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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBE1PBE/6-311G*

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/6-311G*
 hartrees
Energy at 0K-398.613798
Energy at 298.15K-398.623892
HF Energy-398.613798
Nuclear repulsion energy327.056701
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/6-311G*
Mode Number Symmetry Frequency
(cm-1)
Scaled Frequency
(cm-1)
IR Intensities
(km mol-1)
Raman Act
(Å4/u)
Dep P Dep U
1 A 3792 3635 48.31      
2 A 3779 3622 62.40      
3 A 3625 3475 2.37      
4 A 3539 3393 0.53      
5 A 3144 3013 23.09      
6 A 3066 2939 15.82      
7 A 2996 2872 64.33      
8 A 1832 1756 278.14      
9 A 1724 1653 43.80      
10 A 1516 1453 2.97      
11 A 1461 1400 51.71      
12 A 1413 1355 4.99      
13 A 1408 1350 50.65      
14 A 1395 1337 28.68      
15 A 1337 1281 8.20      
16 A 1259 1206 19.07      
17 A 1217 1167 69.14      
18 A 1199 1149 170.25      
19 A 1163 1115 22.52      
20 A 1128 1082 115.31      
21 A 1047 1003 36.68      
22 A 1010 968 0.56      
23 A 900 863 198.35      
24 A 829 795 33.95      
25 A 758 727 39.46      
26 A 663 635 103.57      
27 A 584 560 42.41      
28 A 573 549 200.64      
29 A 529 507 16.32      
30 A 439 421 8.17      
31 A 309 296 6.01      
32 A 293 281 10.29      
33 A 257 247 33.38      
34 A 224 215 8.50      
35 A 170 163 2.55      
36 A 31 29 0.69      

Unscaled Zero Point Vibrational Energy (zpe) 25304.6 cm-1
Scaled (by 0.9585) Zero Point Vibrational Energy (zpe) 24254.5 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/6-311G*
ABC
0.12056 0.07952 0.05137

See section I.F.4 to change rotational constant units
Geometric Data calculated at PBE1PBE/6-311G*

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.766 -0.547 -0.005
O2 2.048 -0.357 -0.344
O3 0.376 -1.556 0.529
C4 -0.083 0.678 -0.313
C5 -1.505 0.455 0.186
O6 -2.093 -0.687 -0.371
N7 0.454 1.916 0.224
H8 2.534 -1.156 -0.106
H9 -0.122 0.767 -1.405
H10 -1.496 0.409 1.286
H11 -2.103 1.320 -0.107
H12 -1.637 -1.445 0.004
H13 1.355 2.126 -0.184
H14 0.578 1.850 1.227

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.33951.20581.52202.48972.88632.49321.87302.11522.77413.42412.56512.74342.7014
O21.33952.23432.36913.68294.15442.83370.96522.66363.97504.48273.85752.58333.0822
O31.20582.23432.43102.77532.76853.48612.28463.06272.81773.84952.08343.87613.4825
C41.52202.36912.43101.52342.43071.45233.20261.09592.15052.12922.64992.04512.0449
C52.48973.68292.77531.52341.40062.44384.35872.13091.10071.09091.91373.33302.7140
O62.88634.15442.76852.43071.40063.69044.65902.65872.07452.02410.96114.45454.0156
N72.49322.83373.48611.45232.44383.69043.72492.07482.68332.64593.96441.01121.0128
H81.87300.96522.28463.20264.35874.65903.72493.52664.54205.25654.18253.48873.8265
H92.11522.66363.06271.09592.13092.65872.07483.52663.04212.43193.02822.34962.9305
H102.77413.97502.81772.15051.10072.07452.68334.54203.04211.77102.25863.63822.5258
H113.42414.48273.84952.12921.09092.02412.64595.25652.43191.77102.80593.55143.0404
H122.56513.85752.08342.64991.91370.96113.96444.18253.02822.25862.80594.66274.1542
H132.74342.58333.87612.04513.33304.45451.01123.48872.34963.63823.55144.66271.6342
H142.70143.08223.48252.04492.71404.01561.01283.82652.93052.52583.04044.15421.6342

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 107.612 C1 C4 C5 109.676
C1 C4 N7 113.889 C1 C4 H9 106.657
O2 C1 O3 122.675 O2 C1 C4 111.614
O3 C1 C4 125.644 C4 C5 O6 112.396
C4 C5 H10 109.011 C4 C5 H11 107.918
C4 N7 H13 110.962 C4 N7 H14 110.837
C5 C4 N7 110.398 C5 C4 H9 107.766
C5 O6 H12 106.772 O6 C5 H10 111.507
O6 C5 H11 108.015 N7 C4 H9 108.203
H10 C5 H11 107.824 H13 N7 H14 107.692
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBE1PBE/6-311G* Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.468      
2 O -0.515      
3 O -0.368      
4 C -0.255      
5 C -0.206      
6 O -0.562      
7 N -0.745      
8 H 0.410      
9 H 0.265      
10 H 0.190      
11 H 0.242      
12 H 0.406      
13 H 0.344      
14 H 0.326      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.527 0.237 0.775 3.619
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.632 -2.220 -1.141
y -2.220 -44.242 1.423
z -1.141 1.423 -39.722
Traceless
 xyz
x 0.350 -2.220 -1.141
y -2.220 -3.565 1.423
z -1.141 1.423 3.215
Polar
3z2-r26.430
x2-y22.610
xy-2.220
xz-1.141
yz1.423


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 7.961 0.144 -0.173
y 0.144 7.734 -0.126
z -0.173 -0.126 5.823


<r2> (average value of r2) Å2
<r2> 214.551
(<r2>)1/2 14.648