Lab 5 creating walsh diagrams from computed molecular orbital energies lab report by Hanna Thomson PDF

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constructing walsh diagrams from computed molecular orbital energies at different bond angles of several molecules and analyzing to differentiate the possible correct bond angles...

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Hanna Thomson Lab 5 Wed. 4pm

Lab 5: Creating Walsh Diagrams from Computed Molecular Orbital Energies Background The objective of this lab was to determine how changes in molecular geometry in a molecule can affect molecular stability by modifying atomic orbital overlaps using computational modeling to observe molecules with differing bond angles, molecular orbital values, and energies by graphing all the information in to Walsh diagrams. VSEPR is a typical way of predicting molecular geometries but does not accurately account for electron placement within molecular orbitals, which is why we create Walsh diagrams accounting for the change in energy in molecular orbitals with differing bond angles. The lowest energy level corresponds to the likeliness of the bonds being arranged in that particular position or angle. The energy of the system refers to electron repulsion within the molecular orbitals, or in other words the overlap of molecular orbitals within the molecule. A Walsh diagram graphs the correlation between electron energies and bond angles. In this lab we change the bond angles of water, ammonia, and borane on computer generated molecules, which also then tells us the electron energies at each of these bond angles as well as the molecular orbital and symmetry. Looking at these diagrams we can see at which bond angle the electron energy is at the lowest, giving us the most probable conformation of that Figure one, Walsh diagram. Image obtained from https://uic.blackboard.com/bbcswebdav/pid6391582-dt-content-rid66224369_2/courses/2019.spring.chem.314.1875 2/CHEM314%20Lab%20Manual.pdf

molecule. pictured

Hanna Thomson Lab 5 Wed. 4pm

above in figure one is an example of a Walsh diagram for CH3I. We observe that the HCH angle is lowest in energy at 120 degrees, meaning this is the most probable conformation of the molecule. We can look at the VSEPR geometries for each molecule and get a general idea of what bond angle we would expect the electrons to behave, corresponding to the lower electron energy. For H2O, we expect the energy to be lowest at 105 degrees since the molecule holds a “bent” geometry and VSEPR predicts a 104.5 degree angle between the oxygen central atom and the hydrogens, pictured below in figure two.

Figure 2, VSEPR for H2O. image obtained from http://chemistrydesk.blogspot.com/2011/05/p rediction-of-shape-ofmolecules-by.html

For ammonia, according to VSEPR we expect the energy to be lowest around 110 degrees, because VSEPR predicts a 107 degree angle between the nitrogen central atom and the surrounding three hydrogens. These bond angles would give a trigonal pyramidal geometry pictured below in figure three. And for

Figure 3, VSEPR for NH3. Image obtained from BH3, https://www.zigya.com/study/book? class=11&board=hbse&subject=Chem VSEPR istry&book=Chemistry%20Part %20I&chapter=Chemical%20Bonding tells us %20and%20Molecular %20Structure&q_type=&q_topic=Vale nce%20Bond%20Theory Figure 4, BH VSEPR. Image obtained %20(VBT)&question_id=CHEN110865 3 from 97 http://ion.chem.usu.edu/~ensigns/Jm

Hanna Thomson Lab 5 Wed. 4pm

the molecule is trigonal planar and we would expect the energy to be lowest around 120 degree bond angles between the central boron atom and the three surrounding hydrogens. The molecule is planar unlike the trigonal pyramidal geometry of ammonia because there are no lone pairs surrounding the central atom like there are in ammonia, causing bending of the bond angles. Pictured below in figure four is the geometry and bond angles of borane.

After plotting each molecule and changing the bond angles we observed the molecular orbitals at the endpoints of each of our analysis, they are pictured below in figure five six and seven.

Orbital # diagram

1

NH3 at 120 degrees figure five 2

NH3 90 degrees figure five

3

4

Hanna Thomson Lab 5 Wed. 4pm

Orbital # diagram

1

Orbital # Diagram

Orbital # diagram

Orbital # Diagram

1

1

2

H2O at 90 degrees figure six 2

H2O at 180 degrees figure six 2

BH3 at 100 degrees figure 7 1 2

BH3 at 180 degrees figure 7

3

4

3

4

3

4

3

Hanna Thomson Lab 5 Wed. 4pm

Orbital # diagram

1

2

3

We can see with the adjustment of the bond angles, changes the molecular orbitals due to electron repulsion as they move closer to each other with each angle adjustment. In the second and third orbitals we observe a node, where there does not exist orbital overlapping within the molecule. After graphing the Walsh diagrams (pictured in figure five, six, and seven in the data and calculations section), we observe an unusual pattern in the diagrams for H2O, the lowest energy tends to be at the higher bond angles around 160-180 degrees the energy in kcal/mol seems to be lower. However, according to VSEPR theory for water the bond angle is estimated to be around 104.5. Before the conversions to kcal/mol the original energies displayed this trend with the lowest energy around 105 degrees, this could be due to calculation error and/or experimental error when graphing the molecule. The energy is lowest for ammonia around 110 degrees according to figure seven pictured below, this is what we would expect according to VSEPR theory the bond angle of the lowest energy is around 107 degrees. For BH3, the lowest energy looks to be around 180 degree bond angles, this doesn’t make much sense according to VSEPR we should observe lower bond energies around 120 degrees because the molecule is planar and does not possess any lone pairs resulting in particular bond angles. This could be a fault in my graphing or converting to kcal/mol from the original energies from the website.

Hanna Thomson Lab 5 Wed. 4pm

Procedure First we opened webmo.net, and clicked on working demo. We then clicked on the link titled ‘webmo demo server’ and signed in as a guest. We then created a new job, and selected a central atom, for example oxygen for H 2O and then attached the two hydrogens. By selecting each atom in order we then adjusted the bond angle to 90 degrees and pressed run job under guassian, molecular orbitals, and G3LYP. Scrolling to the bottom we entered the molecular orbital energies for orbitals 2-5 in an excel spreadsheet along with the overall G3LYP energy. We then repeated this same process in 5 degree intervals up to 180 degrees for a linear molecule until we obtained all the energy range. We repeated all the previous steps for NH3 and BH3 as well. After we obtained molecular orbital data for all three molecules at every bond angle specified, we made three Walsh diagrams for every molecule. one consisting of all the individual molecular orbital energies and the bond angles, another consisting of the sum of the molecular orbital energies and the bond angles, and the last one consisting of the G3LYP energies and the bond angles. We made sure to convert all the energies in to kcal/mol before graphing. Data and calculations H2O Molecular Orbital Energies Energy Sym Energy Energy Orb metr Occup Energy Energy Energy Energy Energy Energy Energy @ ancy @ 90° @ 100° @ 110° @ 120° @ 130° @ 140° @ 150° 160° @ 170° @ 180° ital y 1

2 A1

2 -9.774

0.9693 0.9618 0.9545 0.9469 0.9389 0.9304 0.9223 0.9161 0.9137 9 5 6 8 2 6 2 4 2

3B2

4A1

5B1

Total Energy

Energy @ 90°

2

Hanna Thomson Lab 5 Wed. 4pm - 0.4832 0.4975 0.5093 - 0.5250 0.5290 0.5308 0.5312 0.5312 0.4666 9 6 2 0.5185 5 5 6 9 9

2

0.3958 0.3749 0.3544 0.3341 0.3142 0.2951 0.2776 0.2631 0.2533 0.2498 6 5 2 6 8 8 7 2 1 4

2

- 0.2877 0.2838 0.2794 - 0.2686 - 0.2562 0.2516 0.2498 0.2912 2 4 4 0.2744 6 0.2624 9 1 4 76.395 76.399 76.397 76.387 76.377 76.364 76.350 76.228 76.329 76.329 96498 22599 06152 76265 19482 25466 58995 2737 59205 88983

Energy @ 100°

Energy @ 110°

H20 ENERGY in kcal/mol Energy Energy Energy Energy @ 120° @ 130° @ 140° @ 150°

Energy @ 160°

Energy @ 170°

Energy @ 180°

A1

6133.27 608.257 603.563 598.969 594.225 589.180 583.884 578.789 574.892 573.411 0239 2566 8907 9226 7503 5743 2012 3704 4491 2966

B2

292.795 303.268 312.223 319.602 325.363 329.473 331.983 333.119 333.389 333.389 6994 8246 378 8839 4165 6005 6365 4277 2566 2566

A1

248.405 235.284 222.401 209.688 197.213 185.228 174.240 165.110 158.954 156.776 7127 4996 7398 4074 5285 1066 424 1681 3048 8486

B1

182.730 180.546 178.112 175.351 172.188 168.586 164.658 160.824 157.887 156.776 6208 8895 1546 115 4696 5679 3616 2816 5395 8486

Total Ener 47939.1 47941.2 47939.8 47934.0 47927.3 47919.2 47910.6 47833.9 47897.5 47897.6 9284 0598 278 8235 5707 7714 0855 4368 019 5559 gy

energy (kcal/mol)

individual MO energies vs. bond angle 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% ° 0° 0° 0° 0° 0° 0° 0° 0° 0° 90 12 13 10 11 14 15 17 16 18 @ y@ y@ y@ y@ y@ y@ y@ y@ y@ gy rg rg rg er rg rg rg rg rg rg e e e e e e e e e n E En En En En En En En En En bond angle

Walsh Diagrams for H2O

Hanna Thomson Lab 5 Wed. 4pm

energy kcal/mol

G3LYP energies vs. bond angle -47780 ° 0° 0° 0° 0° 0° 0° 0° 0° 0° -4780090 12 15 10 11 16 17 13 14 18 @ @ @ @ @ @ @ @ @ @ -47820 gy gy gy gy gy gy gy gy gy gy er er er er er er er er er er n n n n n n n n n En-47840 E E E E E E E E E -47860 -47880 -47900 -47920 -47940 -47960 bond angle

Hanna Thomson Lab 5 Wed. 4pm

energy kcal/mol

sum MO energies vs. bond angle 0 ° ° ° ° ° ° ° 0° 0° 0° 30 40 60 70 50 80 -100090 11 12 10 1 1 1 1 1 1 @ y@ y@ y@ y@ y@ y@ y@ y@ y@ gy -2000 rg rg rg rg rg rg er rg rg rg e e e e e e e e e n E -3000 En En En En En En En En En -4000 -5000 -6000 -7000 -8000 bond angle

BH3 Molecular Orbital Energies Orb Sym Occup Energy Energy Energy Energy Energy Energy Energy Energy Energy ital metry ancy @ 100° @ 110° @ 120° @ 130° @ 140° @ 150° @ 160° @ 170° @ 180° 1 0.5280 0.5267 0.5280 0.5274 0.5323 0.5460 0.5462 0.5515 4 2 4 2 5 -0.5335 4 6 5 2 0.3863 0.3810 0.3863 0.3847 0.3974 0.3981 0.3995 0.4079 0.4075 2 6 6 6 8 4 4 2 7 2

2 A1'

3 E'

0.3252 0.3252 0.3282 0.3090 0.3059 0.2805 0.2742 2 9 -0.3323 9 3 7 2 -0.2998 1 9

4 E' 5 6 7

Total Energy

100 A1'

-

26.593 26.596 26.593 26.595 26.583 26.579 26.560 26.552 26.528 65873 92825 65861 83666 7948 99924 82586 93417 91095

BH3 ENERGY in kcal/mol @ different Bond Angles 110 120 130 140 150 160 -

-

-

-

-

-

170

180

-

-

Hanna Thomson Lab 5 Wed. 4pm 331.3498 330.5215 331.3498 330.9607 334.0544 334.7760 342.6450 342.7830 346.1025 524 405 524 968 162 515 144 663 89

E'

242.4443 239.1185 242.4443 241.4529 249.3971 249.8364 250.7023 256.0048 255.7224 772 795 772 13 77 333 957 467 677

E'

204.1224 208.5212 204.1224 205.9672 193.9442 191.9675 188.1271 176.0225 172.1194 026 407 026 791 066 533 982 496 436

Total Ener 16687.76 16689.81 16687.76 16689.12 16681.57 16679.18 16667.15 16662.20 16647.13 gy 038 517 727 874 049 687 012 185 02

Walsh diagrams for BH3

energy kcal/mol

individual MO energy vs. bond angle 0 s s s s s s s s -100es ee ee ee ee ee ee e ee ee -200 gr gr gr gr gr gr gr gr gr e e e e e e e e e 0d-300 0d 0d 0d 0d 0d 0d 0d 0d 10 -400 11 12 13 14 15 16 17 18 -500 -600 -700 -800 -900 bond angle

Hanna Thomson Lab 5 Wed. 4pm

B3LYP energies vs. bond angle

energy kcal/mol

-16620 s s s s s s s s s ee ee ee ee ee ee ee ee ee -16630 gr gr gr gr gr gr gr gr gr e e e e e e e e e d 0d 0d 0d 0d 0d 0d 0d 0d 00 18 17 16 15 14 13 12 11 1-16640 -16650 -16660 -16670 -16680 -16690 -16700 bond angle

energy kcal/mol

sum MO energy vs. bond angle -770 es es es es es es es es es re re re re re re re re re -772 g g g g g g g g g e e e e e e e e e 0d 0d 0d 0d 0d 0d 0d 0d 0d 18 17 16 15 14 13 12 10 -774 11 -776 -778 -780 -782 -784 bond angle

NH3 Molecular Orbital Energies Orbi Symmet Occupan Energy tal ry cy @ 90°

Energy @ 95°

Energy Energy Energy @ 100° @ 105° @ 110°

Energy @ 115°

Energy @ 120°

Energy @ 125°

1 1A1'

2

-0.78671

-0.7905 -0.78963 -0.78847

-0.78764

-0.78711 -0.78671 -0.78685

1E'

2

-0.44016 -0.47791 -0.47288 -0.46635

-0.45978

-0.45337 -0.44016

1E'

2

-0.44016 -0.39545 -0.40165 -0.41032

-0.41856

-0.42609 -0.44016 -0.43183

1A2''

2

-0.20805 -0.20822

0.20809

-0.20806 -0.20805 -0.20805

Total Energy

56.49276 56.50108 329 282

-0.2081 -0.20812

56.5078 56.51319 56.514993 19 99 9828

NH3

-0.4482

56.51783 56.52001 56.5192 5761 457 599

Hanna Thomson Lab 5 Wed. 4pm Energy in kcal/mol

Energy @ 90°

Total energy

Energy @ 95°

Energy @ 100°

Energy @ 105°

Energy @ 110°

Energy @ 115°

Energy @ 120°

Energy @ 125°

493.6676 496.0458 495.4999 317 645 054 276.2043 299.8928 296.7364 614 262 559

494.2511 493.9186 493.6676 493.755456 7 054 09 888 -494.7720212 288.5160 284.4937 276.2043 281.249533 -292.6388222 88 553 614 8

276.2043 248.1484 252.0389 899 341 614 130.5532 130.6599 130.5846 229 24 475

262.6501 267.3753 276.2043 270.977211 5 614 098 67 -257.4794929 130.5783 130.5595 130.5532 130.553247 5 475 225 -130.5971731 478

35449.71 35454.93 35459.21 474 827 711

35463.66 35465.45 35466.81 35466.3428 3 782 074 686 -35462.54156

Walsh diagrams for NH3

Individual MO Energies vs. Bond Angles

MO energies (kcal/mol)

100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% ° ° 5° 0° 5° 5° 0° 0° 90 95 12 11 11 10 10 12 @ @ gy gy y@ y@ y@ y@ y@ y@ er er rg rg rg rg rg rg e e e e e e En En En En En En En En Bond angle

Hanna Thomson Lab 5 Wed. 4pm

energy (kcal/mol)

B3LYP Energy vs. Bond Angle -35440 ° ° 5° 5° 5° 0° 0° 0° 90 95 12 11 10 12 11 10 -35445 @ @ @ @ @ @ @ @ gy gy gy gy gy gy gy gy er er er er er er er er n n n n n n En-35450 En E E E E E E -35455 -35460 -35465 -35470 bond angle

energy (kcal/mol)

MO sum of energies vs. bond angle 0 ° ° 0° 5° 5° 5° 0° 0° 95 90 12 11 10 12 11 10 -200 @ @ @ @ @ @ @ @ gy gy gy gy gy gy gy gy er -400 ner er er er er er er n n n n n n E En E E E E E E -600 -800 -1000 -1200 -1400 bond angle

Conclusion The purpose of this lab was to study molecular orbital energies by creating Walsh diagrams from computed molecular orbitals and comparing the energies to the VSEPR angles of the same molecules, and observing trends in Walsh diagrams as well as changes and overlaps in orbitals. Overall we observed odd trends in the Walsh diagrams that didn’t exactly match up to the expected lowest energy bond angles we know from VSEPR. The ammonia Walsh diagram

Hanna Thomson Lab 5 Wed. 4pm

was the closest to the expected lowest energy bond angle with the lowest energy being around 110 degrees, and VSEPR predicts about a 107 degree angle between the nitrogen and three hydrogens, the molecule should possess a trigonal pyramidal geometry because of the lone pair on nitrogen resulting in electron repulsion against the three bonds. The molecular orbitals at 90 degrees are similar to the ones of the 120 degree bond angles, however with the second and third orbitals we observe a node on both, and between the 90 and 120 degree angles the orbitals seem to have switched axis. The trends between borane and water did not match up very closely with the expected VSEPR energies and angles, with H2O the lowest energy being at 160-180 degrees which differs from the expected 104.5 degree angle from VSEPR. The lowest energy bond angle from BH3 is around 180 degrees even though we would expect a 120 degree bond angle from VSEPR. The molecular orbitals of the highest and lowest angle of water appear to have the same trend as NH3 where they appear the same with a node between the second and third orbital, but between the highest bond angle and the 90 degree angle they look to have switched axis. The borane molecular orbitals have the same trend with nodes in the second and third orbital and switch or rotate axis between the highest angle and the lowest angle. The change in axis or rotation of the orbitals could be resulting from different orientation of electrons around the atom due to changes in bond angles, meaning more or less electron repulsion happening between the orbitals. The symbols attached to each molecular orbital and energy correspond to the mulliken symbols that you see in the related character tables for the symmetry of each molecule. H2O symmetry is C2v, and with the C2v character table we observe the related mulliken symbols we obtained from the specific orbitals of H2O (A1, B2, and B1). Looking at these symbols in a

Hanna Thomson Lab 5 Wed. 4pm

character table we can view how the bonds within the molecule vibrate. The mulliken symbols for BH3 (D3h symmetry) are A1’ and E’. for NH3 (C3v symmetry) they’re A1’, E’, and A2’’. From these symbols we could also obtain the reducible form of the character tables, giving us how many IR peaks and raman peaks we could expect to see in the molecules as well.

Citations structure of boron trihydride. http://ion.chem.usu.edu/~ensigns/Jmol/VSEPR/BH3 VSEPR.htm (accessed Mar 13, 2019). With the help of VSEPR theory, explain the shape of: (i) NH3 (ii) H2O. from Chemistry Chemical Bonding and Molecular Structure Class 11 Haryana Board - English Medium. https://www.zigya.com/study/book? class=11&board=hbse&subject=Chemistry&book=Chemistry Part I&chapter=Chemical Bonding and Molecular Structure&q_type=&q_topic=Valence Bond Theory (VBT)&question_id=CHEN11086597 (accessed Mar 13, 2019). Agray, S. Prediction of Shape of Molecules by VSEPR Theory. http://chemistrydesk.blogspot.com/2011/05/prediction-of-shape-of-molecules-by.html (accessed Mar 13, 2019)....