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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: PBEPBEultrafine/cc-pVTZ

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/cc-pVTZ
 hartrees
Energy at 0K-398.667861
Energy at 298.15K-398.677638
HF Energy-398.667861
Nuclear repulsion energy324.260537
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/cc-pVTZ
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 3631 3606 52.82      
2 A 3612 3587 54.85      
3 A 3490 3466 2.54      
4 A 3403 3380 0.99      
5 A 3030 3010 18.78      
6 A 2974 2954 13.18      
7 A 2900 2880 52.70      
8 A 1727 1715 239.96      
9 A 1605 1593 28.35      
10 A 1444 1434 3.75      
11 A 1385 1376 46.93      
12 A 1344 1335 2.46      
13 A 1336 1327 19.98      
14 A 1327 1318 27.59      
15 A 1268 1260 6.27      
16 A 1201 1193 11.97      
17 A 1147 1139 1.90      
18 A 1112 1104 153.05      
19 A 1089 1081 90.32      
20 A 1054 1047 102.35      
21 A 990 983 32.58      
22 A 962 956 0.87      
23 A 841 835 155.84      
24 A 789 784 23.17      
25 A 718 713 20.45      
26 A 612 608 78.87      
27 A 566 562 8.40      
28 A 538 535 162.42      
29 A 494 490 17.99      
30 A 433 430 9.60      
31 A 280 278 3.44      
32 A 274 272 17.27      
33 A 257 256 18.54      
34 A 201 200 3.65      
35 A 148 147 3.94      
36 A 28 28 1.20      

Unscaled Zero Point Vibrational Energy (zpe) 24106.2 cm-1
Scaled (by 0.9931) Zero Point Vibrational Energy (zpe) 23939.9 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 PBEPBEultrafine/cc-pVTZ
ABC
0.11662 0.07748 0.05191

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

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.794 -0.539 0.008
O2 2.073 -0.331 -0.382
O3 0.431 -1.556 0.569
C4 -0.094 0.674 -0.307
C5 -1.525 0.426 0.191
O6 -2.124 -0.711 -0.395
N7 0.415 1.936 0.231
H8 2.580 -1.129 -0.143
H9 -0.133 0.760 -1.404
H10 -1.510 0.363 1.296
H11 -2.128 1.300 -0.084
H12 -1.658 -1.484 -0.038
H13 1.317 2.176 -0.174
H14 0.535 1.879 1.242

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.35331.21671.53542.51802.95042.51381.88732.13082.78963.45392.62742.77102.7276
O21.35332.25812.38963.72084.21412.87490.97502.66494.01704.51663.91962.62673.1447
O31.21672.25812.45242.81042.85873.50832.30373.09462.82533.89042.17653.90693.5022
C41.53542.38962.45241.53502.45901.46353.22901.10142.16122.14032.67802.06542.0613
C52.51803.72082.81041.53501.41282.45824.40222.14321.10631.09711.92833.35732.7311
O62.95044.21412.85872.45901.41283.72094.72962.67372.09462.03530.97044.49744.0572
N72.51382.87493.50831.46352.45823.72093.77102.08732.70422.64014.00771.01801.0197
H81.88730.97502.30373.22904.40224.72963.77103.53854.58575.29844.25413.53773.8920
H92.13082.66493.09461.10142.14322.67372.08733.53853.05672.45293.03752.37092.9499
H102.78964.01702.82532.16121.10632.09462.70424.58573.05671.77812.28293.66622.5466
H113.45394.51663.89042.14031.09712.03532.64015.29842.45291.77812.82393.55623.0309
H122.62743.91962.17652.67801.92830.97044.00774.25413.03752.28292.82394.71824.2139
H132.77102.62673.90692.06543.35734.49741.01803.53772.37093.66623.55624.71821.6448
H142.72763.14473.50222.06132.73114.05721.01973.89202.94992.54663.03094.21391.6448

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 107.196 C1 C4 C5 110.185
C1 C4 N7 113.889 C1 C4 H9 106.664
O2 C1 O3 122.872 O2 C1 C4 111.472
O3 C1 C4 125.626 C4 C5 O6 112.999
C4 C5 H10 108.725 C4 C5 H11 107.647
C4 N7 H13 111.414 C4 N7 H14 110.957
C5 C4 N7 110.103 C5 C4 H9 107.625
C5 O6 H12 106.543 O6 C5 H10 111.931
O6 C5 H11 107.709 N7 C4 H9 108.111
H10 C5 H11 107.600 H13 N7 H14 107.648
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at PBEPBEultrafine/cc-pVTZ Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.240      
2 O -0.229      
3 O -0.295      
4 C -0.037      
5 C 0.023      
6 O -0.330      
7 N -0.285      
8 H 0.208      
9 H 0.103      
10 H 0.045      
11 H 0.095      
12 H 0.206      
13 H 0.133      
14 H 0.124      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  2.982 0.597 0.536 3.088
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.199 -1.910 -1.125
y -1.910 -43.764 1.678
z -1.125 1.678 -40.983
Traceless
 xyz
x 1.174 -1.910 -1.125
y -1.910 -2.673 1.678
z -1.125 1.678 1.499
Polar
3z2-r22.997
x2-y22.565
xy-1.910
xz-1.125
yz1.678


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 9.371 -0.051 -0.277
y -0.051 9.080 -0.158
z -0.277 -0.158 6.940


<r2> (average value of r2) Å2
<r2> 216.554
(<r2>)1/2 14.716