Equilibrium Molecular Structure and
Spectroscopic Parameters
of Methyl Carbamate
J. Demaison, A. G. Császár, V. Szalay, I.
Kleiner, H. Møllendal
GOALS OF THIS STUDY:
-check predictive power of different ab initio methods for
larger molecules of biological interest.
-structure is planar or not?
-Methyl carbamate (H2NC(O)OCH3) : isomer of the simplest
aminoacid, glycine (H2NCH2COOH). Biological effects and
pharmaceutical applications.
-possible detection in interstellar space : might be more
abundant than glycine and rotational spectrum more intense
(bigger dipole moment).
-Previous works : Microwave
1) K-M. Marstokk and H. Møllendal, Acta
Chem. Scand. 53 (1999) 79-84:
a) Only one conformer found (syn
conformation).
b)Approximate values of the barrier to
internal rotation of the methyl group, the
14N quadrupole coupling constants and
dipole moments.
c) ab initio geometrical structure but no
accurate centrifugal distortion constants.
[2] Bakri, J. Demaison, I. Kleiner, L. Margulès, H. Møllendal, D.
Petitprez, G. Wlodarczak, J. Mol. Spectrosc. 215 (2002) 312-316.
-FT MW and millimeterwave: 415 A-type and 98 E type transitions
in vt= 0 ground torsional state
-Accurate values for 14N quadrupole coupling constants and
centrifugal distortion constants for vt=0.
-Different ab initio methods (Gaussian 98) - syn conformation of
methyl carbamate significantly more stable than the most stable
isomer (Ip) of glycine
HOWEVER!
-Contrary to glycine, there is NO ACCURATE STRUCTURE
available for methyl carbamate.
-Need for a MORE COMPLETE EXPERIMENTAL WORK
CAN WE CALCULATE SPECTROSCOPIC
PARAMETERS AT REASONABLE COST
FOR LARGER MOLECULES OF
BIOLOGICAL INTEREST?
Comparison between experimental and Predicted rotational constants (MHz).
Method a
basis
Exp Const. Fundam.
(A species) Watson Ir
AR
e - c[A]
%
10719.4
BR
e – c[B]
%
4399.1
CR
e – c[C]
%
3182.9
?
b
Time
CPU
3.247
3-21G* 10778.3 -0.55 4340.7 1.33 3154.6 0.89
3.112 1’31”
VDZ
VTZ
11066.7
11160.2
-3.24
-4.11
4442.8 -0.99
4453.6 -1.24
3238.8 -1.76
3249.2 -2.08
3.381
3.221 11 h
MP2(ae)
VDZ
VTZ
AVTZ
VQZ
6-311 c
10509.3
10680.2
10730.3
10733.7
10762.4
1.96
0.37
-0.10
-0.13
-0.40
4408.7
4442.0
4367.7
4449.4
4452.4
-0.22
-0.97
0.71
-1.14
-1.21
3176.0 0.22
3204.5 -0.68
3167.3 0.49
3212.2 -0.92
3214.9 -1.01
3.598
3.384
3.245
3.335
3.265
CCSD(T)(ae)
V(D,T)Z
10755.2
-0.33
4444.1 -1.02
3212.2 -0.94
3.407
B3LYP
VTZ
B3LYP
B3LYP planar
B3LYP planar
AVTZ
VTZ d
AVTZ d
RHF
MP2
a
10722.8 -0.03 4375.8 0.53 3171.8 0.35
10730.3
10725.4
10733.0
-0.10
-0.06
-0.13
4367.7
4380.4
4369.7
0.71
0.43
0.67
frozen core approximation unless otherwise stated: ae = all electrons correlated.
Ia + Ib – Ic (in uÅ2) ,c MP2(ae)/6-311+G(3df,2p) .d heavy atom skeleton planar (Cs symmetry)
b
3167.3
3172.0
3167.1
0.49
0.34
0.63
1h 10’
14h52’
3 days
5 days
3.292 4h 50’
3.245
3.165
3.171
Equilibrium B3LYP/VTZ values apparently closest to the
Experimental ground states. Second best RHF/3-21G* (computation
Less than 1 min!)
BUT
Equilibrium computed constants from ab initio ARE NOT ground state
Values!!!
Corrections from force field calculation using MP2/6-31G*:
Ae – A0 = 82.1 MHz
Be – B0 = 39.6
Ce – C0 = 30.8
So the agreement with B3LYP values can be an accident…
However: the force field correction MP2/6-31G* is also an approximation:
-small amplitude vibrations (not true)
-not the best method
-ab initio structure are found to be non-planar…
Observed and calculated vibrational frequencies for methyl carbamate.
Assignment
exp.
cm-1
HF/6-31G*
e – c in %
B3LYP/VTZ
e – c in %
a' species
1
NH2 antisym stretch
3551
-0.1
-2.6
2
NH2 sym stretch
3435
-0.1
-2.4
3
CH3 antisym stretch
2957
-1.1
-1.7
4
CH3 sym stretch
2874
-1.1
-2.3
5
C=O stretch
1747
-2.2
-1.0
6
NH2 bending
1583 SCALING
-0.9
SCALING 0.5
7
CH3 antisym deform
1460 FACTOR
-1.0
FACTOR -0.6
8
CH3 sym deform
1369
-6.8
-5.4
a
b
9
C-N stretch
1345
0.8929
-1.1
0.975
1.7
10
OC-O stretch
1195
-0.7
0.8
11
NH2 rock
1108
-1.3
1.4
12
CH3 rock
1075
-0.1
1.5
13
H3C-O stretch
880
0.8
3.7
14
C=O rock
702
7.2
7.3
15
OCN deform
520
11.6
11.4
16
COC deform
320
11.9
8.2
a" species
17
CH3 antisym stretch
2998
0.6
-1.3
18
CH3 antisym deform
1447
-1.3
-0.1
19
CH3 rock
1071
-8.4
-7.5
20
NH2 wag
793
1.1
3.4
21
C=O wag
673
24.1
24.7
22
NH2 inversion
203
23
?
24
?
a [Pople et al 1981]. b 0.965 for all CH stretchings and 0.975 for all others [Martin et al 1996].
Observed and calculated quartic centrifugal distortion constants for
methyl carbamate.
Exp. (kHz)a
Calc.B3LYP/
VTZ (I) b
Torsion
contr.c
Calc.
e - c(II) (%)
∆j
0.7794 (7)
0.7574
0.0032
0.7606
2.4
∆jk
4.5326 (29)
4.6700
0.5684
5.2385
-15.6
∆k
8.9474 (22)
3.9092
5.2117
9.1209
-1.9
j
0.2164 (3)
0.2040
0.0016
0.2056
5.0
k
2.4033 (33)
2.1777
0.3057
2.4835
-3.3
a
For the A component of the internal rotation doublet.
b "Unperturbed" constant.
c Contribution of the internal rotation. Calculated with F = 167.26 GHz,
s = 28, and a = 0.9137 [Hersbach].
Computed and experimental dipole moment components
of methyl carbamate.
a
b
c
tot
Debye
Debye
Debye
Debye
0.163(2)
2.294(9)
0a
VTZ
0.222
2.412
0.757 2.538
AVTZ
0.204
2.462
0.671 2.560
VQZ
0.238
2.459
0.673 2.560
CCSD(T)(ae)b
V(T,D)Z
0.234
2.215
0.710 2.338
B3LYP
VTZ
0.347
2.353
0.512 2.433
AVTZ
0.200
2.410
0.374 2.447
method
basis
exp.
MP2
a
(c)2 = –0.001.
b
ae =all electrons correlated.
2.300(9)
Observed and calculated 14N nuclear quadrupole coupling constants
for methyl carbamate
Exp. (I)
[Martskok
Mollendal
1999]
MHz
Exp. (II).
[Bakri et al
2002]
MHz
Calc.
MHz
e – c(II)
(%)
Calc.
MHz
e – c(II)
(%)
eQqaa
1.52 (27)
2.2833 (7)
1.99
12.8
1.85
18.9
eQqbb
3.51 (20)
2.0128 (8)
1.82
9.5
1.68
16.4
eQqcc
-5.03 (33)
-4.2961 (8)
-3.81
11.3
-3.54
17.7
HF/VTZ
B3LYP/AVTZ
IS IT POSSIBLE TO CALCULATE ab initio AN ACCURATE TORSIONAL
BARRIER AT A REASONABLE COST FOR METHYL CARBAMATE?
Methyl barrier to internal rotation for methyl
carbamate
V3
exp. –
-1
cm
calc. (%)
exp.
352.179
G3
396.902 –12.7
MP2(ae)/6-311+G(3df,2p) 366.223
–4.0
MP2(ae)/6-31G(d)
282.964
19.7
B3LYP/VTZ
203.550
42.2
Planarity of the C(O)NH2 linkage:
-The peptide linkage is generally assumed to
have a planar structure due to the contribution
of a resonance structure O-CX=N+HY, which
induces a partial double bond character of the
C–N bond. However, the contribution of each
resonance structure can be changed with
interactions with the environment.
-non planarity of some peptide linkages
attributed to a low potential methyl top
barrier?
. Structure of carbamic acid H2NCOOH (distances in Å and angles in degree).
HF
MP2
CCSD(T) (ae) a
B3LYP
VTZ AVQZ VTZ AVTZ VQZ V(T,D)Z VTZ AVTZ VTZ
C-N
1.3446 1.3426 1.3604 1.3587 1.3557 1.3568 1.3581 1.3577 1.3569
N-Hcis/=O
0.9887 0.9879 1.0021 1.0029 1.0008 1.0091 1.0009 1.0014 1.0025
N-H/trans
0.9886 0.9878 1.0023 1.0032 1.0010 1.0096 1.0012 1.0020 1.0031
C=O
1.1878 1.1871 1.2105 1.2128 1.2088 1.2070 1.2066 1.2076 1.2083
C-O
1.3301 1.3286 1.3599 1.3605 1.3571 1.3544 1.3552 1.3547 1.3622
O-H
0.9437 0.9427 0.9655 0.9670 0.9639 0.9722 0.9630 0.9634 0.9654
CNHcis
117.85 118.37 116.06 116.69 116.72 116.37 116.16 116.38 117.58
CNHtrans
120.39 120.91 118.59 119.21 119.27 118.84 118.63 118.85 120.40
HNH
119.87 120.35 118.40 118.98 119.11 118.67 118.38 118.66 119.48
N-C=O
125.47 125.38 126.02 125.95 125.97 125.88 125.90 125.86 125.88
N-C-O
111.33 111.44 110.20 110.27 110.31 110.50 110.48 110.42 110.62
O=C-O
123.19 123.18 123.75 123.75 123.70 123.60 123.60 123.70 123.49
C-O-H
107.70 107.92 104.56 105.02 104.94 104.90 104.88 105.43 105.77
O-C-N-Hcis
7.64
3.40 14.79 12.92 12.54
13.72 14.57 14.00
9.10
O=C-N-Hcis -173.08 -176.92 -166.97 -168.63 -168.94 -167.84 -167.06 -167.65 -171.90
O-C-N-Htrans 172.02 176.49 165.19 167.39 167.59 165.88 165.22 166.18 170.93
O=C-N-Htrans -8.70 -3.84 -16.57 -14.16 -13.90 -15.68 -16.41 -15.46 -10.07
NCOH
-178.97 -179.52 -178.05 -178.12 -178.28 -178.10 -178.16 -177.74 -178.75
OCOH
0.33
0.17
0.25
0.37
0.28
0.38
0.25
0.66
0.28
a
all electrons correlated.
CLEARLY NON PLANAR BUT the energy difference between planar and non
planar is small: about 20-30 cm-1
Table 12. Computed Born/Oppenheimer equilibrium structures of methyl carbamate.
Method
Basis
N1-C2
N1-H9
N1-H10
C2=O3
C2-O4
O4-C5
C5-H6
C5-H7
C5-H8
C2N1H9
C2N1H10
H9N1H10
N1C2O3
N1C2O4
O3C2O4
C2O4C5
O4C5H6
O4C5H7
O4C5H8
H6C5H7
H6C5H8
H7C5H8
H9N1C2O3
H9N1C2O4
H10N1C2O3
H10N1C2O4
N1C2O4C5
O3C2O4C5
C2O4C5H6
C2O4C5H7
C2O4C5Hs
B3LYP
B3LYP
MP2
CCSD(T)b
re
a
c
VTZ
AVTZ
VTZ
AVTZ
VQZ
V(D,T)Z
1.363
1.361
1.359
1.367
1.365
1.362
1.363
1.362
1.003
1.003
1.002
1.003
1.004
1.002
1.010
1.002
1.004
1.003
1.002
1.003
1.004
1.002
1.011
1.002
1.209
1.210
1.209
1.211
1.214
1.209
1.207
1.207
1.356
1.356
1.348
1.354
1.354
1.351
1.349
1.351
1.433
1.435
1.426
1.431
1.434
1.429
1.428
1.429
1.089
1.088
1.085
1.086
1.087
1.085
1.095
1.087
1.089
1.088
1.085
1.086
1.087
1.085
1.095
1.087
1.086
1.086
1.083
1.084
1.084
1.083
1.092
1.084
116.73
117.47
116.92
115.25
115.90
115.88
115.57
115.88
119.42
120.16
119.35
117.57
118.23
118.23
117.87
118.23
118.67
119.35
119.03
117.58
118.20
118.25
117.90
118.25
125.33
125.23
125.47
125.61
125.49
125.51
125.40
125.51
110.10
110.24
110.00
109.76
109.92
109.92
110.06
109.92
124.56
124.52
124.51
124.60
124.57
124.54
124.51
124.54
115.00
115.21
113.91
113.22
113.42
113.49
113.63
113.49
110.75
110.65
110.60
110.66
110.45
110.57
110.76
110.57
110.70
110.60
110.55
110.60
110.37
110.50
110.69
110.50
105.55
105.48
105.54
105.50
105.32
105.44
105.59
105.44
108.97
109.14
109.11
109.00
109.26
109.11
108.87
109.11
110.44
110.48
110.51
110.55
110.71
110.61
110.47
110.61
110.40
110.46
110.49
110.51
110.69
110.58
110.45
110.58
13.12
10.18
12.59
17.59
16.02
15.88
16.52
15.88
-168.25 -170.90 -168.83 -164.39 -165.79 -165.90
-165.25 -165.90
167.39
170.41
168.09
163.05
165.00
164.91
163.64
164.91
-13.98
-10.67
-13.33
-18.93
-16.81
-16.86
-18.12
-16.86
-177.85 -178.22 -177.93 -177.31 -177.30 -177.46
-177.39 -177.46
0.79
0.71
0.67
0.74
0.90
0.79
0.87
0.79
-60.22
-60.34
-60.44
-60.12
-60.36
-60.24
-60.40
-60.24
60.76
60.72
60.52
60.77
60.57
60.66
60.45
60.66
-179.76 -179.84 -180.01 -179.72 -179.93 -179.82
-179.99 -179.82
-ALL ab initio optimizations indicate that the amide group is non planar
(difference between planar and non planar is 53 cm-1 CCSD(T)/V(T,D)Z
in contradiction with experimental results (c is zero)
WHAT’s GOING ON?
MC behaves like other molecules containing the amino group.
small barrier between planar and non planar and the ground torsional state is above this
barrier.
Kydd and Rauk,
J. Mol. Struct.
1981
Brown, Godfrey, Kleibomer
JMS 124, 34 1987
Acetamide
JMS 440, 165 1998
cyanamide
JMS 114, 257 1985
CH2CHNH
2
vinylamine
JMS 124, 21 1987
Woods program
V3 / cm-1
F / cm-1

A / MHz
B/MHz
C / MHz
Dab / MHz
220
Fv / MHz
c2 / MHz
422
ΔJ / kHz
ΔJK / kHz
404
ΔK / kHz
211
202
½(1-cos3)
P2
P ap 
P a2
Pb2
P c2
(PaPb+PbPa)
352.3(3)
5.579(4)
0.0638
(1-cos3)P2
(1-cos3)(Pb2-Pc2)
-P4
-P2Pa2
Root-mean square / kHz
Number of parameters
351.94(9)
5.597fixed
0.06150(8)
10657.355(600)
4356.345(300)
3177.060(900)
-376.536fixed
187.1(3)
158.(2)
0.330(9)
4.17(1)
3.93(2)
-Pa4
Number of assigned lines in global fit
RAM global program
98 splittings
147
3
Dab NEEDS TO BE DETERMINED!
NEED FOR vt = 1 measurements
124 A + 53 E
158 (A), 295 (E)
10
CONCLUSIONS
-ab initio methods can give us information.
Different methods/basis set
should be tried before conclusions.
-near-planarity in methyl carbamate should be
investigated further.
Need for new experimental MW data (Kharkov)
and FIR high resolution.
This will also provide a line list for astrophysical
purpose.
propianamide
______________________________
Godfrey, Brown and Hunter, J.
Mol. Struct. 413, 405 (1997) :
UREA
Ground-state inertial defects ?
For a molecule with a plane of symmetry and two out-of-plan H :
= I0a+I0b-I0c = mHHd2HH –Dv
dHH = 1.7737 Å
-computed ground-state inertial defect (B3LYP/AVTZ) mHHd2HH=
3.1706 uÅ2.
Dexp = 3.247 uÅ2
the vibrational contribution Dv = 0.076 uÅ2.
Such a small positive contribution is compatible with a planar structure
but at
the other hand the
Computed G-S inertial defects for the planar and non planar forms are
very close
(3.171 and 3.245 uÅ2)
cc(14N) quadrupole coupling constants (MHz) and vibrational contribution to
inertial defect ? v/uÅ2 of some NH2 derivatives.
Molecule
cc
?v
Planarity a Ref.
BH2NH2
–2.186(8)
0.048 planar
K. Vorman
BF2NH2
–3.193(8)
0.152 planar
K. Vorman
FCH2C(O)NH2
–3.2(3)
0.078 Planar
Marstokk 74
0.332 planar
Ohashi
CH3C(O)NHCH3 –3.823(3)
HCCC(O)NH2
–3.82(8)
0.182 planar
Little
NH2CHO
–3.848(4)
0.007 planar
Kukolich
CH3C(O)NH2
–3.9433(9)
0.130 planar
Ilyushin
OC(NH2)2
–4.0889(29) –0.425 non-planar Kretschmer
H2C=CHNH2
–4.147(19)
NH2C(O)OCH3
–4.2961(8)
–0.330 non-planar Brown
0.076
[Bakri et al]
H2C=CHC(O)NH2 –4.6(3)
0.131 planar
Marstokk 00
CH3CH2C(O)NH2 –4.7(9)
0.314 Planar
Marstokk 96
a
heavy atom skeleton in the (a, b) symmetry plane.