthesis are shown below:<br /> <br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=It07:Coniine&diff=13480 2007-12-06T14:15:13Z

<p>Se506: New page: &lt;jmol&gt; &lt;jmolApplet&gt; &lt;size&gt;200&lt;/size&gt; &lt;color&gt;white&lt;/color&gt; &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt; &lt;inlineContents&gt;HEADER NONAME 06-Dec-07 ...</p> <hr /> <div>&lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 06-Dec-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 06-Dec-07 0 NONE 4<br /> ATOM 1 N 0 0.354 1.006 -0.376 0.00 0.00 N+0<br /> ATOM 2 C 0 -0.031 -0.266 0.245 0.00 0.00 C+0<br /> ATOM 3 C 0 -1.446 -0.642 -0.200 0.00 0.00 C+0<br /> ATOM 4 C 0 -2.441 0.390 0.338 0.00 0.00 C+0<br /> ATOM 5 C 0 -3.855 0.014 -0.107 0.00 0.00 C+0<br /> ATOM 6 C 0 0.944 -1.366 -0.179 0.00 0.00 C+0<br /> ATOM 7 C 0 2.352 -1.003 0.301 0.00 0.00 C+0<br /> ATOM 8 C 0 2.721 0.382 -0.242 0.00 0.00 C+0<br /> ATOM 9 C 0 1.653 1.390 0.186 0.00 0.00 C+0<br /> ATOM 10 H 0 -0.313 1.695 -0.063 0.00 0.00 H+0<br /> ATOM 11 H 0 -0.008 -0.161 1.330 0.00 0.00 H+0<br /> ATOM 12 H 0 -1.493 -0.658 -1.288 0.00 0.00 H+0<br /> ATOM 13 H 0 -1.700 -1.628 0.190 0.00 0.00 H+0<br /> ATOM 14 H 0 -2.394 0.406 1.427 0.00 0.00 H+0<br /> ATOM 15 H 0 -2.187 1.376 -0.051 0.00 0.00 H+0<br /> ATOM 16 H 0 -3.902 -0.002 -1.196 0.00 0.00 H+0<br /> ATOM 17 H 0 -4.109 -0.972 0.282 0.00 0.00 H+0<br /> ATOM 18 H 0 -4.564 0.749 0.276 0.00 0.00 H+0<br /> ATOM 19 H 0 0.640 -2.313 0.266 0.00 0.00 H+0<br /> ATOM 20 H 0 0.941 -1.456 -1.266 0.00 0.00 H+0<br /> ATOM 21 H 0 2.374 -0.985 1.390 0.00 0.00 H+0<br /> ATOM 22 H 0 3.065 -1.740 -0.068 0.00 0.00 H+0<br /> ATOM 23 H 0 3.688 0.684 0.159 0.00 0.00 H+0<br /> ATOM 24 H 0 2.772 0.345 -1.330 0.00 0.00 H+0<br /> ATOM 25 H 0 1.925 2.382 -0.176 0.00 0.00 H+0<br /> ATOM 26 H 0 1.586 1.408 1.273 0.00 0.00 H+0<br /> CONECT 1 9 2 10 0 NONE 31<br /> CONECT 2 1 3 6 11 NONE 32<br /> CONECT 3 2 4 12 13 NONE 33<br /> CONECT 4 3 5 14 15 NONE 34<br /> CONECT 5 4 16 17 18 NONE 35<br /> CONECT 6 2 7 19 20 NONE 36<br /> CONECT 7 6 8 21 22 NONE 37<br /> CONECT 8 7 9 23 24 NONE 38<br /> CONECT 9 8 1 25 26 NONE 39<br /> END&lt;/inlineContents&gt;<br /> NONE 4<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=It:projects&diff=13479 2007-12-06T14:13:28Z

<p>Se506: /* Supplemental Project Page */</p> <hr /> <div>__FORCETOC__<br /> <br /> '''''You MUST use the Edit buttons on the right to edit this content. Do NOT use the Edit button on the top of this page.'''''<br /> == Sandbox (Play-Pen) == <br /> <br /> This is an area where you can play without worrying what you do. Enter it by pressing the [Edit] button '''on the right''' and '''not''' at the top. Go here for a [http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet ''cheat sheet''] summary of how to create a Wiki page. It's a free-for-all in here! Learn how to use a Wiki by coming here! PS This is how to do Greek:&amp;alpha;, &amp;beta; &amp;Delta;, &amp;delta; <br /> Try copying/pasting some of the [http://www.ch.ic.ac.uk/local/it/lab1.html examples in the course work] into this page. See the effect by selecting '''Show Preview'''. Do not use '''Save Page''' so as to leave this area uncluttered for others.<br /> ----<br /> {| summary=&quot;CIT Project Titles&quot; border=&quot;1&quot;<br /> |NEW: This demonstrates the use of Jmol loading discrete molecule files (rather than having to paste them into the wiki page). Upload the molecule file, and invoke it as shown here. Use it for eg loading large proteins etc.--[[User:Rzepa|Rzepa]] 16:07, 4 December 2006 (UTC) and --[[User:Rzepa|Rzepa]] 07:41, 16 October 2007 (BST) and --[[User:Rzepa|Rzepa]] 15:56, 18 October 2007 (BST)<br /> <br /> If no rotatable molecule appears to the right there my be a problem in the browser cache - reload the page bypassing the cache using ctrl+F5. If this doesn't work check that [http://www.java.com/en/download/help/testvm.xml Java] is correctly functioning on your system.<br /> <br /> ===References ===<br /> This shows how citations&lt;ref&gt;Example of adding a citation {{DOI|10.1021/ja9825332}}&lt;/ref&gt; can be added to <br /> text&lt;ref&gt;adding a further citation {{DOI|10.1021/ja9825332}}&lt;/ref&gt; to produce a nice effect.<br /> <br /> ===Multiple uses of the same footnote ===<br /> <br /> The code for citing multiple quotes from the same source can be found [http://www.mediawiki.org/wiki/Extension:Cite/Cite.php here]. This stops the same reference being stated multiple times at the bottom of the page when you try to reference more than one item from the same source.<br /> <br /> === Collected citations appear below here ===<br /> &lt;references /&gt;--[[User:Rzepa|Rzepa]] 15:18, 25 October 2007 (BST)<br /> |&lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;title&gt;Pentahelicene&lt;/title&gt;&lt;color&gt;yellow&lt;/color&gt;&lt;size&gt;200&lt;/size&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Pentahelicene.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;jmolMenu&gt;<br /> &lt;item&gt;&lt;text&gt;Start spinning&lt;/text&gt;&lt;script&gt;spin on&lt;/script&gt;&lt;/item&gt;<br /> &lt;item&gt;&lt;text&gt;Stop spinning&lt;/text&gt;&lt;script&gt;spin off&lt;/script&gt;&lt;/item&gt;<br /> &lt;menuHeight&gt;-1&lt;/menuHeight&gt;<br /> &lt;/jmolMenu&gt;<br /> &lt;jmolButton&gt;<br /> &lt;script&gt;console&lt;/script&gt;<br /> &lt;text&gt;open a console window&lt;/text&gt;<br /> &lt;/jmolButton&gt;<br /> &lt;/jmol&gt;<br /> &lt;jmol&gt;&lt;jmolAppletButton&gt;&lt;title&gt;Show CIYSIM.cif in popup window&lt;/title&gt;&lt;color&gt;cyan&lt;/color&gt;<br /> &lt;uploadedFileContents&gt;CIYSIM.cif&lt;/uploadedFileContents&gt;&lt;/jmolAppletButton&gt;<br /> &lt;/jmol&gt;<br /> |}<br /> <br /> == Main Project Page ==<br /> <br /> '''''URGENT Announcement''''' <br /> <br /> Whilst the Wiki itself is pretty robust, and although it is difficult to break a page on it, this did happen a few days ago to project 12. What seems to have happened is that some ''bad'' code (HTML or XML) was copied from another Web page, and pasted into the project 12 page. The Wiki system could not cope with this particular bad code, and sulked. Fortunately, by invoking appropriate magic, the page has now been restored to its state prior to the breakage, and I have learnt a valuable lesson in how to fix it if this happens again. So this serves as a warning; if you are copying/pasting blind from other web pages (which in general you should not be doing), you do run the risk of breaking the page. Hopefully, the break will be detected during the preview, and serves to remind that you should ''always'' preview before saving to detect any such breaks. --[[User:Rzepa|Rzepa]] 10:21, 28 November 2007 (UTC)<br /> <br /> '''Please do not edit this page itself'''. Click on one of the titles to start editing.<br /> {| summary=&quot;CIT Project Titles&quot; border=&quot;1&quot;<br /> ! bgcolor=&quot;cyan&quot; |Project&lt;br /&gt; Number<br /> ! bgcolor=&quot;cyan&quot; |General Keywords<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |01<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Lignocaine|Lignocaine (used in dentistry as a &quot;local&quot;)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |02<br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Piperine|Piperine (active ingredient of both black and white pepper)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |03<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Rapamycin|Rapamycin (prevents transplant rejection)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |04<br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Gossypol|Gossypol (male birth control)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |05<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Gentamycin|Gentamicin A (aminoglycoside antibiotic)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |06<br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Herceptin|Herceptin (topical anticancer drug)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |07<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Gingerone|Zingerone (the characteristic smell of ginger)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |08<br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Sucralose|Sucralose (non-metabolizable sweetening agent)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |09<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Bufotoxin|Bufotoxin (active component of the toad ''Bufo vulgaris'')]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |10<br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Roaccutane|Roaccutane (treatment for severe acne)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |11<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Sibutramine|Sibutramine (appetite suppresor)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |12<br /> | bgcolor=&quot;#66FF99&quot; | [[it07a:Anandamide|Anandamide (the &quot;feel-good&quot; factor in chocolate)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |13<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:h3nbh3|Ammonia-borane: H&lt;sub&gt;3&lt;/sub&gt;N-BH&lt;sub&gt;3&lt;/sub&gt; (Hydrogen storage molecule?)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |14<br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Methoxsalen|Methoxsalen (Treatment of psoriasis)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |15<br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Hycocine|Hyoscine (From Mandrake and Witches Henbane, pre-med before surgery)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |16<br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Capreomycin|Capreomycin (Drug-resistant TB)]]<br /> |-<br /> | bgcolor=&quot;#CCFF00&quot; |17 <br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:wilkinson|Wilkinson's catalyst]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |18 <br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Jacobsen|Jacobsen's epoxidation catalyst]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |19 <br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Methylaluminoxane|Methylaluminoxane: MAO - hugely important ethylene polymerisation cocatalyst]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |20 <br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Schwartz|Schwartz reagent for the hydrozirconation of alkenes and alkynes]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |21 <br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Schrock|Schrock metathesis catalyst]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |22 <br /> | bgcolor=&quot;#66FF99&quot; | [[it07:knots|Molecular-scale knots (nanoscale devices)]] <br /> |- <br /> |bgcolor=&quot;#CCFF00&quot; |23 <br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Vioxx|Vioxx (treatment of osteoarthritis symptoms and pain)]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |24 <br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Sertraline|Sertraline HCl (anti-depression)]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |25 <br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Ceftriaxone|Ceftriaxone (Gonorrhoea)]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |26 <br /> | bgcolor=&quot;#66FF99&quot; | [[i07t:Zithromycin|Zithromycin (anti-infective)]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |27 <br /> | bgcolor=&quot;#CCFF00&quot; | [[it07:Lipitor|Lipitor (Cholesterol reducing agent)]] <br /> |- <br /> | bgcolor=&quot;#CCFF00&quot; |28 <br /> | bgcolor=&quot;#66FF99&quot; | [[it07:Cyameluric Acid|Cyameluric acid (Linus Pauling's last idea!)]]<br /> |}<br /> <br /> == Supplemental Project Page ==<br /> <br /> This area is for people who wish to create their own projects if none of the above appeal to them. Click on the '''Edit''' button to the right to open up an editable page,<br /> then add an entry below as follows<br /> <br /> *&lt;nowiki&gt; [[it07:name_of_project|Descriptive name of intended project]]&lt;/nowiki&gt;<br /> *This will produce the effect: [[it07:name_of_project|Descriptive name of intended project]]<br /> ----<br /> #[[it07:sitagliptin_page|An example entry- in edit mode, please copy this line and paste below to add to this list]]<br /> #[[it07:Limonene|Limonene]]<br /> #[[it07:name_of_project|Vitamin C ]]<br /> #[[it07:Cylcophosphamide|Cyclophosphamide]]<br /> #[[it07:Terbutaline Sulphate|Terbutaline Sulphate]]<br /> #[[it07:Caffeine|Caffeine]]<br /> #[[it07:Mefloquine|Mefloquine]]<br /> #[[it07:Cadaverine|Cadaverine]]<br /> #[[it07:Cyanidin|Cyanidin]]<br /> #[[it07:Ezetimibe|Ezetimibe]]<br /> #[[it07:Octanitrocubane|Octanitrocubane]]<br /> #[[it07:Azadirachtin|Azadirachtin]]<br /> #[[it07:Nicotine|Nicotine]]<br /> #[[it07:Cyclopentasiloxane|Cyclopentasiloxane]]<br /> #[[it07:Trinitrotoluene|Trinitrotoluene]]<br /> #[[it07:Hydroxychloroquine|Hydroxychloroquine]]<br /> #[[it07:Aspartame|Aspartame]]<br /> #[[it07:Azulene|Azulene]]<br /> #[[it07:Chlorine Trifluoride|Chlorine Trifluoride]]<br /> #[[it07:Cholesterol|Cholesterol]]<br /> #[[it07:Vitamin E|Vitamin E]]<br /> #[[it07:Phenothiazine|Phenothiazine]]<br /> #[[it07:linalool|linalool]]<br /> #[[it07:Glutamic acid|Glutamic acid]]<br /> #[[it07:N-(4-hydroxyphenyl)ethanamide|N-(4-hydroxyphenyl)ethanamide]]<br /> #[[it07:Epinephrine|Epinephrine]]<br /> #[[it07:Sodium Valproate|Sodium Valproate]]<br /> #[[it07:Hyaluronic acid |Hyaluronic acid ]]<br /> #[[it07:Methylenedioxymethamphetamine |Methylenedioxymethamphetamine ]]<br /> #[[it07:salicylic acid |salicylic acid ]]<br /> #[[it07:Morphine|Morphine]]<br /> #[[Cetirizine]]<br /> #[[it07:Bisacodyl|Bisacodyl]]<br /> #[[it07:Rivaroxaban|Rivaroxaban]]<br /> #[[it07:Sodium Lauryl Sulfate|Sodium Lauryl Sulfate]]<br /> #[[it07:Silicon Dioxide|Silicon Dioxide]]<br /> #[[it07:Vanillin|Vanillin]]<br /> #[[it07:Tetrahydrocannabinol|Tetrahydrocannabinol]]<br /> #[[it07:Capsaicin|Capsaicin]]<br /> #[[it07:Menthol|Menthol]]<br /> #[[it07:Tamoxifen|Tamoxifen]]<br /> #[[it07:Copper arsenate|Scheele's Green]]<br /> #[[it07:Strychnine|Strychnine]]<br /> #[[it07:Testosterone|Testosterone]]<br /> #[[it07:Monosodium glutamate|Monosodium glutamate]]<br /> #[[it07:Taurine|Taurine]]<br /> #[[it07:Phenethylamine|Phenethylamine]]<br /> #[[it07:Verbenone|Verbenone]]<br /> #[[it07:Salbutamol|Salbutamol]]<br /> #[[it07:Lactic acid|Lactic acid]]<br /> #[[it07:Aspirin|Aspirin]]<br /> #[[it07:EDTA|EDTA]]<br /> #[[it07:Heroin|Heroin]]<br /> #[[it07:Cocaine|Cocaine]]<br /> #[[it07:Myristicin|Myristin (The hallucinogen in nutmeg)]]<br /> #[[it07:Encefabol|Encefabol]]<br /> #[[it07:Sarin|Sarin]]<br /> #[[Thebaine]]<br /> #[[Nitroglycerin]]<br /> #[[it07:Methamphetamine|Methamphetamine]]<br /> #[[it07:Sildenafil|Sildenafil]]<br /> #[[Grubbs' Catalyst]]<br /> #[[it07:Warfarin|Warfarin]]<br /> #[[it07:Angelic Acid|Angelic Acid]]<br /> #[[it07:Melem (Melon) |Melem]]<br /> #[[it07:oxazaborolidines|Chiral Oxazaborolidines as Catalysts]]<br /> #[[it07:RDX|RDX (chemical in plastic explosives)]]<br /> #[[it07:Lysergic Acid|Lysergic Acid]]<br /> #[[it07:Oseltamivir Phosphate|Oseltamivir Phosphate(Tamiflu)]]<br /> #[[Fluoxetine Hydrochloride (Prozac)]]<br /> #[[Dimethylmercury]]<br /> #[[it07:Sorafenib(Nexavar®)|Sorafenib (Nexavar®)]]<br /> #[[Rapamycin]]<br /> #[[Rohypnol]]<br /> #[[it07:Vitamin A|Vitamin A (Retinol)]]<br /> #[[it07:THC|Tetrahydrocannabinol]]<br /> #[[2,4-Dinitrophenylhydrazine|2,4-Dinitrophenylhydrazine]]<br /> #[[Acetylcholine]]<br /> #[[it07:Phenolphthalein|Phenolphthalein]]<br /> #[[Carbon Dioxide]]<br /> #[[Domoic Acid]]<br /> #[[Kevlar]]<br /> #[[it07:Erythromycin|Erythromycin]]<br /> #[[it07:DIBAL|DIBAL]]<br /> #[[Ephedrine]]<br /> #[[it07:Lactose|Lactose]]<br /> #[[it07:Thyjone|Thyjone]]<br /> #[[Levothyroxine]]<br /> #[[it07:Tropinone|Tropinone]]<br /> #[[it07:Ozone|Ozone]]<br /> #[[it07:Indinavir|Indinavir (Crixivan®)]]<br /> #[[it07:Tetrodotoxin|Tetrodotoxin]]<br /> #[[it07:Astaxanthin|Astaxanthin]]<br /> #[[Methane]]<br /> #[[it07:2 – Chlorobenzalmalononitrile|2 – Chlorobenzalmalononitrile (CS Gas)]]<br /> #[[it07:Dichloro-Diphenyl-Trichloroethane|Dichloro-Diphenyl-Trichloroethane]]<br /> #[[it07:Ketamine|Ketamine]]<br /> #[[it07:Ethylene Glycol|Ethylene Glycol]]<br /> #[[it07:HMX|HMX]]<br /> #[[it07:Psilocybin|Psilocybin (magic mushrooms)]]<br /> #[[it07:Dopamine|Dopamine]]<br /> #[[it07:Mefenamic Acid|Mefenamic Acid]]<br /> #[[it07:Sesamin|Sesamin]]<br /> #[[it07:Riboflavin|Riboflavin (Vitamin B2)]]<br /> #[[it07:Coniine|Coniine]]<br /> <br /> == Wiki Templates ==<br /> <br /> [[Template:DOI]] and [[Template:Doi-inline]] are providea as (protected) templates for your use. Many other templates exist, often to be found on e.g. Wikipedia pages. You may decide one of these is of particular use, or of interest. If so, you can install it on the wiki here for you and others to use. Add below a line that looks like Template:Template-name, save, and click on the red text to create the new template. If you prefer the task of adding useful templates to that of adding information about molecules, then you will be given full credit for performing this valuable service for others! --Rzepa 14:41, 20 October 2006 (BST) <br /> <br /> [[Template:Chem-Data]]<br /> <br /> [[Template:Drug-Box]] - For pharmaceutical drugs just copy variable names and code generates tables<br /> <br /> [[Template:Chembox supplement]] - to be linked to from the supplementary section of the table in the template above, for usage see [[Template_talk:chembox_supplement|here]]<br /> <br /> [[Template:NFPA_704]] - for notes on how to use, see [[Template_talk:NFPA_704|here]]<br /> <br /> [[R &amp; S Phrases]]<br /> <br /> [[Template:Chembox new]]</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Dimethylmercury&diff=13451 2007-12-06T13:52:59Z

<p>Se506: </p> <hr /> <div>&lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:dimethylmercury3.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 27-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 27-Nov-07 0 NONE 4<br /> ATOM 1 C 0 2.100 0.000 -0.000 0.00 0.00 C+0<br /> ATOM 2 Hg 0 -0.000 0.000 -0.000 0.00 0.00 Hg+0<br /> ATOM 3 C 0 -2.100 -0.000 0.000 0.00 0.00 C+0<br /> ATOM 4 H 0 2.463 -0.010 1.028 0.00 0.00 H+0<br /> ATOM 5 H 0 2.463 -0.885 -0.522 0.00 0.00 H+0<br /> ATOM 6 H 0 2.463 0.895 -0.505 0.00 0.00 H+0<br /> ATOM 7 H 0 -2.463 0.010 -1.028 0.00 0.00 H+0<br /> ATOM 8 H 0 -2.463 -0.895 0.505 0.00 0.00 H+0<br /> ATOM 9 H 0 -2.463 0.885 0.522 0.00 0.00 H+0<br /> CONECT 1 2 4 5 6 NONE 14<br /> CONECT 2 1 3 0 0 NONE 15<br /> CONECT 3 2 7 8 9 NONE 16<br /> END NONE 17<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt; &lt;!-- replace if not identical with the pagename --&gt;<br /> <br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | Dimethylmercury<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;2&lt;/sub&gt;H&lt;sub&gt;6&lt;/sub&gt;Hg<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 230.659 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 593-74-8<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Density Density] &amp; [http://en.wikipedia.org/wiki/Phase_%28matter%29 phase]<br /> | 2.961 g/cm³ &lt;!-- ? g/cm³, solid / ? g/ml, liquid / ? g/l, gas --&gt;<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 270 K &lt;!-- (mention any decomposition) --&gt;<br /> |-<br /> | [http://en.wikipedia.org/wiki/Boiling_point Boiling point]<br /> | 391-392 K<br /> |-}}<br /> <br /> <br /> ==Dimethylmercury== <br /> <br /> '''Dimethylmercury ''' ([[Carbon|C]][[Hydrogen|H]]&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;[[Mercury (element)|Hg]] belongs to the organometallic family of compounds (specifically the alkyl mercuries. It has a linear structure like many HgX&lt;sub&gt;2&lt;/sub&gt; systems. It is a liquid at room temperature and is flamable, colourless and described as having a sweet smelling odour. <br /> <br /> Dimethylmercury is one of the most potent neurotoxins known. Absorption of less than 1ml can be serverely toxic&lt;ref&gt;Blyney MB, JS Winn and DW Nierenberg, 'Letters; chemical safety - handling of dmHg'. Chem and Engineering news (1997, May, 12); 7.&lt;/ref&gt;. The fact that many materials including plastics and rubbers, specifically latex and neoprene are permeable to the compound, makes it even more deadly. Also its high vapour pressure (50-82mmHg @ 293K)&lt;ref&gt;[http://www.osha.gov/dts/hib/hib_data/hib19980309.html]Occupational Safety and Health Administration, US Department of Labor.&lt;/ref&gt; makes inhalation a significant mode of entry.<br /> The recommended handling advice for DMM is to wear a face shield at least 8 inches long with impervious gloves (silver shield laminate gloves have been shown to remain impervious to DMM for at least 4 hours)<br /> <br /> ==Uses==<br /> <br /> Dimethylmercury is primarily used in research. A major use is in the calibration of NMR machines. Although due to the highly toxic nature of the compound, inorganic Hg salts are prefered.<br /> <br /> ==Synthesis==<br /> <br /> One means of producing DMM is by the oxidation of monomethyl hydrazine by mercuric oxide)&lt;ref&gt;Harry H Sisler, Milap A Mathur, Sampat R Jain and Roy W King. J Org Chem 1980, 45, 1329-1330.&lt;/ref&gt; as shown below:<br /> <br /> 2CH&lt;sub&gt;3&lt;/sub&gt;NHNH&lt;sub&gt;2&lt;/sub&gt; + HgO = C&lt;sub&gt;2&lt;/sub&gt;H&lt;sub&gt;6&lt;/sub&gt;Hg + NH&lt;sub&gt;3&lt;/sub&gt; + NO<br /> <br /> ==Neurotoxicity==<br /> <br /> Dimethylmercury crosses the blood brain barrier rapidly due to the formation of a methyl-mercury cysteine complex. Hg is a soft acid and will therefore bind to soft bases (eg Sulphur). Thus Hg will attack the thiol groups of enzymes causing their inhibition.<br /> The removal of the compound from the body occurs over a long period thus it will tend to bioaccumulate in the body. Such that, often, by the time effects are seen the (fatal) damage has been done. Symptoms of DMM poisoning include ataxia, sensory disturbances and changes in mental state.<br /> <br /> ==Death of a scientist==<br /> <br /> [[Image:wetterhahn.JPG|thumb|250px|Karen Wetterhahn]]<br /> <br /> <br /> One of the most famous cases involving DMM poisoning is that of Karen Wetterhahn, who died as a result of exposure to the compound. Wetterhahn, an internationally respected professor of chemistry at Dartmouth College, New Hampshire, was using DMM as a Hg NMR standard reference for her study of the interaction of Hg ions with DNA repair proteins. In January 1997 she reported symptoms such as slurred speech and tingling fingers and toes, all consistent with Hg poisoning. She later recalled spilling a single drop of DMM onto her latex gloved hand. On 28th January of that year she was officially diagnosed with Hg poisoning. Her blood-Mercury level was found to be 4000 micrograms per litre, 80 times the toxic threshold. Despite aggressive chelation treatment she died on 8th June 1997 after falling into a coma. The official verdict was death by encephalopathy as a result of mercury intoxication.<br /> <br /> ==Spectra==<br /> <br /> The Mass Spectrum&lt;ref&gt;[http://webbook.nist.gov/chemistry/]NIST Chemistry WebBook.&lt;/ref&gt; is shown below:<br /> <br /> [[Image:Examdle.jpg]]<br /> <br /> <br /> == References ==<br /> <br /> &lt;references/&gt;<br /> <br /> ==External Links==<br /> <br /> *[http://www.chm.bris.ac.uk/motm/dimethylmercury/dmmh.htm, Full account of the Death of Karen Wetterhahn]</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=File:Examdle.jpg&diff=13448 2007-12-06T13:51:14Z

<p>Se506: </p> <hr /> <div></div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=12414 2007-11-29T17:11:59Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> Domoic acid displays neuroexcitatory properties; it causes neuronal death, literally by exciting cells to death. The actual mechanism for this is similar to that which occurs in sufferers of dementia. Domoic acid and other kainoid derivatives are therefore currently being studied intensively in an effort to develop tools (drugs) to fight other debilitating diseases such as Huntington’s and epilepsy. These neurological properties are believed to derive from the kainoids' structural similarity to the neurotransmitter, glutamic acid.<br /> [[Image:Law speer.jpg|left|thumb|Glutamic Acid.]]<br /> Domoic acid is the causative agent behind a rare condition known as 'Amnesic shellfish poisoning' or ASP. The condition causes short term memory loss (hence 'amnesic'); dizziness, nausea, vomiting and can eventually result in serious brain damage or death. Domoic acid poisons in this fashion by mimicking the action of glutamic in the hippocampus region of the brain (the area of learning and memory). However when the so called molecular trojan horse (dormoic acid) binds to receptors in the hippocampus an excitotoxic event occurs which causes the continuous sending of impulses, eventually leading to 'burn out' resulting in brain lesions and the memory loss characteristic of the condition.<br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=12388 2007-11-29T16:53:05Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> Domoic acid displays neuroexcitatory properties; it causes neuronal death, literally by exciting cells to death. The actual mechanism for this is similar to that which occurs in sufferers of dementia. Domoic acid and other kainoid derivatives are therefore currently being studied intensively in an effort to develop tools (drugs) to fight other debilitating diseases such as Huntington’s and epilepsy. These neurological properties are believed to derive from the kainoids' structural similarity to the neurotransmitter, glutamic acid.<br /> [[Image:Law speer.jpg|left|thumb|Glutamic Acid.]]<br /> <br /> <br /> <br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=File:Law_speer.jpg&diff=12387 2007-11-29T16:52:40Z

<p>Se506: </p> <hr /> <div></div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=File:Law_speaker.jpg&diff=12383 2007-11-29T16:50:21Z

<p>Se506: </p> <hr /> <div></div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=12378 2007-11-29T16:43:14Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> Domoic acid displays neuroexcitatory properties; it causes neuronal death, literally by exciting cells to death. The actual mechanism for this is similar to that which occurs in sufferers of dementia. Domoic acid and other kainoid derivatives are therefore currently being studied intensively in an effort to develop tools (drugs) to fight other debilitating diseases such as Huntington’s and epilepsy. These neurological properties are believed to derive from the kainoids' structural similarity to the neurotransmitter, glutamic acid.<br /> <br /> <br /> <br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=12362 2007-11-29T16:16:47Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> ==Neurological Properties==<br /> <br /> <br /> <br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=12355 2007-11-29T16:10:55Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> ==Biological Properties==<br /> <br /> Members of the Kainoid family display potent biological effects. Domoic acid is no exception; It is well known for is use as an insecticide and as an anthelmintic, a substance that kills or stuns parasitic worms. The latter property was first discovered by the Japanese in the town of Tokunoshima, Kagoshima, where the compound is still used today for that purpose.<br /> <br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=12347 2007-11-29T16:01:01Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> [[Image:Picture 62.jpg|thumb|''General form of a kainoid amino acid'']]<br /> <br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=File:Picture_62.jpg&diff=12346 2007-11-29T16:00:40Z

<p>Se506: </p> <hr /> <div></div>

Se506 https://chemwiki.ch.ic.ac.uk/index.php?title=Domoic_Acid&diff=12333 2007-11-29T15:24:22Z

<p>Se506: </p> <hr /> <div>'''Domoic Acid''' belongs to the family of molecules collectively known as the kainoid amino acids. In Domoic acid the R-group takes the form of an octadienoic side chain.<br /> The acid is also a phycotoxin (a toxin produced by algae).<br /> The compound was first synthesized in 1958 from the red marine agla ''Chondria armanta''.<br /> <br /> <br /> <br /> &lt;noinclude&gt;<br /> &lt;!-- This template has been defined after elaborate discussion in the Chemicals Wikiproject. Please do not add, deleted or otherwise change it unless after due discussion in [[wikipedia talk:WikiProject Chemicals]] --&gt;<br /> &lt;/noinclude&gt;{| class=&quot;toccolours&quot; border=&quot;1&quot; style=&quot;float: right; clear: right; margin: 0 0 1em 1em; border-collapse: collapse; width: 280px&quot;<br /> ! {{chembox header}} | {{PAGENAME}} &lt;!-- replace if not identical with the article name --&gt;<br /> |-<br /> | align=&quot;center&quot; colspan=&quot;2&quot; bgcolor=&quot;#ffffff&quot; | [[Image:gdegdege.png|200px|{{PAGENAME}}]]<br /> &lt;jmol&gt;<br /> &lt;jmolApplet&gt;<br /> &lt;size&gt;200&lt;/size&gt;<br /> &lt;color&gt;white&lt;/color&gt;<br /> &lt;script&gt;zoom 80; cpk on;frame 1; move 10 -20 10 0 0 0 0 0 3; delay 1;&lt;/script&gt;<br /> &lt;inlineContents&gt;HEADER NONAME 29-Nov-07 NONE 1<br /> TITLE NONE 2<br /> AUTHOR WWW daemon apache NONE 3<br /> REVDAT 1 29-Nov-07 0 NONE 4<br /> ATOM 1 C 0 5.454 -1.128 -0.776 0.00 0.00 C+0<br /> ATOM 2 C 0 4.233 -0.213 -0.674 0.00 0.00 C+0<br /> ATOM 3 C 0 3.359 -0.666 0.467 0.00 0.00 C+0<br /> ATOM 4 C 0 2.104 -1.038 0.237 0.00 0.00 C+0<br /> ATOM 5 C 0 1.252 -1.480 1.351 0.00 0.00 C+0<br /> ATOM 6 C 0 -0.031 -1.755 1.138 0.00 0.00 C+0<br /> ATOM 7 C 0 -0.872 -2.331 2.247 0.00 0.00 C+0<br /> ATOM 8 C 0 -0.644 -1.489 -0.213 0.00 0.00 C+0<br /> ATOM 9 H 0 0.133 -1.428 -0.975 0.00 0.00 H+0<br /> ATOM 10 C 0 -1.658 -2.597 -0.569 0.00 0.00 C+0<br /> ATOM 11 N 0 -2.757 -1.887 -1.273 0.00 0.00 N+0<br /> ATOM 12 C 0 -2.912 -0.616 -0.519 0.00 0.00 C+0<br /> ATOM 13 H 0 -3.483 -0.783 0.394 0.00 0.00 H+0<br /> ATOM 14 C 0 -1.466 -0.184 -0.181 0.00 0.00 C+0<br /> ATOM 15 H 0 -1.096 0.518 -0.928 0.00 0.00 H+0<br /> ATOM 16 C 0 -1.412 0.446 1.212 0.00 0.00 C+0<br /> ATOM 17 C 0 -2.162 1.753 1.201 0.00 0.00 C+0<br /> ATOM 18 O 0 -2.536 2.227 0.155 0.00 0.00 O+0<br /> ATOM 19 O 0 -2.416 2.391 2.355 0.00 0.00 O+0<br /> ATOM 20 C 0 -3.586 0.425 -1.376 0.00 0.00 C+0<br /> ATOM 21 O 0 -3.368 0.462 -2.564 0.00 0.00 O+0<br /> ATOM 22 O 0 -4.428 1.310 -0.819 0.00 0.00 O+0<br /> ATOM 23 C 0 4.686 1.203 -0.428 0.00 0.00 C+0<br /> ATOM 24 O 0 4.335 1.785 0.571 0.00 0.00 O+0<br /> ATOM 25 O 0 5.478 1.819 -1.320 0.00 0.00 O+0<br /> ATOM 26 H 0 6.086 -0.801 -1.602 0.00 0.00 H+0<br /> ATOM 27 H 0 6.020 -1.084 0.154 0.00 0.00 H+0<br /> ATOM 28 H 0 5.127 -2.153 -0.954 0.00 0.00 H+0<br /> ATOM 29 H 0 3.667 -0.257 -1.604 0.00 0.00 H+0<br /> ATOM 30 H 0 3.753 -0.689 1.473 0.00 0.00 H+0<br /> ATOM 31 H 0 1.711 -1.015 -0.769 0.00 0.00 H+0<br /> ATOM 32 H 0 1.668 -1.582 2.342 0.00 0.00 H+0<br /> ATOM 33 H 0 -0.290 -2.360 3.168 0.00 0.00 H+0<br /> ATOM 34 H 0 -1.755 -1.709 2.394 0.00 0.00 H+0<br /> ATOM 35 H 0 -1.181 -3.342 1.980 0.00 0.00 H+0<br /> ATOM 36 H 0 -1.199 -3.335 -1.227 0.00 0.00 H+0<br /> ATOM 37 H 0 -2.033 -3.074 0.336 0.00 0.00 H+0<br /> ATOM 38 H 0 -3.597 -2.422 -1.115 0.00 0.00 H+0<br /> ATOM 39 H 0 -1.869 -0.230 1.935 0.00 0.00 H+0<br /> ATOM 40 H 0 -0.373 0.626 1.489 0.00 0.00 H+0<br /> ATOM 41 H 0 -2.897 3.229 2.348 0.00 0.00 H+0<br /> ATOM 42 H 0 -4.860 1.977 -1.369 0.00 0.00 H+0<br /> ATOM 43 H 0 5.769 2.727 -1.162 0.00 0.00 H+0<br /> CONECT 1 2 26 27 28 NONE 48<br /> CONECT 2 1 3 23 29 NONE 49<br /> CONECT 3 2 4 30 0 NONE 50<br /> CONECT 4 3 5 31 0 NONE 51<br /> CONECT 5 4 6 32 0 NONE 52<br /> CONECT 6 5 7 8 0 NONE 53<br /> CONECT 7 6 33 34 35 NONE 54<br /> CONECT 8 6 9 14 10 NONE 55<br /> CONECT 10 8 11 36 37 NONE 56<br /> CONECT 11 10 12 38 0 NONE 57<br /> CONECT 12 11 13 14 20 NONE 58<br /> CONECT 14 12 15 8 16 NONE 59<br /> CONECT 16 14 17 39 40 NONE 60<br /> CONECT 17 16 18 19 0 NONE 61<br /> CONECT 18 17 0 0 0 NONE 62<br /> CONECT 19 17 41 0 0 NONE 63<br /> CONECT 20 12 21 22 0 NONE 64<br /> CONECT 21 20 0 0 0 NONE 65<br /> CONECT 22 20 42 0 0 NONE 66<br /> CONECT 23 2 24 25 0 NONE 67<br /> CONECT 24 23 0 0 0 NONE 68<br /> CONECT 25 23 43 0 0 NONE 69<br /> END NONE 70<br /> &lt;/inlineContents&gt;<br /> &lt;/jmolApplet&gt;<br /> &lt;/jmol&gt;<br /> |-<br /> ! {{chembox header}} | General<br /> |- <br /> | [http://en.wikipedia.org/wiki/IUPAC Systematic name]<br /> | 3-Pyrrolidineacetic acid, 2-Carboxy-4-[(1Z,3E,5R)-5-carboxy-1-methyl-1,3-hexadien-1-yl]-(2S,3S,4S)<br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Chemical_formula Molecular formula]<br /> | C&lt;sub&gt;15&lt;/sub&gt;H&lt;sub&gt;21&lt;/sub&gt;NO&lt;sub&gt;6&lt;/sub&gt;<br /> <br /> <br /> |-<br /> | [http://en.wikipedia.org/wiki/Molar_mass Molar mass]<br /> | 311.33 g/mol<br /> |-<br /> <br /> | [http://en.wikipedia.org/wiki/CAS_registry_number CAS number]<br /> | 14277-97-5<br /> |-<br /> ! {{chembox header}} | Properties<br /> |-<br /> | [http://en.wikipedia.org/wiki/Melting_point Melting point]<br /> | 490 K (Decomposition)<br /> |-<br /> | Optical Rotatory Power<br /> | -109.6 degrees (In water, 589.3nm, 285K)<br /> |-}}</div>

Se506