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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBEPBE/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 PBEPBE/6-31G**
 hartrees
Energy at 0K-398.518946
Energy at 298.15K-398.528836
HF Energy-398.518946
Nuclear repulsion energy323.813834
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/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 3618 3569 29.08      
2 A 3583 3534 116.18      
3 A 3500 3452 1.04      
4 A 3412 3365 0.20      
5 A 3046 3004 22.73      
6 A 2976 2935 11.89      
7 A 2876 2837 75.38      
8 A 1743 1719 200.62      
9 A 1624 1602 29.93      
10 A 1473 1453 1.19      
11 A 1422 1402 64.39      
12 A 1350 1332 12.52      
13 A 1344 1326 13.00      
14 A 1328 1310 52.93      
15 A 1275 1257 11.07      
16 A 1199 1182 5.26      
17 A 1170 1154 9.48      
18 A 1147 1131 129.68      
19 A 1121 1105 91.42      
20 A 1078 1063 109.63      
21 A 1000 986 35.68      
22 A 961 948 3.41      
23 A 862 850 175.60      
24 A 783 772 29.92      
25 A 720 710 43.51      
26 A 646 638 67.06      
27 A 588 580 174.14      
28 A 549 541 5.97      
29 A 523 516 44.21      
30 A 405 399 8.54      
31 A 308 303 3.07      
32 A 293 289 8.30      
33 A 241 238 15.14      
34 A 222 219 25.68      
35 A 162 160 1.20      
36 A 36 36 0.17      

Unscaled Zero Point Vibrational Energy (zpe) 24289.5 cm-1
Scaled (by 0.9863) Zero Point Vibrational Energy (zpe) 23956.8 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/6-31G**
ABC
0.11774 0.07923 0.04981

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

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.781 -0.550 -0.000
O2 2.072 -0.346 -0.362
O3 0.394 -1.574 0.547
C4 -0.087 0.682 -0.311
C5 -1.522 0.447 0.191
O6 -2.120 -0.694 -0.387
N7 0.445 1.934 0.229
H8 2.563 -1.155 -0.119
H9 -0.127 0.772 -1.411
H10 -1.503 0.393 1.300
H11 -2.124 1.325 -0.087
H12 -1.642 -1.455 -0.012
H13 1.355 2.152 -0.180
H14 0.570 1.865 1.242

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.35571.22371.53842.51702.93072.51691.88602.13592.79263.45832.58682.76742.7232
O21.35572.26862.39133.72174.20652.86250.97762.67994.01134.52423.89152.60473.1164
O31.22372.26862.46062.80752.82303.52252.30713.09982.83503.89182.11513.91513.5122
C41.53842.39132.46061.53872.45641.46403.23041.10482.16472.14742.65972.06322.0597
C52.51703.72172.80751.53871.41222.46664.39942.15021.11041.10051.91673.36492.7374
O62.93074.20652.82302.45641.41223.72424.71382.67882.10002.04170.97374.49664.0549
N72.51692.86253.52251.46402.46663.72423.76202.09002.70542.65883.98781.02101.0225
H81.88600.97762.30713.23044.39944.71383.76203.55224.57725.30294.21723.52133.8658
H92.13592.67993.09981.10482.15022.67882.09003.55223.06492.45923.03572.36922.9526
H102.79264.01132.83502.16471.11042.10002.70544.57723.06491.78322.27143.66792.5437
H113.45834.52423.89182.14741.10052.04172.65885.30292.45921.78322.82303.57643.0521
H122.58683.89152.11512.65971.91670.97373.98784.21723.03572.27142.82304.69244.1821
H132.76742.60473.91512.06323.36494.49661.02103.52132.36923.66793.57644.69241.6488
H142.72323.11643.51222.05972.73744.05491.02253.86582.95262.54373.05214.18211.6488

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 106.735 C1 C4 C5 109.766
C1 C4 N7 113.897 C1 C4 H9 106.666
O2 C1 O3 123.088 O2 C1 C4 111.281
O3 C1 C4 125.579 C4 C5 O6 112.626
C4 C5 H10 108.516 C4 C5 H11 107.759
C4 N7 H13 110.990 C4 N7 H14 110.599
C5 C4 N7 110.439 C5 C4 H9 107.727
C5 O6 H12 105.420 O6 C5 H10 112.154
O6 C5 H11 108.051 N7 C4 H9 108.084
H10 C5 H11 107.520 H13 N7 H14 107.577
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBEPBE/6-31G** Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.533      
2 O -0.449      
3 O -0.449      
4 C -0.109      
5 C 0.021      
6 O -0.515      
7 N -0.568      
8 H 0.322      
9 H 0.169      
10 H 0.088      
11 H 0.138      
12 H 0.315      
13 H 0.257      
14 H 0.246      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.592 0.246 0.684 3.665
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.373 -2.277 -0.445
y -2.277 -44.232 0.611
z -0.445 0.611 -38.915
Traceless
 xyz
x 0.201 -2.277 -0.445
y -2.277 -4.088 0.611
z -0.445 0.611 3.888
Polar
3z2-r27.775
x2-y22.859
xy-2.277
xz-0.445
yz0.611


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 8.460 0.153 0.106
y 0.153 7.916 0.032
z 0.106 0.032 5.646


<r2> (average value of r2) Å2
<r2> 217.900
(<r2>)1/2 14.761