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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBE1PBE/6-31G*

19 10 17 12 22

States and conformations

State Conformation minimum conformation conformer description state description
1 1 yes C1 1A
Energy calculated at PBE1PBE/6-31G*
 hartrees
Energy at 0K-398.512820
Energy at 298.15K-398.522913
HF Energy-398.512820
Nuclear repulsion energy326.652725
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 PBE1PBE/6-31G*
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 3738 3552 11.20      
2 A 3732 3547 158.91      
3 A 3618 3438 3.55      
4 A 3526 3351 0.91      
5 A 3153 2996 21.85      
6 A 3075 2922 11.91      
7 A 2996 2847 66.15      
8 A 1845 1753 245.23      
9 A 1709 1624 38.18      
10 A 1537 1460 1.51      
11 A 1475 1401 53.54      
12 A 1414 1344 35.86      
13 A 1409 1339 54.54      
14 A 1401 1331 19.33      
15 A 1340 1273 11.48      
16 A 1256 1193 8.89      
17 A 1226 1165 49.87      
18 A 1209 1149 158.38      
19 A 1174 1116 38.20      
20 A 1139 1083 106.82      
21 A 1046 994 42.76      
22 A 1011 961 0.85      
23 A 905 860 194.67      
24 A 823 782 33.21      
25 A 753 716 44.15      
26 A 665 632 89.53      
27 A 598 568 183.54      
28 A 573 545 31.05      
29 A 540 513 32.80      
30 A 427 406 8.32      
31 A 317 301 5.23      
32 A 302 287 9.77      
33 A 254 241 27.50      
34 A 233 222 16.35      
35 A 169 161 1.71      
36 A 31 29 0.36      

Unscaled Zero Point Vibrational Energy (zpe) 25308.3 cm-1
Scaled (by 0.9503) Zero Point Vibrational Energy (zpe) 24050.5 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 PBE1PBE/6-31G*
ABC
0.12054 0.08006 0.05072

See section I.F.4 to change rotational constant units
Geometric Data calculated at PBE1PBE/6-31G*

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.767 -0.547 -0.004
O2 2.051 -0.353 -0.343
O3 0.373 -1.563 0.526
C4 -0.084 0.680 -0.314
C5 -1.507 0.455 0.188
O6 -2.094 -0.686 -0.373
N7 0.453 1.917 0.224
H8 2.532 -1.162 -0.102
H9 -0.122 0.771 -1.407
H10 -1.494 0.409 1.290
H11 -2.107 1.322 -0.101
H12 -1.617 -1.438 0.005
H13 1.359 2.125 -0.183
H14 0.579 1.846 1.229

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.34251.21131.52492.49292.88762.49511.87122.12012.77453.42972.54502.74332.6989
O21.34252.24412.37203.68784.15852.83380.97072.66803.97644.48963.84132.57853.0782
O31.21132.24412.43752.77852.76743.49422.28403.06992.82013.85522.06063.88303.4864
C41.52492.37202.43751.52612.43071.45263.20561.09752.15222.13332.63372.04652.0445
C52.49293.68782.77851.52611.40082.44624.36032.13641.10241.09301.90523.33792.7144
O62.88764.15852.76742.43071.40083.69104.65762.66062.07972.02640.96684.45644.0149
N72.49512.83383.49421.45262.44623.69103.72902.07512.68372.64893.94891.01421.0155
H81.87120.97072.28403.20564.36034.65763.72903.53244.53925.26174.15943.49103.8250
H92.12012.66803.06991.09752.13642.66062.07513.53243.04702.43913.01772.35042.9319
H102.77453.97642.82012.15221.10242.07972.68374.53923.04701.77352.25333.64022.5223
H113.42974.48963.85522.13331.09302.02642.64895.26172.43911.77352.80483.55863.0427
H122.54503.84132.06062.63371.90520.96683.94894.15943.01772.25332.80484.64634.1356
H132.74332.57853.88302.04653.33794.45641.01423.49102.35043.64023.55864.64631.6377
H142.69893.07823.48642.04452.71444.01491.01553.82502.93192.52233.04274.13561.6377

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 106.879 C1 C4 C5 109.587
C1 C4 N7 113.835 C1 C4 H9 106.757
O2 C1 O3 122.894 O2 C1 C4 111.480
O3 C1 C4 125.571 C4 C5 O6 112.224
C4 C5 H10 108.864 C4 C5 H11 107.937
C4 N7 H13 110.861 C4 N7 H14 110.606
C5 C4 N7 110.389 C5 C4 H9 107.923
C5 O6 H12 105.697 O6 C5 H10 111.810
O6 C5 H11 108.064 N7 C4 H9 108.115
H10 C5 H11 107.771 H13 N7 H14 107.583
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBE1PBE/6-31G* Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.601      
2 O -0.581      
3 O -0.488      
4 C -0.166      
5 C -0.074      
6 O -0.643      
7 N -0.737      
8 H 0.432      
9 H 0.225      
10 H 0.141      
11 H 0.196      
12 H 0.432      
13 H 0.338      
14 H 0.323      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.650 0.261 0.732 3.732
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.342 -2.334 -0.768
y -2.334 -44.243 0.961
z -0.768 0.961 -38.807
Traceless
 xyz
x 0.183 -2.334 -0.768
y -2.334 -4.168 0.961
z -0.768 0.961 3.985
Polar
3z2-r27.969
x2-y22.901
xy-2.334
xz-0.768
yz0.961


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 7.698 0.212 0.010
y 0.212 7.409 -0.031
z 0.010 -0.031 5.402


<r2> (average value of r2) Å2
<r2> 214.855
(<r2>)1/2 14.658