Molecular mechanics calculations of conjugated amides and an ab initio investigation of acrylamide and its β-amino derivative: Conformational analysis and rotational barriers

Conformations and rotational barriers in a series of conjugated primary and tertiary amides have been analyzed by a modified MM2(91) force field, which treats the amide nitrogen as part of the conjugated system by redefining the atom type for the nitrogen. Ab initio molecular orbital calculations at the MP2/6-31G* level have been performed on the stable conformers and transition structures of acrylamide and β-trans-aminoacrylamide. The results have been used, with published experimental and computational data, to generate parameters for the MM2 force field. The force field has been applied to various conjugated amides, such as reduced nicotinamide adenine dinucleotide (NADH) and NAD⁺ analogues, nicotinamide, urea, vinylogous urea derivatives, and nucleic acid bases. The fundamental difference between primary and tertiary conjugated amides with respect to both conformation and barrier is highlighted. © 1996 by John Wiley & Sons, Inc.     

An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions.     

Study of hydrogen bonding interactions relevant to biomolecular structure and function

Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO-3G, 3-21G, 6-31G*, and MP2/6-31G* levels (geometries were fully optimized at each level). For anionic species, 6-31 + G* and MP2/6-31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for O? H-O and N? HO types of hydrogen bonds, but not for hydrogen bonds involving O-H? S and S-H? O, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate–water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.     

Charge localization by molecular orbital calculations. II. Formamide,thioformamide and N-methylated analogues

Ab initio molecular orbital calculations have been used to determine the degree of charge localization associated with the formation of radical cations on electron impact of formamide, thioformamide and their N-methyl and N, N-dimethyl analogues. The charge favours the nitrogen of formamides and the sulphur of thioformamides, but the degree of localization is calculated to be lower than in the radical cations of urea and thiourea.     

A theoretical study of tautomerism: 2- and 4-oxopyrimidine and some of their derivatives

Here we present a detailed study of the theoretical approach to the tautomerization processes considering 2- and 4-oxo-pyrimidine and several of their derivatives. We look into molecular relaxation, suitability of semiempirical methods, and the effect of basis sets size in pseudopotential ab initio calculations. We found that no semiempirical method is suited for studying the relative stability of the tautomers, even ab initio calculations with minimal basis sets. On the other hand MNDO appears to be very useful for molecular relaxation and can be used, as well as Ab initio calculations, for reasonable estimates of relative tautomerization. We also considered the quality of prediction of other parameters, in particular the ionization potentials. We considered the correlation of experimental and theoretical values as a means to adjust the theoretical results to obtain more reliable predictions.     

Ab initio and molecular mechanics study of n-phenyl phthalimide and its crystal structure

Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N-phenyl phthalimide using 3-21G, 6-31G, and 6-31G^** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least-squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.     

Ab initio study of vibrational frequencies,force field and normal coordinate analysis of the cis- and trans-isomets of nitrosomethanol

In this paper, the equilibrium geometries of two isomers of the newly found compound — nitrosomethanol—have been optimized by ab initio SCF MO method with 3–21G basic set by gradient technique. And the second derivatives of potential energy (i. e. the force constant matrix elements) have been calculated analytically. Hence the entire force fields of the two isomers of nitrosomethanol have been obtained theoretically. The theoretical vibrational frequencies and the corresponding normal modes were obtained and compared with the experimental values, and the structures of two isomeric forms of nitrosomethanol are established.     

A theoretical study on the structure and properties of phenothiazine derivatives and their radical cations

Semiempirical CNDO, AM1, PM3 and ab initio HF/STO-3G, HF/3-21G(d), and HF/6-31(d) methods were employed in the geometry optimization of the phenothiazine and the corresponding radical cation. The results obtained from the PM3 performances were as good as those from the ab initio calculations in the structure optimization of both phenothiazine and phenothiazine radical cation. The PM3 method was used to optimize the structures of a series of N-substituted phenothiazine derivatives and their radical cations. The PM3-optimized results were then analyzed with the ab initio calculation at the 6-311G(d,p) level, which yielded the total energy, frontier molecular orbitals, dipole moments, and charge and spin density distributions of the phenothiazine derivatives and their radical cations.     

Force field calculations (MM3) on glyoxal,quinones, and related compounds

A general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.     

Comparison of ab initio,semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems

The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C₅ ? C₈ cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H? H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.     

A CNDO/INDO molecular orbital formalism for the elements H to Br. applications

The CNDO/INDO molecular orbital formalism introduced in the preceding paper has been applied to a large number of atom combinations up to bromine under the inclusion of the first transition metal series. The results are compared with experimental data (geometries, ionization potentials, dipole moments) or with the results of sophisticatedab initio calculations (one electron energies, net charges, atomic populations). The semiempirical model reproduces for a wide range of molecules the experimental andab initio data with remarkable success.     

Ab initio and molecular mechanics (MM2 and MM3) calculations of positively charged conjugated nitrogen-containing compounds

Ab initio calculations have been carried out on s-trans-N-vinylmethyleneammonium, pyridinium, and related compounds to obtain rotational barriers, structures, and vibrational frequencies. The restricted Hartree-Fock (RHF) level of theory with 6-31G** basis set was used for these calculations. In addition, the MM2(91) and MM3(94) force fields have been parameterized to calculate these positively charged nitrogen-containing compounds. A bond order term was incorporated in the force field to reproduce accurately the rotational barriers of s-trans-N-vinylmethyleneammonium and related compounds. Molecular mechanics geometries and vibrational frequencies compare well with those calculated by ab initio methods. © 1996 by John Wiley & Sons, Inc.     

Geometry-dependent atomic charges: Methodology and application to alkanes,aldehydes, ketones,and amides

A general methodology for deriving geometry-dependent atomic charges is presented. The main ingredient of the method is a model that describes the molecular dipole moment in terms of geometry-dependent point charges. The parameters of the model are determined from ab initio calculations of molecular dipole moments and their Cartesian derivatives at various molecular geometries. Transferability of the parameters is built into the model by fitting ab initio calculations for various molecules simultaneously. The results show that charge flux along the bonds is a major contributing factor to the geometry dependence of the atomic charges, with additional contributions from fluxes along valence angles and adjacent bonds. Torsion flux is found to be smaller in magnitude than the bond and valence angle fluxes but is not always unimportant. A set of electrostatic parameters is presented for alkanes, aldehydes, ketones, and amides. Transferability of these parameters for a host of molecules is established to within 3 ?5% error in the predicted dipole moments. A possible extension of the method to include atomic dipoles is outlined. With the inclusion of such atomic dipoles and with the set of transferable point charges and charge flux parameters, it is demonstrated that molecular electrostatic potentials as well as electrostatic forces on nuclei can be reproduced much better than is possible with other models (such as potential derived charges). © 1995 by John Wiley & Sons, Inc.     

A theoretical study of C4H5N isomers: Comparison of cyano and isocyano as substituents

Ab initio molecular orbital calculations using a 3-21G basis set have been used to optimize geometries for pyrrole, CH₃(X)CCH₂, CH₃(H)CCHX (both cis and trans), c-C₃H₅X, and CH₂CHCH₂X, where X is CN and NC. In all the alkenyl derivatives methyl groups are found to adopt the conformation in which the methyl hydrogen eclipses the double bond. 6-31G*∥3-21G level calculations show the alkenyl cyanides to be of similar energy to pyrrole, but the isocyanides are ～20 kcal mol^?1 higher in energy. For both substituents the cyclopropyl derivatives are higher in energy by ～10 kcal mol^?1. At the 6-31G* level ring strain is 27.7 kcal mol^?1 for the cyanide and 30.6 kcal mol^?1 for the isocyanide. Data on the relative energies of RCN and RNC are compared when R is (i) a saturated hydrocarbon, (ii) an unsaturated hydrocarbon, (iii) an α-carbenium ion, (iv) an allyl cation, and (v) an α-carbanion.     

Semiempirical AM1 electrostatic potentials and AM1 electrostatic potential derived charges: A comparison with ab initio values

Electrostatic potentials calculated from AM1 wave functions have been compared with ab initio STO-3G values and qualitative agreement has been found. Atomic charges derived from AM1 electrostatic potentials for both experimental and AM1 optimized geometries are of comparable quality with STO-3G potential derived charges. These results suggest that the AM1 electrostatic potential may be useful both in its own right and also for deriving atomic charges for use in molecular dynamics studies.     

Studies in hydrogen bonding: Association within mixed dimers of water,methanol, ammonia,and methylamine using the empirical potential EPEN

An empirical potential EPEN has been used to find the stable geometries and approximate hydrogenbond energies of the mixed dimers formed between molecules of water, methanol, ammonia, and methylamine. These results are compared with results in the literature obtained using ab initio methods.     

Ab initio and molecular mechanics (MM2 and MM3) calculations of nonconjugated positively charged nitrogen-containing compounds

High-level ab initio calculations have been performed on N-methyl-N-methyleneammonium and related compounds to obtain accurate rotational barriers, structures, and vibrational frequencies. The 6-31G** basis set has been utilized at the Hartree-Fock level of theory for these calculations because little experimental data are available. The MM2(91) and MM3(94) force fields have been parameterized to include these nonconjugated charged nitrogen-containing compounds. Molecular mechanics geometries and vibrational frequencies compare well with the ab initio results. © 1995 John Wiley & Sons, Inc.     

Quantum chemical prediction of the adsorption conformations and dynamics at HCOOH‐covered ZnO(1010) surfaces

Results from ab initio Hartree–Fock and gradient‐corrected density functional theory calculations of formic acid interactions with ZnO (101 0) surfaces are reported. Surface relaxation is found to affect equilibrium geometries and adsorption energies significantly. Large variations in adsorption energy with coverage and ordering of the adsorbates are revealed and explained in terms of strong and highly anisotropic electrostatic adsorbate–adsorbate interactions. The results are compared to published experimental and theoretical results, and differences in suggested binding geometries from the different studies are discussed. Dynamic properties of the adsorption, surface mobility, and surface reactivity are inferred from key elements of the potential energy surface obtained from the quantum chemical computations and supported by ab initio molecular dynamics simulations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

The valence isomers of (CH)8 and (SiH)8: An ab initio MO study

The 22 possible valence isomers of the (CH)₈ and (SiH)₈ systems have been studied by ab initio molecular orbital calculations at the MP2/6-31G*//6-31G* + ZPE level. Optimized geometries, relative energies, and, for some selected compounds, vibrational frequencies are reported. The systematic differences between the carbon and silicon compounds are analyzed. © 1994 by John Wiley & Sons, Inc.