return to home page Computational Chemistry Comparison and Benchmark DataBase Release 22 (May 2022) Standard Reference Database 101 National Institute of Standards and Technology
You are here: Calculated > Energy > Optimized > Energy

All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBE1PBE/aug-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 PBE1PBE/aug-cc-pVDZ
 hartrees
Energy at 0K-398.594840
Energy at 298.15K-398.604825
HF Energy-398.594840
Nuclear repulsion energy326.250704
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/aug-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 3804 3658 66.02      
2 A 3789 3643 93.51      
3 A 3625 3485 7.72      
4 A 3530 3395 2.30      
5 A 3141 3020 16.41      
6 A 3074 2956 12.98      
7 A 3011 2896 48.19      
8 A 1813 1744 281.98      
9 A 1646 1582 34.36      
10 A 1478 1421 5.87      
11 A 1430 1375 32.94      
12 A 1400 1346 53.65      
13 A 1384 1331 31.94      
14 A 1367 1314 5.37      
15 A 1310 1259 6.06      
16 A 1239 1192 19.78      
17 A 1194 1148 20.25      
18 A 1177 1132 192.74      
19 A 1148 1103 15.55      
20 A 1121 1078 114.22      
21 A 1037 997 34.54      
22 A 996 958 3.01      
23 A 861 828 130.79      
24 A 817 785 44.43      
25 A 749 720 20.39      
26 A 626 602 88.74      
27 A 585 563 10.55      
28 A 540 519 180.01      
29 A 515 495 8.07      
30 A 448 431 8.43      
31 A 296 285 5.49      
32 A 285 274 10.11      
33 A 261 251 27.51      
34 A 209 201 3.97      
35 A 154 148 4.27      
36 A 31 30 1.20      

Unscaled Zero Point Vibrational Energy (zpe) 25044.4 cm-1
Scaled (by 0.9616) Zero Point Vibrational Energy (zpe) 24082.7 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/aug-cc-pVDZ
ABC
0.11875 0.07860 0.05207

See section I.F.4 to change rotational constant units
Geometric Data calculated at PBE1PBE/aug-cc-pVDZ

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.790 -0.530 0.014
O2 2.060 -0.333 -0.380
O3 0.426 -1.543 0.567
C4 -0.094 0.671 -0.307
C5 -1.517 0.424 0.188
O6 -2.102 -0.714 -0.393
N7 0.409 1.927 0.229
H8 2.561 -1.127 -0.149
H9 -0.125 0.753 -1.404
H10 -1.510 0.361 1.291
H11 -2.124 1.292 -0.095
H12 -1.640 -1.482 -0.040
H13 1.308 2.168 -0.172
H14 0.524 1.878 1.237

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.34381.21041.52522.50222.92622.49531.87642.12012.77703.43872.61012.75392.7134
O21.34382.24272.37693.69934.17892.86400.96722.64604.00154.49743.88832.62003.1402
O31.21042.24272.43662.79072.82823.48652.29053.07602.81013.87062.15373.88613.4873
C41.52522.37692.43661.52672.44121.45453.21051.10072.15722.13402.66432.05542.0542
C52.50223.69932.79071.52671.40512.44264.37612.13971.10461.09671.92403.33942.7159
O62.92624.17892.82822.44121.40513.69624.68792.66152.08282.02830.96354.47044.0330
N72.49532.86403.48651.45452.44263.69623.75542.08032.69452.63103.98611.01411.0160
H81.87640.96722.29053.21054.37614.68793.75543.51104.56745.27364.21723.52583.8862
H92.12012.64603.07601.10072.13972.66152.08033.51103.05482.44963.02502.36082.9427
H102.77704.00152.81012.15721.10462.08282.69454.56743.05481.77892.27713.65362.5374
H113.43874.49743.87062.13401.09672.02832.63105.27362.44961.77892.81723.54323.0211
H122.61013.88832.15372.66431.92400.96353.98614.21723.02502.27712.81724.69404.1953
H132.75392.62003.88612.05543.33944.47041.01413.52582.36083.65363.54324.69401.6392
H142.71343.14023.48732.05422.71594.03301.01603.88622.94272.53743.02114.19531.6392

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 107.459 C1 C4 C5 110.147
C1 C4 N7 113.719 C1 C4 H9 106.563
O2 C1 O3 122.732 O2 C1 C4 111.733
O3 C1 C4 125.530 C4 C5 O6 112.680
C4 C5 H10 109.083 C4 C5 H11 107.745
C4 N7 H13 111.487 C4 N7 H14 111.270
C5 C4 N7 110.017 C5 C4 H9 107.955
C5 O6 H12 107.162 O6 C5 H10 111.617
O6 C5 H11 107.698 N7 C4 H9 108.211
H10 C5 H11 107.821 H13 N7 H14 107.689
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBE1PBE/aug-cc-pVDZ Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.902      
2 O -0.526      
3 O -0.600      
4 C 0.082      
5 C 1.213      
6 O -0.513      
7 N -0.181      
8 H 0.175      
9 H -0.229      
10 H -0.242      
11 H -0.178      
12 H 0.123      
13 H -0.005      
14 H -0.020      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.097 0.675 0.547 3.217
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.792 -2.133 -1.343
y -2.133 -44.634 1.698
z -1.343 1.698 -40.911
Traceless
 xyz
x 0.980 -2.133 -1.343
y -2.133 -3.283 1.698
z -1.343 1.698 2.302
Polar
3z2-r24.605
x2-y22.842
xy-2.133
xz-1.343
yz1.698


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 9.551 0.017 -0.210
y 0.017 9.485 -0.147
z -0.210 -0.147 7.341


<r2> (average value of r2) Å2
<r2> 215.080
(<r2>)1/2 14.666