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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBE1PBE/cc-pVDZ

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/cc-pVDZ
 hartrees
Energy at 0K-398.555090
Energy at 298.15K-398.565253
HF Energy-398.555090
Nuclear repulsion energy326.964911
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/cc-pVDZ
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 3752 3608 53.84      
2 A 3732 3588 161.32      
3 A 3598 3459 4.55      
4 A 3515 3380 1.06      
5 A 3128 3008 22.51      
6 A 3054 2937 12.42      
7 A 2969 2854 70.42      
8 A 1833 1763 252.53      
9 A 1656 1592 32.57      
10 A 1488 1430 3.34      
11 A 1461 1404 45.38      
12 A 1400 1346 116.26      
13 A 1387 1334 9.00      
14 A 1378 1325 3.59      
15 A 1316 1266 11.01      
16 A 1238 1190 12.14      
17 A 1220 1173 30.23      
18 A 1204 1158 150.43      
19 A 1170 1125 48.25      
20 A 1137 1093 94.31      
21 A 1041 1001 39.42      
22 A 1005 966 0.77      
23 A 906 871 160.68      
24 A 821 789 30.82      
25 A 755 726 36.97      
26 A 660 635 79.49      
27 A 602 579 147.76      
28 A 572 550 15.13      
29 A 549 528 45.52      
30 A 423 407 7.50      
31 A 322 309 4.41      
32 A 307 295 8.95      
33 A 249 240 16.52      
34 A 230 221 20.31      
35 A 168 162 1.64      
36 A 41 40 0.29      

Unscaled Zero Point Vibrational Energy (zpe) 25142.4 cm-1
Scaled (by 0.9615) Zero Point Vibrational Energy (zpe) 24174.4 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/cc-pVDZ
ABC
0.12043 0.08056 0.05079

See section I.F.4 to change rotational constant units
Geometric Data calculated at PBE1PBE/cc-pVDZ

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.766 -0.546 -0.003
O2 2.049 -0.353 -0.343
O3 0.373 -1.561 0.525
C4 -0.084 0.678 -0.312
C5 -1.505 0.453 0.193
O6 -2.097 -0.681 -0.375
N7 0.455 1.916 0.221
H8 2.524 -1.163 -0.099
H9 -0.124 0.763 -1.412
H10 -1.484 0.401 1.300
H11 -2.106 1.329 -0.088
H12 -1.615 -1.435 -0.011
H13 1.367 2.112 -0.186
H14 0.588 1.838 1.228

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.34121.20991.52292.48942.89062.49161.86512.11942.76713.43172.54162.73132.6889
O21.34122.24182.37003.68384.15912.82950.97002.66613.96864.49023.83482.56253.0665
O31.20992.24182.43422.77372.77183.49132.27543.06582.80983.85682.06223.87123.4778
C41.52292.37002.43421.52452.42931.45143.19991.10342.15272.13572.62622.04372.0416
C52.48943.68382.77371.52451.40012.44584.35092.14011.10831.09911.90203.33782.7143
O62.89064.15912.77182.42931.40013.68944.65402.65582.08652.03090.96594.45334.0153
N72.49162.82953.49131.45142.44583.68943.72302.08042.68692.64563.94501.01721.0187
H81.86510.97002.27543.19994.35094.65403.72303.52724.52375.25824.14863.47453.8099
H92.11942.66613.06581.10342.14012.65582.08043.52723.05522.45003.00272.35412.9372
H102.76713.96862.80982.15271.10832.08652.68694.52373.05521.78252.25913.64152.5223
H113.43174.49023.85682.13571.09912.03092.64565.25822.45001.78252.80833.56113.0409
H122.54163.83482.06222.62621.90200.96593.94504.14863.00272.25912.80834.63654.1346
H132.73132.56253.87122.04373.33784.45331.01723.47452.35413.64153.56114.63651.6372
H142.68893.06653.47782.04162.71434.01531.01873.80992.93722.52233.04094.13461.6372

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 106.489 C1 C4 C5 109.546
C1 C4 N7 113.779 C1 C4 H9 106.505
O2 C1 O3 122.894 O2 C1 C4 111.524
O3 C1 C4 125.538 C4 C5 O6 112.261
C4 C5 H10 108.671 C4 C5 H11 107.881
C4 N7 H13 110.536 C4 N7 H14 110.256
C5 C4 N7 110.524 C5 C4 H9 107.979
C5 O6 H12 105.532 O6 C5 H10 112.044
O6 C5 H11 108.100 N7 C4 H9 108.268
H10 C5 H11 107.700 H13 N7 H14 107.058
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBE1PBE/cc-pVDZ Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.239      
2 O -0.176      
3 O -0.283      
4 C -0.135      
5 C 0.164      
6 O -0.282      
7 N -0.173      
8 H 0.165      
9 H 0.080      
10 H 0.015      
11 H 0.051      
12 H 0.148      
13 H 0.098      
14 H 0.090      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.517 0.400 0.639 3.597
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.273 -2.353 -0.442
y -2.353 -44.097 0.747
z -0.442 0.747 -38.855
Traceless
 xyz
x 0.203 -2.353 -0.442
y -2.353 -4.033 0.747
z -0.442 0.747 3.830
Polar
3z2-r27.660
x2-y22.824
xy-2.353
xz-0.442
yz0.747


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 8.004 0.153 0.039
y 0.153 7.542 0.035
z 0.039 0.035 5.637


<r2> (average value of r2) Å2
<r2> 214.272
(<r2>)1/2 14.638