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All results from a given calculation for HO2CCHNH2CH2OH (Serine)

using model chemistry: B3LYP/TZVP

19 10 17 12 22

States and conformations

State Conformation minimum conformation conformer description state description
1 1 yes C1 1A
Energy calculated at B3LYP/TZVP
 hartrees
Energy at 0K-399.116472
Energy at 298.15K-399.126425
HF Energy-399.116472
Nuclear repulsion energy324.985481
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 B3LYP/TZVP
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 3773 3642 53.77      
2 A 3732 3602 70.67      
3 A 3588 3464 5.75      
4 A 3501 3379 2.33      
5 A 3116 3008 17.40      
6 A 3058 2952 13.12      
7 A 2998 2894 45.50      
8 A 1788 1726 281.12      
9 A 1665 1608 35.87      
10 A 1503 1451 4.65      
11 A 1429 1380 27.54      
12 A 1404 1355 4.68      
13 A 1389 1341 18.18      
14 A 1377 1329 31.43      
15 A 1314 1269 11.48      
16 A 1247 1204 19.12      
17 A 1187 1146 8.58      
18 A 1152 1112 223.75      
19 A 1116 1077 49.99      
20 A 1074 1037 107.56      
21 A 1024 988 33.53      
22 A 993 958 1.00      
23 A 844 815 137.15      
24 A 808 780 70.66      
25 A 741 715 22.09      
26 A 623 601 90.10      
27 A 587 567 23.48      
28 A 526 508 197.72      
29 A 504 487 17.84      
30 A 451 435 9.15      
31 A 293 283 5.13      
32 A 285 276 24.32      
33 A 272 262 17.01      
34 A 208 200 2.11      
35 A 152 147 4.91      
36 A 39 38 1.41      

Unscaled Zero Point Vibrational Energy (zpe) 24878.7 cm-1
Scaled (by 0.9654) Zero Point Vibrational Energy (zpe) 24017.9 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 B3LYP/TZVP
ABC
0.11696 0.07719 0.05229

See section I.F.4 to change rotational constant units
Geometric Data calculated at B3LYP/TZVP

Point Group is C1

Cartesians (Å)
Atom x (Å) y (Å) z (Å)
C1 0.801 -0.532 0.012
O2 2.073 -0.329 -0.385
O3 0.449 -1.543 0.573
C4 -0.097 0.669 -0.305
C5 -1.527 0.419 0.188
O6 -2.125 -0.720 -0.393
N7 0.404 1.934 0.229
H8 2.593 -1.114 -0.155
H9 -0.133 0.751 -1.395
H10 -1.523 0.359 1.285
H11 -2.127 1.284 -0.093
H12 -1.683 -1.500 -0.037
H13 1.296 2.190 -0.176
H14 0.513 1.901 1.236

Atom - Atom Distances (Å)
  C1 O2 O3 C4 C5 O6 N7 H8 H9 H10 H11 H12 H13 H14
C11.34751.20841.53302.52142.96032.50741.89132.12152.79643.44702.66652.77312.7393
O21.34752.24212.38953.72144.21642.87780.96912.65614.02444.50823.94972.64443.1677
O31.20842.24212.44192.81132.87033.49422.30453.07852.83163.88202.21833.90023.5080
C41.53302.38952.44191.53382.46051.46123.23051.09402.15872.13182.70072.06582.0651
C52.52143.72142.81131.53381.41162.45514.40962.13581.09841.08921.93803.35232.7309
O62.96034.21642.87032.46051.41163.71874.74092.67202.08392.02610.96444.49654.0603
N72.50742.87783.49421.46122.45513.71873.77192.07962.70382.63304.02711.01201.0138
H81.89130.96912.30453.23054.40964.74093.77193.52844.60345.29434.29543.54933.9182
H92.12152.65613.07851.09402.13582.67202.07963.52843.04482.44023.05222.36592.9436
H102.79644.02442.83162.15871.09842.08392.70384.60343.04481.76562.28673.66512.5547
H113.44704.50823.88202.13181.08922.02612.63305.29432.44021.76562.81913.54153.0195
H122.66653.94972.21832.70071.93800.96444.02714.29543.05222.28672.81914.74414.2438
H132.77312.64443.90022.06583.35234.49651.01203.54932.36593.66513.54154.74411.6403
H142.73933.16773.50802.06512.73094.06031.01383.91822.94362.55473.01954.24381.6403

picture of Serine state 1 conformation 1
More geometry information
Calculated Bond Angles
atom1 atom2 atom3 angle atom1 atom2 atom3 angle
C1 O2 H8 108.349 C1 C4 C5 110.600
C1 C4 N7 113.712 C1 C4 H9 106.522
O2 C1 O3 122.524 O2 C1 C4 111.939
O3 C1 C4 125.520 C4 C5 O6 113.239
C4 C5 H10 109.069 C4 C5 H11 107.510
C4 N7 H13 112.006 C4 N7 H14 111.829
C5 C4 N7 110.089 C5 C4 H9 107.554
C5 O6 H12 107.824 O6 C5 H10 111.637
O6 C5 H11 107.522 N7 C4 H9 108.090
H10 C5 H11 107.620 H13 N7 H14 108.131
Electronic energy levels
Charges, Dipole, Quadrupole and Polarizability
Charges from optimized geometry at B3LYP/TZVP Charges (e)
Number Element Mulliken CHELPG AIM ESP
1 C 0.169      
2 O -0.279      
3 O -0.335      
4 C -0.056      
5 C -0.109      
6 O -0.377      
7 N -0.408      
8 H 0.291      
9 H 0.161      
10 H 0.102      
11 H 0.143      
12 H 0.283      
13 H 0.218      
14 H 0.197      


Electric dipole moments
Electric dipole components in Debye
(What's a Debye? See section VII.A.3)
  x y z Total
  3.019 0.641 0.666 3.157
CHELPG        
AIM        
ESP        


Electric Quadrupole moment
Quadrupole components in D Å
Primitive
 xyz
x -41.780 -1.800 -1.566
y -1.800 -44.208 1.885
z -1.566 1.885 -41.557
Traceless
 xyz
x 1.103 -1.800 -1.566
y -1.800 -2.539 1.885
z -1.566 1.885 1.437
Polar
3z2-r22.873
x2-y22.428
xy-1.800
xz-1.566
yz1.885


Polarizabilities
Components of the polarizability tensor.
Units are Å3 (Angstrom cubed)
Change units.
  x y z
x 8.603 0.041 -0.303
y 0.041 8.598 -0.255
z -0.303 -0.255 6.715


<r2> (average value of r2) Å2
<r2> 216.555
(<r2>)1/2 14.716