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 : Microwave1) 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 AR

e - c[A] % BR

e – c[B] % CR

e – c[C] %

? b Time CPU

Exp Const. Fundam. (A species) Watson Ir 10719.4 4399.1 3182.9

3.247

RHF 3-21G* 10778.3 -0.55 4340.7 1.33 3154.6 0.89

3.112 1’31”

VDZ 11066.7 -3.24 4442.8 -0.99 3238.8 -1.76 3.381 VTZ 11160.2 -4.11 4453.6 -1.24 3249.2 -2.08 3.221 11 h MP2 VDZ 10509.3 1.96 4408.7 -0.22 3176.0 0.22 3.598 1h 10’ VTZ 10680.2 0.37 4442.0 -0.97 3204.5 -0.68 3.384 14h52’ AVTZ 10730.3 -0.10 4367.7 0.71 3167.3 0.49 3.245 3 days VQZ 10733.7 -0.13 4449.4 -1.14 3212.2 -0.92 3.335 5 days MP2(ae) 6-311 c 10762.4 -0.40 4452.4 -1.21 3214.9 -1.01 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 10722.8 -0.03 4375.8 0.53 3171.8 0.35

3.292

4h 50’ B3LYP AVTZ 10730.3 -0.10 4367.7 0.71 3167.3 0.49 3.245 B3LYP planar VTZ d 10725.4 -0.06 4380.4 0.43 3172.0 0.34 3.165 B3LYP planar AVTZ d 10733.0 -0.13 4369.7 0.67 3167.1 0.63 3.171 a frozen core approximation unless otherwise stated: ae = all electrons correlated. b Ia + Ib – Ic (in uÅ2) ,c MP2(ae)/6-311+G(3df,2p) .d heavy atom skeleton planar (Cs symmetry)

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 stateValues!!!

Corrections from force field calculation using MP2/6-31G*:Ae – A0 = 82.1 MHzBe – B0 = 39.6Ce – 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.

exp. HF/6-31G* B3LYP/VTZ Assignment cm-1 e – c in % e – c in %a' species1 NH2 antisym stretch 3551 0.1 2.62 NH2 sym stretch 3435 0.1 2.43 CH3 antisym stretch 2957 1.1 1.74 CH3 sym stretch 2874 1.1 2.35 C=O stretch 1747 2.2 1.06 NH2 bending 1583 SCALING 0.9 SCALING 0.57 CH3 antisym deform 1460 FACTOR 1.0 FACTOR 0.68 CH3 sym deform 1369 6.8 5.49 C-N stretch 1345 0.8929a 1.1 0.975b 1.710 OC-O stretch 1195 0.7 0.811 NH2 rock 1108 1.3 1.412 CH3 rock 1075 0.1 1.513 H3C-O stretch 880 0.8 3.714 C=O rock 702 7.2 7.315 OCN deform 520 11.6 11.416 COC deform 320 11.9 8.2a" species17 CH3 antisym stretch 2998 0.6 1.318 CH3 antisym deform 1447 1.3 0.119 CH3 rock 1071 8.4 7.520 NH2 wag 793 1.1 3.421 C=O wag 673 24.1 24.722 NH2 inversion 20323 ?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

Torsioncontr.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].

method basis

a

Debye

b

Debye

c

Debye

tot

Debye

exp. 0.163(2) 2.294(9) 0a 2.300(9)

MP2 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

a (c)2 = –0.001.

b ae =all electrons correlated.

Computed and experimental dipole moment components of methyl carbamate.

Observed and calculated 14N nuclear quadrupole coupling constants for methyl carbamate

Exp. (I) [MartskokMollendal

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 TORSIONALBARRIER AT A REASONABLE COST FOR METHYL CARBAMATE?

Methyl barrier to internal rotation for methyl

carbamate

V3

cm-1 exp. – 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 B3LYP B3LYP MP2 CCSD(T)b re

Basis VTZ AVTZ a VTZ AVTZ VQZ V(D,T)Z c

N1 C2 1.363 1.361 1.359 1.367 1.365 1.362 1.363 1.362 N1 H9 1.003 1.003 1.002 1.003 1.004 1.002 1.010 1.002 N1 H10 1.004 1.003 1.002 1.003 1.004 1.002 1.011 1.002 C2=O3 1.209 1.210 1.209 1.211 1.214 1.209 1.207 1.207 C2 O4 1.356 1.356 1.348 1.354 1.354 1.351 1.349 1.351 O4 C5 1.433 1.435 1.426 1.431 1.434 1.429 1.428 1.429 C5 H6 1.089 1.088 1.085 1.086 1.087 1.085 1.095 1.087 C5 H7 1.089 1.088 1.085 1.086 1.087 1.085 1.095 1.087 C5 H8 1.086 1.086 1.083 1.084 1.084 1.083 1.092 1.084 C2N1H9 116.73 117.47 116.92 115.25 115.90 115.88 115.57 115.88 C2N1H10 119.42 120.16 119.35 117.57 118.23 118.23 117.87 118.23 H9N1H10 118.67 119.35 119.03 117.58 118.20 118.25 117.90 118.25 N1C2O3 125.33 125.23 125.47 125.61 125.49 125.51 125.40 125.51 N1C2O4 110.10 110.24 110.00 109.76 109.92 109.92 110.06 109.92 O3C2O4 124.56 124.52 124.51 124.60 124.57 124.54 124.51 124.54 C2O4C5 115.00 115.21 113.91 113.22 113.42 113.49 113.63 113.49 O4C5H6 110.75 110.65 110.60 110.66 110.45 110.57 110.76 110.57 O4C5H7 110.70 110.60 110.55 110.60 110.37 110.50 110.69 110.50 O4C5H8 105.55 105.48 105.54 105.50 105.32 105.44 105.59 105.44 H6C5H7 108.97 109.14 109.11 109.00 109.26 109.11 108.87 109.11 H6C5H8 110.44 110.48 110.51 110.55 110.71 110.61 110.47 110.61 H7C5H8 110.40 110.46 110.49 110.51 110.69 110.58 110.45 110.58 H9N1C2O3 13.12 10.18 12.59 17.59 16.02 15.88 16.52 15.88 H9N1C2O4 168.25 170.90 168.83 164.39 165.79 165.90 165.25 165.90 H10N1C2O3 167.39 170.41 168.09 163.05 165.00 164.91 163.64 164.91 H10N1C2O4 13.98 10.67 13.33 18.93 16.81 16.86 18.12 16.86 N1C2O4C5 177.85 178.22 177.93 177.31 -177.30 177.46 177.39 177.46 O3C2O4C5 0.79 0.71 0.67 0.74 0.90 0.79 0.87 0.79 C2O4C5H6 60.22 60.34 60.44 60.12 -60.36 -60.24 60.40 60.24 C2O4C5H7 60.76 60.72 60.52 60.77 60.57 60.66 60.45 60.66 C2O4C5Hs 179.76 179.84 180.01 179.72 179.93 179.82 179.99 179.82 a 6-311+G(3df,2p), all electrons correlated., b All electrons correlated.c MP2/VQZ + offset

-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, KleibomerJMS 124, 34 1987

Acetamide JMS 440, 165 1998

cyanamide

vinylamine

CH2CHNH2

JMS 114, 257 1985

JMS 124, 21 1987

V3 / cm-1 220 ½(1-cos3) 352.3(3) 351.94(9)F / cm-1 P

2 5.579(4) 5.597fixed

211 Pap 0.0638 0.06150(8)A / MHzB/MHz

202 Pa2 10657.355(600)

Pb2 4356.345(300)

C / MHz Pc2 3177.060(900)

Dab / MHz (PaPb+PbPa) -376.536fixed

Fv / MHz 422 (1-cos3)P2 187.1(3)158.(2)(1-cos3)(Pb

2-Pc2)

RAM global programWoods program

c2 / MHz

ΔJ / kHz

ΔJK / kHz

ΔK / kHz

404 -P4

-P2Pa2

-Pa4

0.330(9)

4.17(1)

Number of assigned lines in global fit

Root-mean square / kHzNumber of parameters

98 splittings1473

124 A + 53 E158 (A), 295 (E)

10

3.93(2)

Dab NEEDS TO BE DETERMINED!

NEED FOR vt = 1 measurements

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+I0

b-I0c = mHHd2

HH –v

dHH = 1.7737 Å-computed ground-state inertial defect (B3LYP/AVTZ) mHHd2

HH= 3.1706 uÅ2. exp = 3.247 uÅ2

the vibrational contribution v = 0.076 uÅ2.

Such a small positive contribution is compatible with a planar structure but atthe 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

CH3C(O)NHCH3 –3.823(3) 0.332 planar Ohashi

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) –0.330 non-planar Brown

NH2C(O)OCH3 –4.2961(8) 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.