The geometry of some amides obtained from ab initio calculations

Fogarasi, Géza; Pulay, Péter; Török, Ferenc; Boggs, James E.

doi:10.1016/0022-2860(79)80252-5

Cited by 83 publications

(27 citation statements)

References 25 publications

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“…For instance, the formation of a H bond to the NH group by formamide in NMA + (FM and H20) (I11 and I) "turns on" the cooperative interactions and leads to an energy of interaction equal to 10.5 kcal/mol at the HF/6-31G level. This is 2.6 kcal/mol larger than the H bond energy (7.9 kcal/mol) for the corresponding H bond in NMA + FM (11). Furthermore, since the cooperative effect is larger for formamide than for water, the hydrogen bonding of formamide to the NH in NMA + (FM and H20) (I11 and I) is more favorable than the hydrogen bonding of water where the energy of interaction for the system is -9.5 kcal/mol (i.e., -1 kcal/mol smaller) at the HF/6-3 1G Similar conclusions apply for the other hydrogen bonded NMA complexes in Table VI and Figures 2-7; the arrangements of the molecules in the hydrogen bonded complexes are also given in Figures 2-7.…”

Section: H Bond Geometries and Interactionmentioning

confidence: 88%

“…The formation of a H bond at position I1 leads to an increase of the barrier by 0.15423 kcal/mol for the N-methyl and by -0.32 kcal/mol for the C'methyl. From Tables IX and X, for NMA + HzO (11) with t +b = Oo, there is a relatively large overlap population (-0.01 1) between H1 and the oxygen of HzO (11) which stabilizes the eclipsed C'-methyl group. In contrast, there is only a small overlap population (0.0007) between the hydrogem of a staggered C'-methyl and the oxygen of H20 (11) (see Table XI).…”

Section: H Bond Geometries and Interactionmentioning

confidence: 94%

“…The MP2/6-31G*,.st) values for NMA + 2H20 (I and 111), NM-. + FM(11), and NM (FM and H20) (111 and I) 31G* values. cSeeTable I,footnote c. dFrom ref 2 and as refined in ref 19.…”

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confidence: 99%

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Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers

Guo¹,

Karplus²

1992

J. Phys. Chem.

198

170

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Hydrogen bonding interactions and their effect on the structure and the energetics of the rotation about N-Cu and Cu-C' bonds are studied for N-methylacetamide (NMA) by use of ab initio quantum mechanical calculations. The structure and methyl rotational barriers for isolated NMA have k e n determined at the Hartree-Fock (HF) level with 6-31G. 6-31G*, and 6-31 1G** basis sets and at the second-order Mdler-Plesset perturbation (MP2) level with a 6-31G* basis set including geometry optimization for the different methyl orientations. The optimized geometries, the hydrogen bonding interaction energies, and the methyl rotational barriers for 11 complexes in which NMA is hydrogen bonded to H20 and/or formamide (FM) [i.e., NMA + H20 (3 complexes), NMA + 2H20 (2 complexes), NMA + 3H20 (1 complex), NMA + FM (2 complexes), NMA + (FM and H20) (1 complex), NMA + 2FM (1 complex), and NMA + (2FM and 1H2O) (1 complex)] have been calculated at the HF/6-31G level; HF/6-31G* calculations were performed for the 3 NMA + H20 complexes and 1 of the NMA + 2H20 complexes. For isolated NMA, the torsional potentials for both methyl group are predicted to be very flat and the rotational bamers are only -0.1 kcal/mol. This contrasts with some of the earlier calculations in which larger barriers were obtained due to lack of geometry optimization of the rotated conformers. The bamers in the hydrogen bonded systems are calculated to be significantly larger (0.2-0.9 kcaljmol). The increase of the C'=O bond length from the gas-phase to crystallinestate NMA componds to that found in the ab initio calculations with hydrogen bonding ligand^, but the d8erence (0.1 A) in the experimental C'(0)-N bond distance is significantly larger than the calculated value. This suggests that the crystal structure may be in error. In agreement with the crystal structure, the lowest energy conformation in all the hydrogen bonded systems is predicted to have an ecliped (C')CH3 group and a staggered (N)CHp group with respect to the C'(0)-N bond; this contrasts with isolated NMA, where the conformations with the different methyl orientations have similar energies with a difference of only -0.1 kcaljmol. In accord with the general trend observed in hydrogen bonding in a crystal data base, the ab initio calculations show that the hydrogen bond distance involving 'multiple acceptors" (i.e., the C ' 4 group that accepts two hydrogen bonds) is 0.02-0.06 A longer than that involving a 'single acceptor". The calculated hydrogen bond energy is -0.5-1.5 kcal/mol smaller when two acceptors are present. By contrast, the formation of a hydrogen bond to the NH group reduces the hydrogen bond distance for the hydrogen bond to the C ' 4 group by -0.02-0.045 A and increases the corresponding hydrogen bond energy by -0.3-0.9 kcal/mol. Correspondingly, the formation of each hydrogen bond to C ' 4 reduces the hydrogen bond distance for the hydrogen bond to the NH and increases the corresponding hydrogen bond energy by about the same amount. When one ligand is bound to the carbonyl group,...

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Section: H Bond Geometries and Interactionmentioning

confidence: 88%

Section: H Bond Geometries and Interactionmentioning

confidence: 94%

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Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers

Guo¹,

Karplus²

1992

J. Phys. Chem.

198

170

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“…[8][9][10][11][12][13][14][15][16][17][18][19][20] In the most recent ab initio theoretical studies, (a) 4-3 1G vibrational frequencies modified through nonuniform scaling were reported for the NMA conformers with C, symmetry by Williams,16 (b) 3-21G vibrational frequencies modified through nonuniform scaling were reported by Cheam17 for the same conformer (with C, symmetry) as that assumed in electron diffraction study, (c) 4-3 lG* optimized geometries and vibrational frequencies were reported by Mirkin and KIk"m5 for four conformers of trans-NMA, all with C, symmetry, (d) a preliminary 4-31G* study for the cis-NMA conformers with C, symmetry was also reported by Mirkin and Krimm,14 and (e) 6-31G* optimized geometries for trans-and cis-NMA conformers with C, symmetry were reported by Jorgenson and Gao. 13 In all these studies, C, symmetry for isolated NMA has been either assumed or supported.…”

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confidence: 97%

Vibrational properties of the peptide group: achiral and chiral conformers of N-methylacetamide

Polavarapu¹,

Deng²,

Ewig³

1994

J. Phys. Chem.

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Vibrational optical activity associated with the peptide group vibrations has been examined with Nmethylacetamide (NMA) as a model compound. In this process, the structures and vibrational infrared and Raman spectra of NMA are also examined. The a b initio Hartree-Fock investigations with the 6-31G* basis set and higher level calculations using electron correlation (MP2/6-31G*) and a larger TZP basis set indicate that the chiral structures have energies comparable to, and some times slightly lower than, the energies of the achiral structures. The predicted absorption spectra for chiral and achiral NMA conformers are similar and consistent with the corresponding experimental spectra of NMA. However, the predicted Raman spectra of the chiral and achiral conformers show significant differences. The predictions for vibrational optical activity of the chiral conformers suggest that the vibrations of carbonyl and of methyl groups are especially sensitive to the conformation of peptide groups. These investigations are expected to serve as reference points for the interpretation of the experimental vibrational optical activity spectra of peptides.Spectral properties of the peptide group [C-C(0)-N(H)-C] represent active areas of current research. Natural optical activity in vibrational transitions, referred to as vibrational optical activity (VOA), is supported by chiral molecules.' Vibrational circular dichroism (VCD) and Raman optical activity (VROA) are two phenomenologically different, yet complementary, branches of VOA s p e c t r o~c o p y~~~ that are gaining increased attention for three-dimensional structural determination of biological molecules in the solution phase. For example, the absolute configurations of chiral anesthetics were determined4 for the first time using VOA. A large body of experimental VOA data is now available on molecules containing the peptide group^,^ and some VCD calculations were undertaken recently assuming planar peptide skeleton^.^^ The interpretation of this experimental data will be facilitated by an understanding of the VOA associated with the peptide group. Since the experimental VOA measurements on NMA are not possible (because resolution of the chiral antipodes is unlikely to be achievable), theoretical investigations of VOA in chiral conformers of NMA will provide an altemative route to gain an understanding of the VOA associated with the peptide group. In order to understand the VOA properties of peptide groups in peptides and proteins, a careful and reliable analysis for molecules containing a single peptide group is useful. NMethylacetamide (NMA, CH3CONHCH3) is one of such simple model molecules.Despite widespread studies on NMA, several fundamental questions remain. The experimental data for the structure of NMA were derived from X-ray and electron diffraction studies. The X-ray diffraction results of Katz and Post6 indicated that in the crystalline phase the five heavy atoms of NMA are coplanar with a trans structure (trans-and cis-NMA refer to the trans and cis orientation...

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“…The microscopic description of solute-solvent interactions in aqueous solutions of amides is of particular interest [2], since it represents a suitable model for studying of both hydrophilic and hydrophobic interactions in peptides and proteins [3][4][5][6][7][8]. The N-methylacetamide (NMA) molecule contains a single amide group and can represent the protein as a model peptide group linkage, and as such it is the subject of extensive experimental [9][10][11][12][13] and theoretical investigations [14][15][16][17][18][19][20][21][22]. The strong hydrogen bond cooperativity in liquid NMA with its solvation structure and dynamics at different thermodynamic conditions are also available within the literature [23][24][25][26][27][28][29][30].…”

Section: Introductionmentioning

confidence: 99%

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

Pattanayak

Chowdhuri

2013

Molecular Physics

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The effects of salt concentrations on the structure, dynamics and hydrogen bond structural relaxation properties of ∼1.10 M aqueous N-methylacetamide (NMA) solution at 308 K are studied by classical molecular dynamics simulations. We have considered the concentration range of salts solution from 0.222 to 3.756 M to investigate the behaviour of aqueous environment of peptide bonds in the presence of concentrated NaCl and KCl solution. It is found that the addition of salt solution facilitates the structural breaking of aqueous NMA hydrogen bonds, as a result the number of hydrogen bonds per NMA molecule and their stability decreases. The water and NMA molecule shows slower translational and rotational dynamics with increasing salt concentrations due to additional ion atmospheric friction. Our result shows that the cation-O NMA radial distribution function decreases whereas the Cl − ৄH NMA radial distribution function increases with ion concentration. On the other hand, the cation-O water and Cl − ৄH water radial distribution function shows very negligible change with respect to ion concentration.We have also calculated NMA-water and water-water hydrogen bond structural relaxation times. It is observed that the hydrogen bond structural relaxation of O NMA ৄH water is comparatively slower than the H NMA ৄO water hydrogen bond, which can be attributed to higher number and greater stability of the former hydrogen bond than the latter. The change of the dynamical quantities observed here is more prominent in addition of NaCl rather than the KCl solution.

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The geometry of some amides obtained from ab initio calculations

Cited by 83 publications

References 25 publications

Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers

Ab initio studies of hydrogen bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers

Vibrational properties of the peptide group: achiral and chiral conformers of N-methylacetamide

Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation

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