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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBEPBEultrafine/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 PBEPBEultrafine/6-31G*
 hartrees
Energy at 0K-398.497872
Energy at 298.15K-398.507772
HF Energy-398.497872
Nuclear repulsion energy323.678812
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 PBEPBEultrafine/6-31G*
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 3546 3488 24.15      
2 A 3518 3460 112.02      
3 A 3475 3418 0.70      
4 A 3386 3330 0.24      
5 A 3052 3002 23.74      
6 A 2978 2929 12.28      
7 A 2879 2832 76.99      
8 A 1745 1716 201.64      
9 A 1655 1628 30.35      
10 A 1488 1463 1.07      
11 A 1437 1413 75.00      
12 A 1359 1337 14.23      
13 A 1356 1334 4.55      
14 A 1333 1311 48.08      
15 A 1286 1265 10.90      
16 A 1208 1188 5.71      
17 A 1177 1158 11.07      
18 A 1153 1134 141.14      
19 A 1126 1108 83.76      
20 A 1080 1062 109.33      
21 A 1006 990 37.77      
22 A 966 950 3.74      
23 A 879 865 179.58      
24 A 785 772 27.56      
25 A 722 710 47.01      
26 A 650 639 63.70      
27 A 596 586 185.47      
28 A 550 541 3.81      
29 A 523 515 43.51      
30 A 406 399 8.64      
31 A 307 302 3.24      
32 A 295 290 9.39      
33 A 243 239 15.68      
34 A 227 223 24.88      
35 A 165 162 1.08      
36 A 33 33 0.16      

Unscaled Zero Point Vibrational Energy (zpe) 24294.1 cm-1
Scaled (by 0.9835) Zero Point Vibrational Energy (zpe) 23893.3 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 PBEPBEultrafine/6-31G*
ABC
0.11768 0.07920 0.04980

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

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.781 -0.549 -0.000
O2 2.072 -0.346 -0.362
O3 0.394 -1.574 0.547
C4 -0.087 0.682 -0.311
C5 -1.523 0.447 0.191
O6 -2.119 -0.696 -0.387
N7 0.444 1.936 0.230
H8 2.565 -1.158 -0.119
H9 -0.127 0.776 -1.412
H10 -1.506 0.391 1.301
H11 -2.127 1.323 -0.089
H12 -1.638 -1.457 -0.011
H13 1.355 2.155 -0.180
H14 0.570 1.865 1.243

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.35641.22371.53862.51662.92892.51841.88872.13822.79403.45942.58312.77042.7239
O21.35642.26902.39203.72214.20552.86460.98052.68204.01384.52663.88852.60793.1175
O31.22372.26902.46122.80742.82123.52402.30813.10282.83533.89232.11033.91823.5128
C41.53862.39202.46121.53892.45621.46473.23361.10522.16742.14952.65942.06512.0608
C52.51663.72212.80741.53891.41232.46704.40182.15111.11121.10091.91783.36672.7384
O62.92894.20552.82122.45621.41233.72454.71402.68052.09892.04020.97634.49834.0555
N72.51842.86463.52401.46472.46703.72453.76702.08922.70872.66223.98781.02241.0238
H81.88870.98052.30813.23364.40184.71403.76703.55724.58115.30734.21443.52753.8692
H92.13822.68203.10281.10522.15112.68052.08923.55723.06772.45983.03862.36932.9531
H102.79404.01382.83532.16741.11122.09892.70874.58113.06771.78512.27003.67272.5473
H113.45944.52663.89232.14951.10092.04022.66225.30732.45981.78512.82373.58103.0571
H122.58313.88852.11032.65941.91780.97633.98784.21443.03862.27002.82374.69364.1815
H132.77042.60793.91822.06513.36674.49831.02243.52752.36933.67273.58104.69361.6504
H142.72393.11753.51282.06082.73844.05551.02383.86922.95312.54733.05714.18151.6504

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 106.736 C1 C4 C5 109.713
C1 C4 N7 113.949 C1 C4 H9 106.801
O2 C1 O3 123.058 O2 C1 C4 111.274
O3 C1 C4 125.617 C4 C5 O6 112.589
C4 C5 H10 108.663 C4 C5 H11 107.877
C4 N7 H13 111.016 C4 N7 H14 110.562
C5 C4 N7 110.414 C5 C4 H9 107.752
C5 O6 H12 105.353 O6 C5 H10 112.004
O6 C5 H11 107.901 N7 C4 H9 107.955
H10 C5 H11 107.605 H13 N7 H14 107.529
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBEPBEultrafine/6-31G* Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.534      
2 O -0.529      
3 O -0.446      
4 C -0.145      
5 C -0.072      
6 O -0.592      
7 N -0.682      
8 H 0.405      
9 H 0.203      
10 H 0.124      
11 H 0.178      
12 H 0.403      
13 H 0.315      
14 H 0.303      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.638 0.193 0.693 3.709
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.490 -2.298 -0.480
y -2.298 -44.341 0.610
z -0.480 0.610 -38.952
Traceless
 xyz
x 0.156 -2.298 -0.480
y -2.298 -4.120 0.610
z -0.480 0.610 3.963
Polar
3z2-r27.926
x2-y22.851
xy-2.298
xz-0.480
yz0.610


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 8.393 0.153 0.098
y 0.153 7.860 0.017
z 0.098 0.017 5.583


<r2> (average value of r2) Å2
<r2> 218.066
(<r2>)1/2 14.767