https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&feedformat=atom&user=Jw13918ChemWiki - User contributions [en]2026-04-07T09:16:12ZUser contributionsMediaWiki 1.43.0https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=801184MRD:jw139182020-05-08T21:52:10Z<p>Jw13918: /* PES inspection */</p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to products first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. The activation barrier is recrossed and It goes back to the reagents again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}<br />
The figure below shows the last set of conditions in the table. The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
<br />
[[File:Figure 2 (jw13918).png]]<br />
<br />
From the table, we can know that the momenta condition should be controlled in a range to make the trajectory reactive. If the momenta are too small, the system has no enough kinetic energy to overcome activation barrier, and the reaction cannot happen. If the momenta are too large, the activation barrier will be recrossed and the system will go back to reagents. But it may bounce back to product again if momenta is larger.<br />
<br />
* Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?<br />
Answer:<br />
<br />
The reaction rate value by Transition State Theory predictions will be larger than experimental value.<br />
<br />
== EXERCISE 2: F - H - H system ==<br />
<br />
=== PES inspection ===<br />
* By inspecting the potential energy surfaces, classify the F + H<sub>2</sub> and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?<br />
Answer:<br />
<br />
The F + H<sub>2</sub> reaction is exothermic, and H + HF reaction is endothermic. The bond strength of HF is very high because it is hydrogen bond between a H atom with a more electronegative atom F, which is dipole-dipole interaction. The bond strength of H<sub>2</sub> is relatively lower because it is non-polar covalent bond. Therefore, it will release heat while HF bond is formed from breaking H<sub>2 </sub>bond, and it will absorb heat while breaking HF bond to form H<sub>2</sub> bond.<br />
<br />
* Locate the approximate position of the transition state.<br />
Answer:<br />
<br />
The position of transition state is at around r<sub>ts</sub> = 92 pm. The diagram below shows that the distances between atoms are flat on this transition state position.<br />
<br />
[[File:Figure 3 (jw13918).png]]<br />
<br />
* Report the activation energy for both reactions.<br />
Answer:<br />
<br />
The activation energy is equal to the difference between the potential energy of reagents and the potential energy of transition state. In the F + H<sub>2</sub> reaction, the potential energy of reagents is about -550 kJ/mol, and the potential energy of transition state is about -500 kJ/mol. So the activation energy is (-500)-(-550)= 50 kJ/mol. In the H + HF reaction, the potential energy of reagents is about -580 kJ/mol, and the potential energy of transition state is about -450 kJ/mol. So the activation energy is (-450)-(-580)= 130 kJ/mol. <br />
<br />
=== Reaction dynamics ===<br />
* In light of the fact that energy is conserved, discuss the mechanism of release of the reaction energy. Explain how this could be confirmed experimentally.<br />
Answer:<br />
<br />
In F + H<sub>2 </sub>reaction, when the H-H bond is broken and H-F bond is formed, the bond length increases so that the potential energy will be in lower value. Since energy is conserved, the lost potential energy will be converted into reaction energy released. Then, it causes the exothermic reaction. That can be confirmed experimentally, and we can feel the temperature of reaction mixture increases while the system is releasing heat to the environment. <br />
<br />
* Discuss how the distribution of energy between different modes (translation and vibration) affect the efficiency of the reaction, and how this is influenced by the position of the transition state.<br />
Answer:<br />
<br />
In H + HF reaction, when the vibrational energy of H-F bond (low momentum) is very low and translational energy of HH (high momentum of incoming H atom) is very high initially, it is difficult to obtain a reactive trajectory. If the vibrational energy of H-F bond is increase to a much higher level (higher momentum) and the momentum of the incoming H atom is decreased to a much lower level, and p<sub>HF </sub>is larger than p<sub>HH</sub>, we can obtain a reactive trajectory that from H + HF to H<sub>2</sub> +F. If the position of the transition state is on a large distance of atoms, low vibrational energy and high translational energy will bring a reactive trajectory. Inversely, if the position of the transition state is on a small distance of atoms, high vibrational energy and low translational energy will bring a reactive trajectory.<br />
<br />
== References ==<br />
<br />
1 John C. Polanyi and Jerry L. Schreiber, in ''Faraday Discussions of the Chemical Society,'' 1977, 62, 267-290.<br />
<br />
2 PetersBaron, in ''Reaction Rate Theory and Rare Events Simulations'', 2017</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=801163MRD:jw139182020-05-08T21:36:00Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to products first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. The activation barrier is recrossed and It goes back to the reagents again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}<br />
The figure below shows the last set of conditions in the table. The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
<br />
[[File:Figure 2 (jw13918).png]]<br />
<br />
From the table, we can know that the momenta condition should be controlled in a range to make the trajectory reactive. If the momenta are too small, the system has no enough kinetic energy to overcome activation barrier, and the reaction cannot happen. If the momenta are too large, the activation barrier will be recrossed and the system will go back to reagents. But it may bounce back to product again if momenta is larger.<br />
<br />
* Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?<br />
Answer:<br />
<br />
The reaction rate value by Transition State Theory predictions will be larger than experimental value.<br />
<br />
== EXERCISE 2: F - H - H system ==<br />
<br />
=== PES inspection ===<br />
* By inspecting the potential energy surfaces, classify the F + H<sub>2</sub> and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?<br />
Answer:<br />
<br />
The F + H<sub>2</sub> reaction is exothermic, and H + HF reaction is endothermic. The bond strength of HF is very high because it is hydrogen bond between a H atom with a more electronegative atom F, which is dipole-dipole interaction. The bond strength of H<sub>2</sub> is relatively lower because it is non-polar covalent bond. Therefore, it will release heat while HF bond is formed from breaking H<sub>2</sub>, and it will absorb heat while breaking HF bond to form H<sub>2</sub> bond.<br />
<br />
* Locate the approximate position of the transition state.<br />
Answer:<br />
<br />
The position of transition state is at around r<sub>ts</sub> = 92 pm. The diagram below shows that the distances between atoms are flat on this transition state position.<br />
<br />
[[File:Figure 3 (jw13918).png]]<br />
<br />
* Report the activation energy for both reactions.<br />
Answer:<br />
<br />
The activation energy is equal to the difference between the potential energy of reagents and the potential energy of transition state. In the F + H<sub>2</sub> reaction, the potential energy of reagents is about -550 kJ/mol, and the potential energy of transition state is about -500 kJ/mol. So the activation energy is (-500)-(-550)= 50 kJ/mol. In the H + HF reaction, the potential energy of reagents is about -580 kJ/mol, and the potential energy of transition state is about -450 kJ/mol. So the activation energy is (-450)-(-580)= 130 kJ/mol. <br />
<br />
=== Reaction dynamics ===<br />
* In light of the fact that energy is conserved, discuss the mechanism of release of the reaction energy. Explain how this could be confirmed experimentally.<br />
Answer:<br />
<br />
In F + H<sub>2 </sub>reaction, when the H-H bond is broken and H-F bond is formed, the bond length increases so that the potential energy will be in lower value. Since energy is conserved, the lost potential energy will be converted into reaction energy released. Then, it causes the exothermic reaction. That can be confirmed experimentally, and we can feel the temperature of reaction mixture increases while the system is releasing heat to the environment. <br />
<br />
* Discuss how the distribution of energy between different modes (translation and vibration) affect the efficiency of the reaction, and how this is influenced by the position of the transition state.<br />
Answer:<br />
<br />
In H + HF reaction, when the vibrational energy of H-F bond (low momentum) is very low and translational energy of HH (high momentum of incoming H atom) is very high initially, it is difficult to obtain a reactive trajectory. If the vibrational energy of H-F bond is increase to a much higher level (higher momentum) and the momentum of the incoming H atom is decreased to a much lower level, and p<sub>HF </sub>is larger than p<sub>HH</sub>, we can obtain a reactive trajectory that from H + HF to H<sub>2</sub> +F. If the position of the transition state is on a large distance of atoms, low vibrational energy and high translational energy will bring a reactive trajectory. Inversely, if the position of the transition state is on a small distance of atoms, high vibrational energy and low translational energy will bring a reactive trajectory.<br />
<br />
== References ==<br />
<br />
1 John C. Polanyi and Jerry L. Schreiber, in ''Faraday Discussions of the Chemical Society,'' 1977, 62, 267-290.<br />
<br />
2 PetersBaron, in ''Reaction Rate Theory and Rare Events Simulations'', 2017</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800980MRD:jw139182020-05-08T19:25:54Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to products first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. The activation barrier is recrossed and It goes back to the reagents again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}<br />
The figure below shows the last set of conditions in the table. The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
<br />
[[File:Figure 2 (jw13918).png]]<br />
<br />
From the table, we can know that the momenta condition should be controlled in a range to make the trajectory reactive. If the momenta are too small, the system has no enough kinetic energy to overcome activation barrier, and the reaction cannot happen. If the momenta are too large, the activation barrier will be recrossed and the system will go back to reagents. But it may bounce back to product again if momenta is larger.<br />
<br />
* Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?<br />
Answer:<br />
<br />
The reaction rate value by Transition State Theory predictions will be larger than experimental value.<br />
<br />
== EXERCISE 2: F - H - H system ==<br />
<br />
=== PES inspection ===<br />
* By inspecting the potential energy surfaces, classify the F + H<sub>2</sub> and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?<br />
Answer:<br />
<br />
The F + H<sub>2</sub> reaction is exothermic, and H + HF reaction is endothermic. The bond strength of HF is very high because it is hydrogen bond between a H atom with a more electronegative atom F, which is dipole-dipole interaction. The bond strength of H<sub>2</sub> is relatively lower because it is non-polar covalent bond. Therefore, it will release heat while HF bond is formed from breaking H<sub>2</sub>, and it will absorb heat while breaking HF bond to form H<sub>2</sub> bond.<br />
<br />
* Locate the approximate position of the transition state.<br />
Answer:<br />
<br />
The position of transition state is at around r<sub>ts</sub> = 92 pm. The diagram below shows that the distances between atoms are flat on this transition state position.<br />
<br />
[[File:Figure 3 (jw13918).png]]<br />
<br />
* Report the activation energy for both reactions.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800971MRD:jw139182020-05-08T19:18:55Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to products first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. The activation barrier is recrossed and It goes back to the reagents again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}<br />
The figure below shows the last set of conditions in the table. The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
<br />
[[File:Figure 2 (jw13918).png]]<br />
<br />
From the table, we can know that the momenta condition should be controlled in a range to make the trajectory reactive. If the momenta are too small, the system has no enough kinetic energy to overcome activation barrier, and the reaction cannot happen. If the momenta are too large, the activation barrier will be recrossed and the system will go back to reagents. But it may bounce back to product again if momenta is larger.<br />
<br />
* Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?<br />
Answer:<br />
<br />
The reaction rate value by Transition State Theory predictions will be larger than experimental value.<br />
<br />
== EXERCISE 2: F - H - H system ==<br />
<br />
=== PES inspection ===<br />
* By inspecting the potential energy surfaces, classify the F + H<sub>2</sub> and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?<br />
Answer:<br />
<br />
The F + H<sub>2</sub> reaction is exothermic, and H + HF reaction is endothermic. The bond strength of HF is very high because it is hydrogen bond between a H atom with a more electronegative atom F, which is dipole-dipole interaction. The bond strength of H<sub>2</sub> is relatively lower because it is non-polar covalent bond. Therefore, it will release heat while HF bond is formed from breaking H<sub>2</sub>, and it will absorb heat while breaking HF bond to form H<sub>2</sub> bond.<br />
[[File:Figure 3 (jw13918).png]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800969MRD:jw139182020-05-08T19:17:49Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to products first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. The activation barrier is recrossed and It goes back to the reagents again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}<br />
The figure below shows the last set of conditions in the table. The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
<br />
[[File:Figure 2 (jw13918).png]]<br />
<br />
From the table, we can know that the momenta condition should be controlled in a range to make the trajectory reactive. If the momenta are too small, the system has no enough kinetic energy to overcome activation barrier, and the reaction cannot happen. If the momenta are too large, the activation barrier will be recrossed and the system will go back to reagents. But it may bounce back to product again if momenta is larger.<br />
<br />
* Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?<br />
Answer:<br />
<br />
The reaction rate value by Transition State Theory predictions will be larger than experimental value.<br />
<br />
== EXERCISE 2: F - H - H system ==<br />
<br />
=== PES inspection ===<br />
* By inspecting the potential energy surfaces, classify the F + H<sub>2</sub> and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?<br />
Answer:<br />
<br />
The F + H<sub>2</sub> reaction is exothermic, and H + HF reaction is endothermic. The bond strength of HF is very high because it is hydrogen bond between a H atom with a more electronegative atom F, which is dipole-dipole interaction. The bond strength of H<sub>2</sub> is relatively lower because it is non-polar covalent bond. Therefore, it will release heat while HF bond is formed from breaking H<sub>2</sub>, and it will absorb heat while breaking HF bond to form H<sub>2</sub> bond.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Figure_3_(jw13918).png&diff=800968File:Figure 3 (jw13918).png2020-05-08T19:17:26Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800838MRD:jw139182020-05-08T17:46:33Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to products first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. The activation barrier is recrossed and It goes back to the reagents again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}<br />
The figure below shows the last set of conditions in the table. The trajectory moves to products first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
<br />
[[File:Figure 2 (jw13918).png]]<br />
<br />
From the table, we can know that the momenta condition should be controlled in a range to make the trajectory reactive. If the momenta are too small, the system has no enough kinetic energy to overcome activation barrier, and the reaction cannot happen. If the momenta are too large, the activation barrier will be recrossed and the system will go back to reagents. But it may bounce back to product again if momenta is larger.<br />
<br />
* Given the results you have obtained, how will Transition State Theory predictions for reaction rate values compare with experimental values?<br />
Answer:<br />
<br />
The reaction rate value by Transition State Theory predictions will be larger than experimental value.<br />
<br />
== EXERCISE 2: F - H - H system ==<br />
<br />
=== PES inspection ===<br />
* By inspecting the potential energy surfaces, classify the F + H<sub>2</sub> and H + HF reactions according to their energetics (endothermic or exothermic). How does this relate to the bond strength of the chemical species involved?<br />
Answer:</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800783MRD:jw139182020-05-08T17:00:06Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to transition state first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. They go back to the initial state again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to transition state first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}<br />
[[File:Figure 2 (jw13918).png]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Figure_2_(jw13918).png&diff=800780File:Figure 2 (jw13918).png2020-05-08T16:58:02Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800776MRD:jw139182020-05-08T16:56:46Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.<br />
<br />
=== Reactive and unreactive trajectories ===<br />
* Complete the table below by adding the total energy, whether the trajectory is reactive or unreactive, and provide a plot of the trajectory and a small description for what happens along the trajectory. What can you conclude from the table?<br />
Answer:<br />
{| class="wikitable"<br />
!p<sub>1</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!p<sub>2</sub>/ g.mol<sup>-1</sup>.pm.fs<sup>-1</sup><br />
!E<sub>tot</sub><br />
!Reactive? <br />
!Description of the dynamics <br />
!Illustration of the trajectory<br />
|-<br />
|<nowiki>-2.56 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-414.280</nowiki><br />
|reactive<br />
|The trajectory moves smoothly to transition state first and then falls off to products with slight oscillation.<br />
|The diatomic reagent does not have vibrational energy so the distance between the two atoms does not oscillate. The diatomic product has vibrational energy so the distance between the two atoms oscillates. <br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-4.1 </nowiki><br />
|<nowiki>-420.077</nowiki><br />
|unreactive<br />
|The trajectory shows the atom moves closer to the diatomic molecule until one point first, but goes back further from the point.<br />
|The momentum between the atom and diatomic molecule (p2) is not large enough to make enough kinetic energy to overcome the activation barrier.<br />
|-<br />
|<nowiki>-3.1 </nowiki><br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-413.977</nowiki><br />
|reactive<br />
|The trajectory moves to transition state with slight oscillation first and then falls off to products with larger oscillation.<br />
|The diatomic reagent has a small vibrational energy so the distance between the two atoms oscillates slightly. The diatomic product has larger vibrational energy so the distance between the two atoms oscillates obviously. <br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.1 </nowiki><br />
|<nowiki>-357.277</nowiki><br />
|reactive<br />
|The trajectory is very disordered. It moves to transition state first and then bounces back vigorously. <br />
|The momentum is too large so that the diatomic molecule (product) vibrates too vigorously to break the bond. They go back to the initial state again.<br />
|-<br />
|<nowiki>-5.1 </nowiki><br />
|<nowiki>-10.6 </nowiki><br />
|<nowiki>-349.477</nowiki><br />
|reactive<br />
|The trajectory moves to transition state first and then bounces back a little. Finally it falls off to product with vigorous oscillation.<br />
|The momentum of the diatomic product is even larger than above one, so it vibrates more vigorously and breaks the bond but bounces back to diatomic product again.<br />
|}</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800702MRD:jw139182020-05-08T15:49:41Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]<br />
<br />
* Comment on how the ''mep'' and the trajectory you just calculated differ.<br />
Answer:<br />
<br />
When the calculation type is MEP, the ''mep ''shows that the trajectory falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub> smoothly, and the distance between H<sub>2 </sub>and H<sub>3</sub> is almost constant. When the calculation type is Dynamics, the trajectory still falls off from the valley floor to H<sub>1</sub>+ H<sub>2</sub>-H<sub>3</sub>, but the distance between H<sub>2 </sub>and H<sub>3</sub> oscillates slightly because the molecule has vibrational energy. Also, the distance between H<sub>1</sub> and H<sub>2</sub> increases to a larger value in dynamics calculation type than that in MEP calculation type. The reason is that the atoms have mass and they have inertia when they are moving. Therefore, the atoms will move further in reality.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800671MRD:jw139182020-05-08T15:05:16Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position (r<sub>ts</sub>) and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
<br />
To locate the transition state of the reaction, the first step was to check the main range of r<sub>ts</sub> on the saddle point, and the range was r=80-100 pm. Then the initial conditions were changed into r1=r2, p1=p2=0.0 g.mol<sup>-1</sup>.pm.fs<sup>-1</sup>, and the r value was testing in the range. Finally, the best transition state position was found at r<sub>ts</sub> =91 pm. If the trajectory starts at this point, it will not fall off due to no gradient, and the distance between the atoms will not change. So r1 and r2 is always constant at 91 pm. This can be shown in a "Internuclear Distances vs Time" plot below.<br />
<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800627MRD:jw139182020-05-08T14:35:50Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position ('''r<sub>ts</sub>''') and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:<br />
[[File:Figure 1 (jw13918) Internuclear distances vs Time.png]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Figure_1_(jw13918)_Internuclear_distances_vs_Time.png&diff=800609File:Figure 1 (jw13918) Internuclear distances vs Time.png2020-05-08T14:21:01Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800588MRD:jw139182020-05-08T14:03:06Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
* On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?<br />
Answer: <br />
<br />
On a potential energy surface diagram, the transition state is on the maximum of the minimum energy path, which is the saddle point. On this point, the gradient of potential energy is zero, and it can be defined mathematically as ∂V(ri)/∂ri=0. ri could represent both r1 and r2 in this case because this saddle point on energy path links both reactants and products in two directions separately. In H+H<sub>2</sub> system, r1=r2 at transition state.<br />
<br />
* Report your best estimate of the transition state position ('''r<sub>ts</sub>''') and explain your reasoning illustrating it with a “Internuclear Distances vs Time” plot for a relevant trajectory.<br />
Answer:</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=800381MRD:jw139182020-05-08T10:12:46Z<p>Jw13918: </p>
<hr />
<div>== EXERCISE 1: H+H<sub>2 </sub>system ==<br />
<br />
=== Dynamics from the transition state region ===<br />
On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=MRD:jw13918&diff=799780MRD:jw139182020-05-07T17:38:50Z<p>Jw13918: Created page with "== '''On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished fr..."</p>
<hr />
<div>== '''On a potential energy surface diagram, how is the transition state mathematically defined? How can the transition state be identified, and how can it be distinguished from a local minimum of the potential energy surface?''' ==</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745851User:Jw139182019-03-01T00:38:57Z<p>Jw13918: </p>
<hr />
<div>== NH3 molecule ==<br />
What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
Optimised N-H bond distance: 1.01798 A<br />
<br />
Optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
How many modes do you expect from the 3N-6 rule? 6.<br />
<br />
Which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
Which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
Which mode is highly symmetric? mode 4.<br />
<br />
One mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
How many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
== N2 molecule ==<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
Optimised N-N bond distance: 1.10550 A<br />
<br />
Optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
== H2 molecule ==<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
Optimised H-H bond distance: 0.74279 A<br />
<br />
Optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
== Crystal Structure ==<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
== Energy differences ==<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
== NF3 molecule ==<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
Optimised N-F bond distance: 1.38404 A<br />
Optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
== MOs of NF3 ==<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
== Addition ==<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
== Reference ==<br />
Bond angle of NF3 and NH3:<br />
<rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745850User:Jw139182019-03-01T00:34:02Z<p>Jw13918: </p>
<hr />
<div>== NH3 molecule ==<br />
What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
== N2 molecule ==<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
== H2 molecule ==<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
== Crystal Structure ==<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
== Energy differences ==<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
== NF3 molecule ==<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
== MOs of NF3 ==<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
== Addition ==<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
== Reference ==<br />
Bond angle of NF3 and NH3:<br />
<rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745848User:Jw139182019-03-01T00:23:47Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
<br />
Bond angle of NF3 and NH3:<br />
<rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745847User:Jw139182019-03-01T00:22:50Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
<br />
Bond angle of NF3 and NH3.<br />
<file://icnas4.cc.ic.ac.uk/jw13918/downloads/33.%20shapes%20of%20molecules%20and%20ions%20(3).pdf></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745845User:Jw139182019-03-01T00:21:56Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
<br />
Bond angle of NF3 and NH3.<br />
<rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745844User:Jw139182019-03-01T00:20:43Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
Bond angle of NF3 and NH3:<br />
rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf<br />
Bond angle of NF3 and NH3.<br />
<rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf><br />
</references></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745843User:Jw139182019-03-01T00:19:47Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
Bond angle of NF3 and NH3:<br />
rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf<br />
Bond angle of NF3 and NH3.<br />
<references><br />
rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf<br />
</references></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745841User:Jw139182019-03-01T00:17:16Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.<br />
<br />
Bond angle of NF3 and NH3:<br />
rsc.org/learn-chemistry/resource/download/res00000648/cmp00000674/pdf</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745840User:Jw139182019-03-01T00:14:42Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.<br />
<br />
<br />
The NF3 bond angle in literature is 102°, compared to the optimised NF3 bond angle 101.830°.<br />
<br />
The NH3 bond angle in literature is 107°, compared to the optimised NH3 bond angle 105.741°.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745810User:Jw139182019-02-28T23:41:51Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
<br />
[[File:Jw13918_4mo.png |150px]]<br />
This MO is deep in energy. It is occupied and non-bonding.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Jw13918_4mo.png&diff=745809File:Jw13918 4mo.png2019-02-28T23:40:28Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745805User:Jw139182019-02-28T23:30:02Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_5mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and bonding.<br />
[[File:Jw13918_17mo.png |150px]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Jw13918_5mo.png&diff=745804File:Jw13918 5mo.png2019-02-28T23:27:25Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745803User:Jw139182019-02-28T23:27:05Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_16mo.png |150px]]<br />
This MO is not deep in energy. It is occupied and anti-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
<br />
[[File:Jw13918_17mo.png |150px]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Jw13918_16mo.png&diff=745800File:Jw13918 16mo.png2019-02-28T23:21:20Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745799User:Jw139182019-02-28T23:20:15Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
This MO is HOMO. It is occupied and antibonding.<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
<br />
[[File:Jw13918_17mo.png |150px]]<br />
<br />
[[File:Jw13918_17mo.png |150px]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Jw13918_17mo.png&diff=745797File:Jw13918 17mo.png2019-02-28T23:15:06Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745796User:Jw139182019-02-28T23:13:23Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]<br />
This MO is LUMO. It is unoccupied and non-bonding.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745794User:Jw139182019-02-28T23:05:25Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png|150px]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745793User:Jw139182019-02-28T23:03:58Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_18mo.png]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Jw13918_18mo.png&diff=745792File:Jw13918 18mo.png2019-02-28T23:03:29Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745791User:Jw139182019-02-28T23:01:56Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_mo_18.tif]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Jw13918_mo_18.tif&diff=745790File:Jw13918 mo 18.tif2019-02-28T23:01:37Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745789User:Jw139182019-02-28T23:00:52Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.<br />
<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745778User:Jw139182019-02-28T22:35:32Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NH3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>N2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>H2</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>NF3</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745773User:Jw139182019-02-28T22:31:45Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
<br />
Charge on the N-atom is +0.660, charge on F-atoms is -0.200 because F has higher electronegativity than N.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745770User:Jw139182019-02-28T22:27:55Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!482!!482!!644!!930!!930!!1062<br />
|-<br />
| symmetry ||E||E||A1||E||E||A1<br />
|-<br />
| intensity/arbitrary units ||1||1||3||208||208||40<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745763User:Jw139182019-02-28T22:22:25Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_nf3.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:Jw13918_screenshot_nf3.PNG&diff=745761File:Jw13918 screenshot nf3.PNG2019-02-28T22:21:52Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745760User:Jw139182019-02-28T22:19:24Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_NF3_OPT.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745759User:Jw139182019-02-28T22:18:32Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=User:Jw13918&diff=745758User:Jw139182019-02-28T22:17:53Z<p>Jw13918: </p>
<hr />
<div>What is the molecule? Ammonia.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -56.55776873 a.u.<br />
<br />
What is the RMS gradient? 0.00000485 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-H bond distance: 1.01798 A<br />
<br />
optimised H-N-H bond angle: 105.741°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000004 0.000450 YES<br />
RMS Force 0.000004 0.000300 YES<br />
Maximum Displacement 0.000072 0.001800 YES<br />
RMS Displacement 0.000035 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>NH3_OPTIMISATION_JW13918.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.<br />
<br />
<br />
What is the molecule? N2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -109.52412868 a.u.<br />
<br />
What is the RMS gradient? 0.00000060 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised N-N bond distance: 1.10550 A<br />
<br />
optimised N-N bond angle: 180°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000001 0.000450 YES<br />
RMS Force 0.000001 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000000 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_N2_OPT.LOG</uploadedFileContents><br />
<script>frame 10</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:JW13918_N2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_n2.PNG]]<br />
<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!2457<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on N-atoms is 0.<br />
<br />
<br />
<br />
What is the molecule? H2.<br />
<br />
What is the calculation method? RB3LYP <br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -1.17853936 a.u.<br />
<br />
What is the RMS gradient? 0.00000017 a.u.<br />
<br />
What is the point group of your molecule? D*H<br />
<br />
optimised H-H bond distance: 0.74279 A<br />
<br />
optimised H-H bond angle: 180°<br />
<br />
<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000000 0.000450 YES<br />
RMS Force 0.000000 0.000300 YES<br />
Maximum Displacement 0.000000 0.001800 YES<br />
RMS Displacement 0.000001 0.001200 YES<br />
</pre><br />
<br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_H2_OPT.LOG</uploadedFileContents><br />
<script>frame 12</script></jmolApplet></jmol><br />
<br />
<br />
The optimisation file is liked to [[Media:JW13918_H2_OPT.LOG| here]]<br />
<br />
[[File:Jw13918_screenshot_h2.PNG]]<br />
<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!4466<br />
|-<br />
<br />
<br />
| intensity/arbitrary units ||0<br />
|}<br />
<br />
<br />
Charge on H-atoms is 0.<br />
<br />
<br />
<br />
[[https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=TAGLAO&DatabaseToSearch=Published| N2_LAGLAO10]]<br />
<br />
<br />
N-N bond distance in crystal structure is 1.112(9)A.<br />
The crystal structure and computational distances are different. The N-N bond distance in crystal is larger because there is attraction force between N-atom and the metal ion, and then the attraction force between N-N atoms is weaker than that in N2 molecule.<br />
<br />
<br />
E(NH3)= -56.55776873 a.u.<br />
<br />
2*E(NH3)= -113.11553746 a.u.<br />
<br />
E(N2)= -109.52412868 a.u.<br />
<br />
E(H2)= -1.17853936 a.u.<br />
<br />
3*E(H2)= -3.53561808 a.u.<br />
<br />
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557907= -146.8kJ/mol<br />
<br />
So the ammonia product is more stable because its energy level is deeper.<br />
<br />
<br />
<br />
What is the molecule? NF3.<br />
<br />
What is the calculation method? RB3LYP<br />
<br />
What is the basis set? 6-31G(d,p)<br />
<br />
What is the final energy E(RB3LYP) in atomic units (au)? -354.07131058 a.u.<br />
<br />
What is the RMS gradient? 0.00010256 a.u.<br />
<br />
What is the point group of your molecule? C3V<br />
<br />
optimised N-F bond distance: 1.38404 A<br />
<br />
optimised F-N-F bond angle: 101.830°<br />
<br />
<pre><br />
Item Value Threshold Converged?<br />
Maximum Force 0.000164 0.000450 YES<br />
RMS Force 0.000108 0.000300 YES<br />
Maximum Displacement 0.000612 0.001800 YES<br />
RMS Displacement 0.000296 0.001200 YES<br />
</pre><br />
<br />
<jmol><jmolApplet><br />
<title>test molecule</title><br />
<color>black</color><br />
<size>200</size><br />
<uploadedFileContents>JW13918_NF3_OPT.LOG</uploadedFileContents><br />
<script>frame 16</script></jmolApplet></jmol><br />
<br />
The optimisation file is liked to [[Media:NH3_OPTIMISATION_JW13918.LOG| here]]<br />
<br />
[[File:Screenshot display vib.PNG]]<br />
<br />
{| class="wikitable" border="1"<br />
|+ <br />
!wavenumber/cm-1 !!1090!!1694!!1694!!3461!!3590!!3590<br />
|-<br />
| symmetry ||A1||E||E||A1||E||E<br />
|-<br />
| intensity/arbitrary units ||145||14||14||1||0||0<br />
|}<br />
<br />
how many modes do you expect from the 3N-6 rule? 6.<br />
<br />
which modes are degenerate (ie have the same energy)? 2 and 3 are degenerate, 5 and 6 are degenerate.<br />
<br />
which modes are "bending" vibrations and which are "bond stretch" vibrations? "bending" vibrations: 1,2,3. "bond stretch" vibrations: 4,5,6.<br />
<br />
which mode is highly symmetric? mode 4.<br />
<br />
one mode is known as the "umbrella" mode, which one is this? mode 1.<br />
<br />
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? 2.<br />
<br />
Charge on the N-atom is -1.125, charge on H-atoms is +0.375 because N has higher electronegativity than H.</div>Jw13918https://chemwiki.ch.ic.ac.uk/index.php?title=File:JW13918_NF3_OPT.LOG&diff=745756File:JW13918 NF3 OPT.LOG2019-02-28T22:17:28Z<p>Jw13918: </p>
<hr />
<div></div>Jw13918