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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBE1PBE/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 PBE1PBE/6-31+G**
 hartrees
Energy at 0K-398.555348
Energy at 298.15K-398.565349
HF Energy-398.555348
Nuclear repulsion energy326.201885
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/6-31+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 3824 3653 72.20      
2 A 3807 3637 97.16      
3 A 3660 3496 10.35      
4 A 3559 3400 2.87      
5 A 3151 3010 15.25      
6 A 3076 2939 11.71      
7 A 3016 2881 50.76      
8 A 1828 1746 297.25      
9 A 1675 1600 43.91      
10 A 1504 1437 4.87      
11 A 1436 1372 25.22      
12 A 1404 1341 51.59      
13 A 1391 1329 45.64      
14 A 1380 1318 13.66      
15 A 1318 1259 12.52      
16 A 1244 1188 15.54      
17 A 1203 1150 19.56      
18 A 1181 1129 185.02      
19 A 1152 1100 28.88      
20 A 1126 1076 122.54      
21 A 1038 992 35.00      
22 A 1001 956 2.94      
23 A 855 817 143.09      
24 A 818 781 69.61      
25 A 748 715 25.65      
26 A 634 606 103.93      
27 A 584 558 8.60      
28 A 552 528 215.06      
29 A 519 496 11.65      
30 A 446 426 8.37      
31 A 303 290 6.36      
32 A 288 275 10.76      
33 A 263 251 33.64      
34 A 215 206 5.14      
35 A 161 154 4.10      
36 A 32 30 1.01      

Unscaled Zero Point Vibrational Energy (zpe) 25195.6 cm-1
Scaled (by 0.9553) Zero Point Vibrational Energy (zpe) 24069.4 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/6-31+G**
ABC
0.11935 0.07875 0.05158

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

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.788 -0.534 0.011
O2 2.062 -0.337 -0.366
O3 0.414 -1.552 0.551
C4 -0.090 0.673 -0.308
C5 -1.516 0.432 0.186
O6 -2.103 -0.708 -0.385
N7 0.417 1.926 0.227
H8 2.566 -1.131 -0.137
H9 -0.123 0.756 -1.402
H10 -1.513 0.377 1.286
H11 -2.117 1.297 -0.102
H12 -1.652 -1.479 -0.021
H13 1.312 2.173 -0.180
H14 0.527 1.885 1.235

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.34271.21181.52622.50402.92282.49661.88112.11892.78383.43562.61712.76342.7229
O21.34272.24322.37793.70044.18092.85930.96812.65364.00194.49453.90082.62603.1386
O31.21182.24322.43782.79132.81463.49272.29783.07082.82363.86652.14523.90053.5057
C41.52622.37792.43781.52782.44191.45363.21541.09762.15722.13042.67462.05732.0568
C52.50403.70042.79131.52781.40402.44314.38232.13721.10141.09261.92733.34062.7172
O62.92284.18092.81462.44191.40403.69614.69392.66382.07852.02540.96444.47234.0329
N72.49662.85933.49271.45362.44313.69613.75422.07702.69182.63133.99221.01331.0148
H81.88110.96812.29783.21544.38234.69393.75423.52004.57535.27494.23363.53423.8900
H92.11892.65363.07081.09762.13722.66382.07703.52003.05012.44083.03992.35842.9412
H102.78384.00192.82362.15721.10142.07852.69184.57533.05011.77232.27493.65412.5372
H113.43564.49453.86652.13041.09262.02542.63135.27492.44081.77232.81643.53963.0207
H122.61713.90082.14522.67461.92730.96443.99224.23363.03992.27492.81644.70624.2004
H132.76342.62603.90052.05733.34064.47231.01333.53422.35843.65413.53964.70621.6427
H142.72293.13863.50572.05682.71724.03291.01483.89002.94122.53723.02074.20041.6427

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 107.891 C1 C4 C5 110.149
C1 C4 N7 113.801 C1 C4 H9 106.572
O2 C1 O3 122.753 O2 C1 C4 111.803
O3 C1 C4 125.439 C4 C5 O6 112.727
C4 C5 H10 109.189 C4 C5 H11 107.623
C4 N7 H13 111.770 C4 N7 H14 111.626
C5 C4 N7 110.030 C5 C4 H9 107.863
C5 O6 H12 107.475 O6 C5 H10 111.550
O6 C5 H11 107.787 N7 C4 H9 108.186
H10 C5 H11 107.759 H13 N7 H14 108.187
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBE1PBE/6-31+G** Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.456      
2 O -0.445      
3 O -0.500      
4 C -0.260      
5 C -0.117      
6 O -0.496      
7 N -0.565      
8 H 0.380      
9 H 0.216      
10 H 0.149      
11 H 0.182      
12 H 0.375      
13 H 0.319      
14 H 0.305      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.363 0.590 0.698 3.484
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -42.273 -2.150 -1.479
y -2.150 -44.926 1.621
z -1.479 1.621 -40.692
Traceless
 xyz
x 0.536 -2.150 -1.479
y -2.150 -3.443 1.621
z -1.479 1.621 2.908
Polar
3z2-r25.815
x2-y22.653
xy-2.150
xz-1.479
yz1.621


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 8.870 0.065 -0.221
y 0.065 8.936 -0.201
z -0.221 -0.201 6.779


<r2> (average value of r2) Å2
<r2> 215.746
(<r2>)1/2 14.688