A computational analysis of the electrostatic potentials and relative bond strengths of hydrazine and some of its 1,1-dimethyl derivatives

We have carried out a computational study of hydrazine and five of its 1,1-dimethyl derivatives, focusing on their electrostatic potentials and relative bond strengths. Our approach has involved the calculation of ab initio self-consistent-field molecular orbital wave functions and molecular properties using the GAUSSIAN 82 system of programs. The electrostatic potentials of the hydrazines possess negative regions of varying sizes and strengths associated with the nitrogens of the α-diamino linkages. Through an analysis of the positions of the most negative potentials of these regions, we have obtained directly the dihedral angles between the nitrogen lone pairs in these systems. Our use of the electrostatic potential to obtain these angles is a direct and general approach, in contrast to indirect procedures used in the past. We find this dihedral angle to be close to 90° in hydrazine, with variations in the substituted hydrazines that depend on the nature of the substituents. A highly polar structure is found for 1-chloromethyl-1-methylhydrazine, which involves a delocalization of electronic charge from the substituted nitrogen towards the CH₂Cl group. We find that substituents able to withdraw significant amounts of electronic density from the central nitrogen lone pair regions, either through resonance or by induction, have a slight bond strengthening effect on the central N-N bond. This is attributed to a decrease in the repulsion between the weakened nitrogen lone pair regions. The difficulties encountered in seeking the controlled oxidation of hydrazine to nitro derivatives may be due, in part, to the fact that two factors which would favor this, highly negative nitrogen potentials and strong N-N bonds, are opposing in nature.     

CNDO/2 (complete neglect of differential overlap)-method for third-row molecules

An extension of the CNDO/2 method to compounds containing third-row elements (Germanium, Arsenic, Selenium and Bromine) is presented. Bond lengths, bond angles, dipole moments, and ionization potentials are considered.     

Towards a quantum chemical software package utilizing transferable fragments as molecular building blocks

Computer programs have been developed or are under development for the IBM personal computer that enable their users to get information on atomic charges, electrostatic potentials, conformational and other properties of molecular systems containing H, C, N, O, F, Si, P, S, or Cl atoms. The zero-order wavefunction is constructed of strictly localized molecular orbitals with fixed atomic orbital coefficients. The wave function can be refined by optimizing these coefficients, i.e., considering inductive effects via a coupled set of 2 × 2 secular equations within the CNDO /2 approximation. Delocalization and exchange effects are accounted for by expanding the wavefunction on a basis of the aforementioned strictly localized orbitals, instead of conventional atomic orbitals, and solving the corresponding SCF equations. Our method has been applied to the study of large systems. We calculated the electrostatic field of the complex of β-trypsin and basic pancreatic trypsin inhibitor and it has been found that strong field regions more or less coincide with hydration sites. A further potential application of protein electrostatic fields is in NMR spectroscopy. We found a linear correlation between C^αH or backbone NH proton chemical shifts and the protein field at the site of the corresponding proton. At last, we propose a simple method to mimic the bulk around atomic clusters modeling crystalline and amorphous silicon. Based on this method we found a linear correlation between atomic net charges and bond angle distortions in silicon clusters with 35 atoms.     

Force constants in hydrogen-bonded crystals

Hydrogen bond stretching force constants in crystals of imidazole, urea and cyanuric acid are calculated using both a modified CNDO/2 method and a constrained least squares fitting of interatomic pair potentials to the lattice vibrations. Results show that the modified CNDO/2 method gives closer agreement with the experimentally derived force constants than the normal CNDO/2 parameterization.     

Molecular orbital and DFT studies of the alimemazine radical cation

Semiempirical molecular orbital methods including CNDO, MNDO, AM1 and PM3, and density function theory method B3LYP/3-21G(d) were employed in the study of the alimemazine radical cation. It was found that PM3 was much better than CNDO, MNDO and AM1 in the structural optimization. The bond lengths and bond angles by PM3 were close to the experimental data, and comparable with the results by the density function theory method.     

Molecular chains with fixed bond lengths and angles: a study based on quantum statistical mechanics

This work studies large three-dimensional open molecular chains at thermal equilibrium in which bond lengths and angles are fixed (hard variables), based upon quantum statistics. A model for a chain formed by N particles interacting through harmonic-like vibrational potentials is treated in the high-frequency limit in which all bond lengths and angles become constrained, while other N angles (soft variables) remain unconstrained. The associated quantum partition function is bounded rigorously, using a variational inequality (related to the Born-Oppenheimer approximation), by another quantum partition function, Z. The total vibrational zero-point energy is shown to be independent of the soft variables thereby solving for this model a generic difficulty in the elimination of hard variables. Z depends only on soft variables and, under certain conditions, it can be approximated by a classical partition function Z_c. The latter satisfies the equipartition principle and it differs from other classical partition functions for related molecular chains. The extension of the model when only part of the bond angles become fixed in the high-frequency limit is outlined. As another generalization, a systematic study of macromolecules, as composed of electrons and heavy particles with Coulomb interactions, is also presented. Its exact quantum partition function is bounded, supposing that the effective molecular potential also tends to constrain all bond lengths and angles, and under suitable assumptions, by another quantum partition function. The latter depends only on the remaining soft variables and it generalizes the one obtained for the first model.     

N—亚硝基二甲胺化学电离的量子化学研究

用质谱化学电离和量子化学方法研究了致癌物质N-亚硝基二甲胺(NDMA)的结构及性质,优化了化学电离质谱中主要离子的构型;探讨了NDMA的质子化合物的形成途径,经NDMA及其质子化合物的静电势计算,阐述了NDMA的可能致癌机理。     

Geometry optimization of periodic systems using internal coordinates

An algorithm is proposed for the structural optimization of periodic systems in internal (chemical) coordinates. Internal coordinates may include in addition to the usual bond lengths, bond angles, out-of-plane and dihedral angles, various "lattice internal coordinates" such as cell edge lengths, cell angles, cell volume, etc. The coordinate transformations between Cartesian (or fractional) and internal coordinates are performed by a generalized Wilson B-matrix, which in contrast to the previous formulation by Kudin et al. [J. Chem. Phys. 114, 2919 (2001)] includes the explicit dependence of the lattice parameters on the positions of all unit cell atoms. The performance of the method, including constrained optimizations, is demonstrated on several examples, such as layered and microporous materials (gibbsite and chabazite) as well as the urea molecular crystal. The calculations used energies and forces from the ab initio density functional theory plane wave method in the projector-augmented wave formalism.     

Calculation of fully optimized geometries of five- and six-membered heterocycles by the CNDO force method

Equilibrium geometries of five- and six-membered aromatic molecules have been calculated by applying the force method of the CNDO/2 procedure. The calculated and experimental geometries agree surprisingly well. The reliable values obtained for bond angles are of special importance in calculating molecular conformations.     

Algorithm for normal mode analysis with general internal coordinates

A technique for performing normal vibrational analysis for biological macromolecules using general internal coordinates is proposed. The technique is based on the conventional algorithm for calculating the second derivatives of potential and kinetic energies using intramolecular dihedral angles, intermolecular translation, and rotation as variables [Braun, W. et al., J Phys Soc Jpn 1984, 53, 3269]. We extend the algorithm to include more general internal coordinates, bond stretching, angle bending, and so forth, without assuming two-body interactions. The essential point is the separation of the variables for potential functions and vibrational analysis. With our technique, we can arbitrarily choose any combination of internal coordinates as variables, free from the functional form of potential energy. We can analyze complex systems such as a multiple molecular system including solvents or a transition state of chemical reactions. In addition, mixed use of the potentials of molecular mechanics and quantum chemistry is possible.     

Molecular orbital studies of conformation

The application of single-configuration molecular orbital theory to the conformations of small organic molecules is reviewed. Emphasis is laid on systematic ab initio studies using simple gaussion-type basis sets for expansion of the molecular orbitals. Topics dealt with include the prediction of bond angles, single-rotor potential functions, effects of single and double (1,2) substitutions on such rotors and double-rotor potentials involving two internal rotation coordinates.     

Efficient parallelization of the energy,surface, and derivative calculations for internal coordinate mechanics

An efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.     

Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters

Summary Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.     

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

Parametrization and testing of a new all-atom force field for organic molecules and peptides with fixed bond lengths and bond angles are described. The van der Waals parameters for both the organic molecules and the peptides were taken from J. Phys. Chem. B 2003, 107, 7143 and J. Phys. Chem. B 2004, 108, 12181. First, the values of the 1-4 nonbonded and electrostatic scale factors appropriate to the new force field were determined by computing the conformational energies of six model molecules, namely, ethanol, ethylamine, propanol, propylamine, 1,2-ethanediol, and 1,3-propanediol with different values of these factors. The partial atomic charges of these molecules were obtained by fitting to the electrostatic potentials calculated with the HF/6-31G quantum-mechanical method. Two different charge models (single- and multiple-conformation-derived) were also considered. We demonstrated that the charge model has a stronger effect on the conformational energies than the 1-4 scaling. The choice of a charge model affected the conformational energies of even the smallest molecules considered, whereas the effect of the 1-4 electrostatic or nonbonded scaling was apparent only for 1,3-propanediol. The best agreement with high-level ab initio data was obtained with the multiple-conformation-derived charges and with no scaling of the 1-4 nonbonded or electrostatic interactions (scale factors of 1.0). Next, the torsional parameters of a large number of neutral and charged organic molecules, assumed to be models of the side chains of the 20 naturally occurring amino acids, were computed by fitting to rotational energy profiles obtained from ab initio MP2/6-31G calculations. The quality of the fits was high with average errors for torsional profiles of less than 0.2 kcal/mol. To derive the torsional parameters for the peptide backbone, the partial atomic charges of the 20 neutral and charged amino acids were obtained by fitting to the electrostatic potentials of terminally blocked amino acids using the HF/6-31G quantum-mechanical method. Then, the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe were computed using MP2/6-31G//HF/6-31G quantum-mechanical methods. The phi-psi energy map of Ac-Ala-NMe was used for refinement of the nonbonded parameters for the backbone nitrogen and hydrogen bonded to it. Subsequently, the main-chain torsional parameters were obtained by fitting the molecular mechanics energies to the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe. The transferability of the entire force field was demonstrated by reproducing the main energy minima of terminally blocked Ala3 from the literature. The performance of the force field was also evaluated by simulating crystal structures of small peptides. By comparison of simulated and experimental data, examination of the torsional-angle and atom-positional root-mean-square deviations of the energy-minimized crystal structures from the corresponding X-ray model structures demonstrated high accuracy of the force field.     

The use of internal coordinates in the variable metric method of molecular geometry optimization

A computational algorithm for the variable metric method of molecular geometry optimization using internal instead of cartesian coordinates is presented. The greater efficiency attainable using internal coordinates is shown using ethylene and methanol as examples. A high degree of accuracy in determining bond lengths and angles was achieved even when, as in the case of some ethers studied, the resulting equilibrium structures were essentially different from the initial ones constructed from experimental data.     

A study on quantum chemical calculations of 3-, 4-nitrobenzaldehyde oximes

The molecular geometry, vibrational frequencies, 1H and 13C NMR chemical shifts, UV-vis spectra, HOMO-LUMO analyses, molecular electrostatic potentials (MEPs), , thermodynamic properties and atomic charges of 3- and 4-Nitrobenzaldehyde oxime (C7H6N2O3) molecules have been investigated by using Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with the 6-311++G(d, p) basis set. The calculated optimized geometric parameters (bond lengths and bond angles), the vibrational frequencies calculated and 13C and 1H NMR chemical shifts values for the mentioned compounds are in a very good agreement with the experimental data. Furthermore, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) have been simulated and the transition states, energy band gaps and molecular electrostatic potential (MEP) maps for each oxime compound have been determined. Additionally, we also report the infrared intensities and Raman activities for the compounds under study.     

Realistic sampling of amino acid geometries for a multipolar polarizable force field

The Quantum Chemical Topological Force Field (QCTFF) uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms in the molecular system. It is important that kriging operates on relevant and realistic training sets of molecular geometries. Therefore, we sampled single amino acid geometries directly from protein crystal structures stored in the Protein Databank (PDB). This sampling enhances the conformational realism (in terms of dihedral angles) of the training geometries. However, these geometries can be fraught with inaccurate bond lengths and valence angles due to artefacts of the refinement process of the X‐ray diffraction patterns, combined with experimentally invisible hydrogen atoms. This is why we developed a hybrid PDB/nonstationary normal modes (NM) sampling approach called PDB/NM. This method is superior over standard NM sampling, which captures only geometries optimized from the stationary points of single amino acids in the gas phase. Indeed, PDB/NM combines the sampling of relevant dihedral angles with chemically correct local geometries. Geometries sampled using PDB/NM were used to build kriging models for alanine and lysine, and their prediction accuracy was compared to models built from geometries sampled from three other sampling approaches. Bond length variation, as opposed to variation in dihedral angles, puts pressure on prediction accuracy, potentially lowering it. Hence, the larger coverage of dihedral angles of the PDB/NM method does not deteriorate the predictive accuracy of kriging models, compared to the NM sampling around local energetic minima used so far in the development of QCTFF. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Ab initio assessment of the electronic structure of 5α-reduced progestins

Progesterone (P) yields to 5α-reduced progestins, namely 5α-pregnanedione (DHP), tetrahydroprogesterone (THP), and allopregnanolone (ALLO-P). The geometries and electronic structure of these steroids were assessed by ab initio calculations using the 6-31G* basis set. The parameters measured were bond distances, valence angles, and dihedral angles. Likewise, the following were calculated: total energy; frontier orbitals, i.e., highest occupied molecular orbital (HOMO); lowest unoccupied molecular orbital (LUMO); dipole moment; atomic charges; and electrostatic potentials. The frontier orbitals of P were located at the π-double bond. However, the HOMO of the 5α-progestins was extended into the molecule, while the LUMO was confined at the C20 carbonyl group. The atomic charges, electronic density surfaces and electrostatic potentials showed patterns according to the stereochemical arrangement of the C3 and C20 carbonyl and hydroxyl functional groups. Interestingly, P and THP showed the larger dipole moment and high electronic density at the A-ring because the double bond and the 3α-hydroxy group, respectively. The present results might explain to some extent the metabolism of the studied progestins. Similarly, some physicochemical properties, such as dipole moments and electrostatic potentials, seem related with important biological actions such as uterine contractility and control of gonadotropin secretion. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 329–338, 1998     

SCF perturbation calculations on metalloporphyrins

The influence of metal ion on the oxidation and ionisation potentials of metalloporphyrins is investigated by the simple electrostatic model using SCF perturbation theory. The zero order wavefunctions are obtained from PPP and CNDO/2 methods. The wide variations in redox potentials with metal and the relative insensitivity of the optical transitions with metal are very well accounted for by the perturbation approach.