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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-398.376821
Energy at 298.15K-398.386773
HF Energy-398.376821
Nuclear repulsion energy324.072350
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 3726 3561 10.67      
2 A 3661 3499 37.59      
3 A 3639 3479 62.34      
4 A 3601 3442 4.20      
5 A 3190 3049 15.95      
6 A 3085 2949 10.56      
7 A 3027 2893 54.58      
8 A 1745 1668 219.27      
9 A 1722 1646 28.22      
10 A 1548 1480 2.87      
11 A 1444 1380 20.95      
12 A 1409 1347 15.41      
13 A 1406 1344 14.20      
14 A 1389 1328 78.99      
15 A 1347 1288 4.33      
16 A 1258 1202 16.15      
17 A 1212 1159 9.89      
18 A 1180 1128 22.48      
19 A 1154 1103 220.17      
20 A 1083 1035 48.37      
21 A 1034 988 111.82      
22 A 1004 959 2.88      
23 A 822 785 24.63      
24 A 736 704 43.93      
25 A 660 631 180.93      
26 A 631 603 315.43      
27 A 588 562 210.30      
28 A 581 555 53.40      
29 A 527 504 28.40      
30 A 437 417 9.81      
31 A 313 299 10.33      
32 A 289 276 6.39      
33 A 255 244 34.02      
34 A 225 215 14.44      
35 A 166 159 3.02      
36 A 30 29 0.92      

Unscaled Zero Point Vibrational Energy (zpe) 25060.8 cm-1
Scaled (by 0.9559) Zero Point Vibrational Energy (zpe) 23955.6 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
0.11847 0.07888 0.05044

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 0.755 -0.558 0.006
O2 2.064 -0.403 -0.344
O3 0.325 -1.579 0.541
C4 -0.068 0.682 -0.313
C5 -1.497 0.491 0.190
O6 -2.123 -0.659 -0.381
N7 0.504 1.917 0.221
H8 2.608 -1.189 -0.139
H9 -0.103 0.764 -1.406
H10 -1.484 0.445 1.290
H11 -2.069 1.372 -0.101
H12 -1.726 -1.476 -0.030
H13 1.387 2.179 -0.208
H14 0.590 1.925 1.234

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.36361.23011.52172.49122.90592.49751.96312.11602.76943.42262.64612.81692.7754
O21.36362.27792.39163.70994.19482.85250.97812.68003.99724.50473.95172.67233.1754
O31.23012.27792.44832.77992.77343.51572.41393.07622.81673.85422.13213.97613.5821
C41.52172.39162.44831.52742.45481.46233.26961.09652.15252.12812.73632.09012.0915
C52.49123.70992.77991.52741.42772.45774.44802.13671.10171.09041.99203.36562.7400
O62.90594.19482.77342.45481.42773.72804.76732.67512.10262.05070.97414.51694.0804
N72.49752.85253.51571.46232.45773.72803.76952.08412.69492.64974.06841.01611.0175
H81.96310.97812.41393.26964.44804.76733.76953.57344.63275.33314.34573.58293.9569
H92.11602.68003.07621.09652.13672.67512.08413.57343.04622.43733.08992.37822.9664
H102.76943.99722.81672.15251.10172.10262.69494.63273.04621.77122.34373.67332.5488
H113.42264.50473.85422.12811.09042.05072.64975.33312.43731.77122.86953.55093.0270
H122.64613.95172.13212.73631.99200.97414.06844.34573.08992.34372.86954.80444.3052
H132.81692.67233.97612.09013.36564.51691.01613.58292.37823.67333.55094.80441.6672
H142.77543.17543.58212.09152.74004.08041.01753.95692.96642.54883.02704.30521.6672

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 112.897 C1 C4 C5 109.576
C1 C4 N7 113.623 C1 C4 H9 106.714
O2 C1 O3 122.784 O2 C1 C4 111.857
O3 C1 C4 125.342 C4 C5 O6 112.298
C4 C5 H10 108.834 C4 C5 H11 107.592
C4 N7 H13 113.767 C4 N7 H14 113.788
C5 C4 N7 110.562 C5 C4 H9 107.910
C5 O6 H12 110.651 O6 C5 H10 111.818
O6 C5 H11 108.310 N7 C4 H9 108.222
H10 C5 H11 107.803 H13 N7 H14 110.132
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 0.540      
2 O -0.577      
3 O -0.456      
4 C -0.134      
5 C -0.060      
6 O -0.638      
7 N -0.720      
8 H 0.408      
9 H 0.239      
10 H 0.151      
11 H 0.208      
12 H 0.400      
13 H 0.328      
14 H 0.312      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.803 0.660 0.906 3.965
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -42.927 -2.659 -1.560
y -2.659 -43.222 1.416
z -1.560 1.416 -39.326
Traceless
 xyz
x -1.653 -2.659 -1.560
y -2.659 -2.096 1.416
z -1.560 1.416 3.749
Polar
3z2-r27.498
x2-y20.295
xy-2.659
xz-1.560
yz1.416


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 7.372 0.360 -0.099
y 0.360 7.347 -0.118
z -0.099 -0.118 5.114


<r2> (average value of r2) Å2
<r2> 217.814
(<r2>)1/2 14.759