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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBEPBE/cc-pVTZ

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/cc-pVTZ
 hartrees
Energy at 0K-398.667859
Energy at 298.15K-398.677631
HF Energy-398.667859
Nuclear repulsion energy324.288107
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/cc-pVTZ
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 3633 3608 53.65      
2 A 3613 3589 54.99      
3 A 3490 3466 2.55      
4 A 3403 3379 0.98      
5 A 3031 3010 18.83      
6 A 2974 2954 13.13      
7 A 2899 2879 52.90      
8 A 1727 1715 239.86      
9 A 1605 1594 28.30      
10 A 1443 1433 3.70      
11 A 1386 1376 46.89      
12 A 1344 1335 2.47      
13 A 1336 1327 18.92      
14 A 1327 1318 28.90      
15 A 1268 1260 6.29      
16 A 1201 1193 11.93      
17 A 1148 1140 1.81      
18 A 1112 1104 154.16      
19 A 1089 1082 88.77      
20 A 1054 1047 103.00      
21 A 990 984 32.03      
22 A 962 956 1.05      
23 A 843 838 157.70      
24 A 789 784 21.64      
25 A 718 713 19.86      
26 A 611 607 78.60      
27 A 566 562 9.20      
28 A 539 536 161.19      
29 A 494 491 19.56      
30 A 433 430 9.54      
31 A 279 277 3.14      
32 A 274 272 14.36      
33 A 254 253 21.41      
34 A 201 199 4.02      
35 A 146 145 3.88      
36 A 30 29 1.22      

Unscaled Zero Point Vibrational Energy (zpe) 24106.5 cm-1
Scaled (by 0.9931) Zero Point Vibrational Energy (zpe) 23940.2 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/cc-pVTZ
ABC
0.11659 0.07754 0.05192

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

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.794 -0.539 0.007
O2 2.073 -0.331 -0.382
O3 0.432 -1.556 0.569
C4 -0.094 0.674 -0.307
C5 -1.525 0.426 0.192
O6 -2.125 -0.711 -0.395
N7 0.415 1.936 0.231
H8 2.580 -1.128 -0.143
H9 -0.134 0.760 -1.404
H10 -1.510 0.362 1.296
H11 -2.128 1.300 -0.082
H12 -1.658 -1.484 -0.039
H13 1.317 2.175 -0.175
H14 0.536 1.879 1.242

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.35321.21671.53562.51822.95102.51381.88732.13092.78933.45402.62832.77042.7275
O21.35322.25792.38983.72104.21472.87480.97502.66544.01674.51693.92042.62603.1442
O31.21672.25792.45252.81052.85993.50812.30343.09492.82443.89062.17813.90623.5018
C41.53562.38982.45251.53512.45921.46353.22921.10142.16112.14042.67842.06502.0613
C52.51823.72102.81051.53511.41272.45864.40232.14321.10631.09711.92823.35742.7318
O62.95104.21472.85992.45921.41273.72114.73032.67342.09462.03520.97044.49724.0579
N72.51382.87483.50811.46352.45863.72113.77072.08732.70492.64034.00831.01801.0197
H81.88730.97502.30343.22924.40234.73033.77073.53904.58505.29864.25503.53703.8913
H92.13092.66543.09491.10142.14322.67342.08733.53903.05662.45313.03732.37042.9499
H102.78934.01672.82442.16111.10632.09462.70494.58503.05661.77822.28273.66662.5477
H113.45404.51693.89062.14041.09712.03522.64035.29862.45311.77822.82383.55633.0311
H122.62833.92042.17812.67841.92820.97044.00834.25503.03732.28272.82384.71834.2149
H132.77042.62603.90622.06503.35744.49721.01803.53702.37043.66663.55634.71831.6448
H142.72753.14423.50182.06132.73184.05791.01973.89132.94992.54773.03114.21491.6448

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 107.191 C1 C4 C5 110.183
C1 C4 N7 113.881 C1 C4 H9 106.661
O2 C1 O3 122.857 O2 C1 C4 111.485
O3 C1 C4 125.626 C4 C5 O6 113.006
C4 C5 H10 108.715 C4 C5 H11 107.642
C4 N7 H13 111.383 C4 N7 H14 110.959
C5 C4 N7 110.126 C5 C4 H9 107.618
C5 O6 H12 106.540 O6 C5 H10 111.936
O6 C5 H11 107.703 N7 C4 H9 108.107
H10 C5 H11 107.609 H13 N7 H14 107.648
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBEPBE/cc-pVTZ Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.240      
2 O -0.229      
3 O -0.295      
4 C -0.037      
5 C 0.024      
6 O -0.330      
7 N -0.285      
8 H 0.208      
9 H 0.103      
10 H 0.045      
11 H 0.095      
12 H 0.206      
13 H 0.133      
14 H 0.124      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  2.986 0.597 0.536 3.092
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.205 -1.929 -1.117
y -1.929 -43.772 1.681
z -1.117 1.681 -40.981
Traceless
 xyz
x 1.172 -1.929 -1.117
y -1.929 -2.680 1.681
z -1.117 1.681 1.508
Polar
3z2-r23.016
x2-y22.568
xy-1.929
xz-1.117
yz1.681


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 9.372 -0.052 -0.276
y -0.052 9.080 -0.157
z -0.276 -0.157 6.940


<r2> (average value of r2) Å2
<r2> 216.501
(<r2>)1/2 14.714