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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBEPBE/3-21G*

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/3-21G*
 hartrees
Energy at 0K-396.295409
Energy at 298.15K-396.305294
HF Energy-396.295409
Nuclear repulsion energy322.088031
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/3-21G*
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 3409 3250 0.12      
2 A 3330 3176 8.82      
3 A 3313 3159 0.65      
4 A 3168 3021 88.38      
5 A 3059 2916 33.08      
6 A 3003 2863 6.94      
7 A 2864 2731 85.51      
8 A 1682 1604 40.58      
9 A 1656 1579 93.81      
10 A 1523 1452 0.98      
11 A 1459 1391 111.41      
12 A 1364 1301 6.50      
13 A 1351 1288 14.87      
14 A 1338 1276 21.16      
15 A 1296 1235 10.31      
16 A 1215 1159 15.46      
17 A 1167 1113 5.67      
18 A 1130 1078 5.98      
19 A 1076 1026 180.47      
20 A 1016 969 127.64      
21 A 1003 956 12.91      
22 A 935 891 5.87      
23 A 777 741 38.64      
24 A 721 687 224.93      
25 A 706 673 106.55      
26 A 685 653 104.52      
27 A 644 614 129.73      
28 A 541 516 7.31      
29 A 518 494 53.55      
30 A 394 376 10.01      
31 A 302 288 1.69      
32 A 284 271 10.48      
33 A 249 237 4.09      
34 A 219 208 48.55      
35 A 167 159 1.08      
36 A 56 54 0.58      

Unscaled Zero Point Vibrational Energy (zpe) 23809.0 cm-1
Scaled (by 0.9535) Zero Point Vibrational Energy (zpe) 22701.9 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/3-21G*
ABC
0.11539 0.08013 0.04991

See section I.F.4 to change rotational constant units
Geometric Data calculated at PBEPBE/3-21G*

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.730 -0.581 0.006
O2 2.051 -0.441 -0.348
O3 0.264 -1.591 0.546
C4 -0.052 0.697 -0.320
C5 -1.488 0.519 0.195
O6 -2.122 -0.630 -0.391
N7 0.554 1.928 0.223
H8 2.556 -1.272 -0.119
H9 -0.088 0.784 -1.420
H10 -1.442 0.473 1.306
H11 -2.055 1.418 -0.082
H12 -1.659 -1.430 -0.022
H13 1.471 2.126 -0.203
H14 0.657 1.884 1.248

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.37381.23711.53372.48292.88032.52451.95592.13672.74283.43002.53642.81362.7614
O21.37382.30532.39153.70624.17712.86010.99882.68813.97154.51533.85332.63553.1459
O31.23712.30532.46712.76432.73743.54612.40803.10312.78403.85082.01153.97903.5675
C41.53372.39152.46711.53552.45971.47553.27431.10392.15082.14222.68272.09152.0909
C52.48293.70622.76431.53551.43732.48104.43352.15341.11221.09931.96833.39032.7522
O62.88034.17712.73742.45971.43733.75254.72962.68182.13512.07230.99524.53194.0907
N72.52452.86013.54611.47552.48103.75253.79022.10242.69722.67624.02931.03011.0316
H81.95590.99882.40803.27434.43354.72963.79023.59334.58945.33884.21943.56753.9287
H92.13672.68813.10311.10392.15342.68182.10243.59333.05922.46193.05342.39032.9809
H102.74283.97152.78402.15081.11222.13512.69724.58943.05921.78742.33073.67352.5306
H113.43004.51533.85082.14221.09932.07232.67625.33882.46191.78742.87613.59883.0573
H122.53643.85332.01152.68271.96830.99524.02934.21943.05342.33072.87614.74074.2385
H132.81362.63553.97902.09153.39034.53191.03013.56752.39033.67353.59884.74071.6809
H142.76143.14593.56752.09092.75224.09071.03163.92872.98092.53063.05734.23851.6809

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 110.039 C1 C4 C5 107.993
C1 C4 N7 114.040 C1 C4 H9 107.086
O2 C1 O3 123.913 O2 C1 C4 110.555
O3 C1 C4 125.503 C4 C5 O6 111.622
C4 C5 H10 107.568 C4 C5 H11 107.638
C4 N7 H13 111.943 C4 N7 H14 111.799
C5 C4 N7 110.953 C5 C4 H9 108.233
C5 O6 H12 106.610 O6 C5 H10 113.127
O6 C5 H11 108.836 N7 C4 H9 108.328
H10 C5 H11 107.845 H13 N7 H14 109.235
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBEPBE/3-21G* Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.590      
2 O -0.507      
3 O -0.458      
4 C -0.248      
5 C -0.152      
6 O -0.534      
7 N -0.629      
8 H 0.363      
9 H 0.275      
10 H 0.170      
11 H 0.239      
12 H 0.335      
13 H 0.283      
14 H 0.273      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  4.106 -0.132 0.691 4.166
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -42.345 -3.151 -0.114
y -3.151 -43.903 0.253
z -0.114 0.253 -38.686
Traceless
 xyz
x -1.051 -3.151 -0.114
y -3.151 -3.388 0.253
z -0.114 0.253 4.438
Polar
3z2-r28.877
x2-y21.558
xy-3.151
xz-0.114
yz0.253


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 7.935 0.131 0.203
y 0.131 7.195 0.071
z 0.203 0.071 4.911


<r2> (average value of r2) Å2
<r2> 218.144
(<r2>)1/2 14.770