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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBEPBE/6-31+G**

19 10 17 12 22

States and conformations

State Conformation minimum conformation conformer description state description
1 1 yes C1 1A
Energy calculated at PBEPBE/6-31+G**
 hartrees
Energy at 0K-398.545399
Energy at 298.15K-398.555157
HF Energy-398.545399
Nuclear repulsion energy323.031217
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 PBEPBE/6-31+G**
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 3641 3599 54.79      
2 A 3626 3585 66.08      
3 A 3526 3486 5.75      
4 A 3427 3388 1.57      
5 A 3060 3025 15.35      
6 A 2989 2955 11.61      
7 A 2920 2886 54.29      
8 A 1728 1708 267.02      
9 A 1618 1600 37.50      
10 A 1449 1432 4.37      
11 A 1381 1366 34.96      
12 A 1342 1326 2.60      
13 A 1337 1322 20.07      
14 A 1322 1307 42.81      
15 A 1263 1248 10.55      
16 A 1198 1185 12.55      
17 A 1148 1135 5.22      
18 A 1116 1103 165.37      
19 A 1095 1082 67.75      
20 A 1059 1047 116.14      
21 A 992 981 36.91      
22 A 962 951 1.75      
23 A 825 816 151.68      
24 A 785 776 38.61      
25 A 712 704 20.62      
26 A 613 606 92.63      
27 A 562 556 7.56      
28 A 536 530 193.79      
29 A 494 489 17.23      
30 A 433 428 10.05      
31 A 286 282 4.34      
32 A 279 275 23.76      
33 A 262 259 19.21      
34 A 204 202 3.62      
35 A 152 150 4.57      
36 A 29 28 1.16      

Unscaled Zero Point Vibrational Energy (zpe) 24184.5 cm-1
Scaled (by 0.9886) Zero Point Vibrational Energy (zpe) 23908.8 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 PBEPBE/6-31+G**
ABC
0.11627 0.07714 0.05108

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

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.801 -0.539 0.010
O2 2.085 -0.330 -0.377
O3 0.433 -1.567 0.563
C4 -0.093 0.675 -0.307
C5 -1.530 0.428 0.189
O6 -2.133 -0.714 -0.393
N7 0.413 1.942 0.231
H8 2.601 -1.128 -0.147
H9 -0.129 0.762 -1.408
H10 -1.525 0.369 1.298
H11 -2.134 1.303 -0.094
H12 -1.684 -1.497 -0.028
H13 1.313 2.198 -0.179
H14 0.527 1.901 1.247

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.35701.22411.54042.53032.96702.52091.90092.13702.80943.46662.66332.79132.7491
O21.35702.26782.39903.73694.23542.88560.97832.67454.04044.53253.96032.65123.1686
O31.22412.26782.46182.82402.86833.52502.32363.10222.84983.90632.19863.93773.5363
C41.54042.39902.46181.54102.47011.46623.24571.10522.17272.14632.70722.07652.0738
C52.53033.73692.82401.54101.41652.46384.42792.15141.10971.10031.94383.36952.7426
O62.96704.23542.86832.47011.41653.73184.75932.68832.09742.03900.97434.51694.0749
N72.52092.88563.52501.46622.46383.73183.78922.09102.71482.64574.03641.02151.0231
H81.90090.97832.32363.24574.42794.75933.78923.55184.62125.32334.30263.56763.9267
H92.13702.67453.10221.10522.15142.68832.09103.55183.07012.45783.07012.37742.9624
H102.80944.04042.84982.17271.10972.09742.71484.62123.07011.78342.29473.68552.5620
H113.46664.53253.90632.14631.10032.03902.64575.32332.45781.78342.83743.56203.0393
H122.66333.96032.19862.70721.94380.97434.03644.30263.07012.29472.83744.76034.2501
H132.79132.65123.93772.07653.36954.51691.02153.56762.37743.68553.56204.76031.6547
H142.74913.16863.53632.07382.74264.07491.02313.92672.96242.56203.03934.25011.6547

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 107.872 C1 C4 C5 110.400
C1 C4 N7 113.931 C1 C4 H9 106.599
O2 C1 O3 122.867 O2 C1 C4 111.631
O3 C1 C4 125.490 C4 C5 O6 113.204
C4 C5 H10 109.017 C4 C5 H11 107.527
C4 N7 H13 111.929 C4 N7 H14 111.592
C5 C4 N7 110.005 C5 C4 H9 107.642
C5 O6 H12 107.338 O6 C5 H10 111.681
O6 C5 H11 107.562 N7 C4 H9 107.993
H10 C5 H11 107.606 H13 N7 H14 108.058
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBEPBE/6-31+G** Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.395      
2 O -0.399      
3 O -0.462      
4 C -0.266      
5 C -0.160      
6 O -0.456      
7 N -0.527      
8 H 0.365      
9 H 0.208      
10 H 0.152      
11 H 0.179      
12 H 0.361      
13 H 0.312      
14 H 0.298      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.248 0.624 0.661 3.373
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -42.625 -2.030 -1.414
y -2.030 -45.144 1.566
z -1.414 1.566 -41.531
Traceless
 xyz
x 0.712 -2.030 -1.414
y -2.030 -3.066 1.566
z -1.414 1.566 2.354
Polar
3z2-r24.707
x2-y22.519
xy-2.030
xz-1.414
yz1.566


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 9.769 -0.062 -0.300
y -0.062 9.785 -0.211
z -0.300 -0.211 7.307


<r2> (average value of r2) Å2
<r2> 219.156
(<r2>)1/2 14.804