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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBEPBEultrafine/cc-pVDZ

19 10 17 12 22

States and conformations

State Conformation minimum conformation conformer description state description
1 1 yes C1 1A
Energy calculated at PBEPBEultrafine/cc-pVDZ
 hartrees
Energy at 0K-398.537320
Energy at 298.15K-398.547287
HF Energy-398.537320
Nuclear repulsion energy324.072696
The energy at 298.15K was derived from the energy at 0K and an integrated heat capacity that used the calculated vibrational frequencies.
Vibrational Frequencies calculated at PBEPBEultrafine/cc-pVDZ
Mode Number Symmetry Frequency
(cm-1)
Scaled Frequency
(cm-1)
IR Intensities
(km mol-1)
Raman Act
4/u)
Dep P Dep U
1 A 3559 3539 34.53      
2 A 3509 3489 146.23      
3 A 3456 3436 1.17      
4 A 3377 3357 0.28      
5 A 3026 3009 25.19      
6 A 2960 2942 12.91      
7 A 2851 2834 83.05      
8 A 1733 1723 207.30      
9 A 1602 1593 25.50      
10 A 1435 1426 5.80      
11 A 1421 1413 63.71      
12 A 1337 1329 36.99      
13 A 1331 1323 12.36      
14 A 1317 1310 30.02      
15 A 1262 1254 10.33      
16 A 1189 1182 2.58      
17 A 1170 1163 13.81      
18 A 1146 1139 128.33      
19 A 1121 1115 79.95      
20 A 1078 1072 101.54      
21 A 1000 994 34.85      
22 A 961 956 2.22      
23 A 878 873 150.07      
24 A 783 778 25.50      
25 A 722 718 36.74      
26 A 645 642 56.67      
27 A 604 600 145.29      
28 A 551 548 2.27      
29 A 528 525 48.83      
30 A 404 402 7.51      
31 A 311 309 2.76      
32 A 296 294 8.35      
33 A 240 239 9.90      
34 A 222 221 24.83      
35 A 165 164 1.16      
36 A 44 44 0.16      

Unscaled Zero Point Vibrational Energy (zpe) 24116.8 cm-1
Scaled (by 0.9942) Zero Point Vibrational Energy (zpe) 23976.9 cm-1
See section III.C.1 List or set vibrational scaling factors to change the scale factors used here.
See section III.C.2 Calculate a vibrational scaling factor for a given set of molecules to determine the least squares best scaling factor.
Rotational Constants (cm-1) from geometry optimized at PBEPBEultrafine/cc-pVDZ
ABC
0.11745 0.07975 0.05000

See section I.F.4 to change rotational constant units
Geometric Data calculated at PBEPBEultrafine/cc-pVDZ

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.779 -0.549 0.001
O2 2.069 -0.347 -0.361
O3 0.391 -1.573 0.544
C4 -0.087 0.682 -0.311
C5 -1.520 0.447 0.194
O6 -2.119 -0.691 -0.387
N7 0.446 1.934 0.227
H8 2.557 -1.161 -0.115
H9 -0.126 0.770 -1.417
H10 -1.497 0.389 1.309
H11 -2.126 1.330 -0.083
H12 -1.635 -1.454 -0.019
H13 1.362 2.145 -0.182
H14 0.578 1.859 1.242

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.35501.22241.53702.51292.92792.51561.88372.13802.78853.46102.57812.76282.7171
O21.35502.26682.38983.71764.20312.86060.98002.68084.00654.52683.88122.59693.1082
O31.22242.26682.45822.80222.81893.52162.30133.09922.82863.89292.10603.91083.5074
C41.53702.38982.45821.53732.45411.46333.22871.11072.16752.15182.65382.06352.0592
C52.51293.71762.80221.53731.41142.46564.39322.15461.11661.10651.91593.36642.7380
O62.92794.20312.81892.45411.41143.72194.70782.67772.10502.04400.97564.49554.0544
N72.51562.86063.52161.46332.46563.72193.76182.09402.70832.66043.98371.02501.0266
H81.88370.98002.30133.22874.39324.70783.76183.55324.56845.30444.20313.51613.8575
H92.13802.68083.09921.11072.15462.67772.09403.55323.07512.46813.02952.37322.9589
H102.78854.00652.82862.16751.11662.10502.70834.56843.07511.79372.27593.67192.5443
H113.46104.52683.89292.15181.10652.04402.66045.30442.46811.79372.82763.58363.0578
H122.57813.88122.10602.65381.91590.97563.98374.20313.02952.27592.82764.68644.1792
H132.76282.59693.91082.06353.36644.49551.02503.51612.37323.67193.58364.68641.6506
H142.71713.10823.50742.05922.73804.05441.02663.85752.95892.54433.05784.17921.6506

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 106.443 C1 C4 C5 109.647
C1 C4 N7 113.931 C1 C4 H9 106.592
O2 C1 O3 123.084 O2 C1 C4 111.292
O3 C1 C4 125.580 C4 C5 O6 112.596
C4 C5 H10 108.475 C4 C5 H11 107.841
C4 N7 H13 110.822 C4 N7 H14 110.362
C5 C4 N7 110.485 C5 C4 H9 107.822
C5 O6 H12 105.306 O6 C5 H10 112.218
O6 C5 H11 107.930 N7 C4 H9 108.107
H10 C5 H11 107.571 H13 N7 H14 107.131
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBEPBEultrafine/cc-pVDZ Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.171      
2 O -0.139      
3 O -0.239      
4 C -0.119      
5 C 0.152      
6 O -0.245      
7 N -0.131      
8 H 0.153      
9 H 0.062      
10 H 0.002      
11 H 0.036      
12 H 0.133      
13 H 0.085      
14 H 0.079      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.486 0.322 0.600 3.552
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.408 -2.281 -0.194
y -2.281 -44.150 0.472
z -0.194 0.472 -39.182
Traceless
 xyz
x 0.258 -2.281 -0.194
y -2.281 -3.855 0.472
z -0.194 0.472 3.597
Polar
3z2-r27.193
x2-y22.742
xy-2.281
xz-0.194
yz0.472


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 8.739 0.080 0.109
y 0.080 8.015 0.066
z 0.109 0.066 5.899


<r2> (average value of r2) Å2
<r2> 217.270
(<r2>)1/2 14.740