Introducing a novel method based on the imperialistic competitive algorithm to determine fluorine intermolecular potential from ab initio calculations and calculation of some properties via MD simulations

In this work, the possibility of obtaining an accurate site-site potential model suitable for use in molecular dynamics (MD) simulations of fluorine from ab initio calculations has been explored. The exploration was made on ab initio calculations. To reduce the ab initio pair potentials into a site-site potential, a higher significance was assigned to the configuration which is more stable. For this purpose, the imperialistic competitive algorithm (ICA) was implemented as a powerful optimisation tool. The calculated second virial coefficients were compared to the experimental values to test the quality of the presented intermolecular potential. The relative error for the calculated second virial coefficient ranged from 0.1 to 5.6%. MD simulations were used to evaluate the ability of the proposed intermolecular potential function. The relative error for the MD simulations ranged from 0.5 to 5.2%. The results are in good agreement with experimental data.     

Investigations of Some Nucleic Acid Component Analogs

Abstract

Ab initio calculations of some nucleic acid bases analogs - 6 thioguanine, 4-thiouracil, 5- and 6-azacytosines, 6-azauracil, 5- and 6-fluorouraciles and 5azaC+Gua dimer had performed. 6-Thioguanine and 4-thiouracil were studied by experimental methods also. Total energies, geometries, charge distributions, entropies, heat capacities, vibrational spectra and solvent effects using high level ab initio methods were calculated.     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

Coordination and Thermodynamics of Stable Zn(II) Complexes in the Gas Phase

Abstract

Ab initio molecular orbital methods in combination with DFT calculations were used to study the structural and thermodynamic properties of 17 complexes containing zinc cation and four first-shell ligands as models of active site of metalloenzymes (e.g. angiotensin converting enzyme, thermolysin). The geometry of the complexes was relaxed by complete optimization by ab initio molecular orbital methods at Hertree-Fock level with 3–21G basis set. Following single point calculation with tight SCF criteria at the B3LYP level with 6–311+G(2d,p) basis set was used to calculate accurate interaction enthalpies. The structure and thermodynamics of optimized complexes are discussed from the point of view of their biological importance.     

Study of the Tautomerism by Experimentally and Theoretically Estimated 13C and 15N Chemical Shifts

2-Substituted 5-Me-7OH-1,2,4-Triazolo[1,5-a]pyrimidines can exist as different tautomeric forms. The tautomeric equilibrium of these compounds were determined by various NMR spectroscopic methods and quantum-chemical calculations. The tautomeric equilibria of 2-substituted 1,2,4-Triazolopyrimidines depend on the used solvent. In order to take solvent effects into account, ab initio calculations using the SCI-PCM method were carried out. The solvation energy depends on the polarity of the substituents in position 2. The comparison of chemical shifts determined by experimental methods and theoretical ab initio methods were used to definitely find out the the tautomeric equilibria of these compounds.     

On the accuracy of analytical potentials: comment on ‘Accurate ab initio calculation of the Ar–CF4 intermolecular potential energy surface’

In a recent study of the Ar–CF₄ intermolecular interaction potential [Shen C-C, Chang R-Y. Accurate ab initio calculation of the Ar–CF₄ intermolecular potential energy surface. Mol Sim. 2010;36:1111–1122], Shen and Chang (SC) illustrated how the use of bond functions can improve the accuracy and basis-set saturation of electronic structure calculations employing perturbation and coupled-cluster theory. SC then used these ab initio data to derive analytic potential energy functions for use in chemical dynamics simulations. We critically examine these analytic potentials and comment on their usage in such simulations. Our analysis highlights the need for care and global validation when deriving analytic potential energy functions.     

A New Potential Model for Carbon Dioxide from AB Initio Calculations

Abstract

Ab initio quantum chemical calculations have been carried out for carbon dioxide dimer and the results have been used to establish potential functions usable in molecular simulations. Since the intermolecular interaction in carbon dioxide is fairly weak, careful treatment is required: this study uses 6–31G* basis set and takes electron correlations by the 2nd order Møller-Plesset theory into account. The potential energy surface is elucidated using the four representative relative configurations of the dimer. A new potential function model has been proposed on the basis of these ab initio data. In the super-critical region, this model is used to calculate the PVT relation of carbon dioxide fluid by the Monte Carlo simulations and confirmed to reproduce reasonably well the experimental isotherms.     

A Modified Version of the Cornell et al. Force Field with Improved Sugar Pucker Phases and Helical Repeat

Abstract

We have examined some subtle parameter modifications to the Cornell et al. force field, which has proven quite successful in reproducing nucleic acid properties, but whose C2′-endo sugar pucker phase and helical repeat for B DNA appear to be somewhat underestimated. Encouragingly, the addition of a single V₂ term involving the atoms C(sp³)-O-(sp³)-C(sp³)- N(sp²), which can be nicely rationalized because of the anomeric effect (lone pairs on oxygen are preferentially oriented relative to the electron withdrawing N), brings the sugar pucker phase of C2′-endo sugars to near perfect agreement with ab initio calculations (W near 162°). Secondly, the use of high level ab initio calculations on entire nucleosides (in contrast to smaller model systems necessitated in 1994–95 by computer limitations) lets one improve the % torsional potential for nucleic acids. Finally, the O(sp³)-C(sp³)- C(sp³)-O(sp³) V₂ torsional potential has been empirically adjusted to reproduce the ab initio calculated relative energy of C2′- endo and C3′-endo nucleosides. These modifications are tested in molecular dynamics simulations of mononucleosides (to assess sugar pucker percentages) and double helices of DNA and RNA (to assess helical and sequence specific structural properties). In both areas, the modified force field leads to improved agreement with experimental data.     

Methane in Water: An Ab Initio Study

Abstract

In preceding publications we discussed some properties of pure water in condensed phases using an ab initio approach. Here this study is used as a basis of comparison for analysing the behaviour of water as a solvent in the presence of an apolar molecule. Our analysis is focused on the process of organization of the hydrogen bonding network around the solute. For this purpose we perform some ab initio calculations for a system of 32 water molecules and one methane molecule at 300 K; in particular, the average molecular dipole moment of water is determined and the result is compared with that of pure water. Next the attention is switched to the methane molecule; related properties such as excluded volume and sphericity of its shape are illustrated and discussed. A comparison with results obtained using classical approaches suggests that some classical models of water can be considered to be still valid when they are used to analyse the water-methane system.     

Molecular Parameterisation and the Theoretical Calculation of Electrode Potentials

The difference in reduction potentials between ortho and para-benzoquinones has been calculated. The employs gas phase ab initio and semi-empirical computations in combination with free energy perturbation theory applied to gas and solution phase Monte Carlo simulations. The effects on calculated results of altering solute electrostatic parameterisation in solution phase simulations is examined. Atom centred charges derived from the molecular electrostatic potentials, MEPs, from optimised ab initio wavefunctions and charges generated by consideration of hydrogen bonded complexes are considered. Parameterisation of hydroxyl torsions in hydroquinone molecules is treated in a physically realistic manner. The coupled torsional system of the ortho-hydrobenzoquinone molecule is described by a potential energy surface calculated using gas phase AM1 semi-empirical computations rather than the simple torsional energy functions frequently employed in such calculations. Calculated differences in electrode potentials show that the electrostatic interactions of quinone and hydroquinone molecules in aqueous solution are not well described by atom centred charges derived from ab initio calculated MEPs. Moreover, results in good agreement with the experimental reduction potential difference can be obtained by employing high level ab initio calculations and solution phase electrostatic parameters developed by consideration of hydrogen bonded complexes.     

Comparison of Different Three-site Interaction Potentials for Liquid Acetonitrile

Abstract

Computer simulations of liquid acetonitrile at normal room conditions are reported. Both static and dynamic properties are analysed. Special attention is paid to the dielectric properties. A three-site interaction potential has been derived from ab initio calculations on the gas phase dimer and a comparison with different three-site interaction potentials available in the literature is presented. The suitability of three-site models to reproduce the properties of the real liquid is discussed by comparing computer simulation results with experimental data.     

Quantum simulation for muoniated and deuterated methyl radicals in implicit water solvent: combined ab initio path integral molecular dynamics and the polarizable continuum model simulation study

We have combined ab initio path integral molecular dynamics (PIMD) simulation and the polarizable continuum model (PCM) method to efficiently incorporate solvent effects into nuclear quantum fluctuation of molecular systems. Our combined ab initio PIMD–PCM simulation was applied to muoniated and deuterated methyl radical immersed in implicit water solvent to gain information on solvent and isotope effects from one simulation run. We found that solvent effects lead to the bond elongation and a decrease in the magnitude of isotropic hyperfine coupling constants. These are consistent with the trends in conventional static calculations and experiments. In addition, the performance of cavity models (universal force field, united atom specified for Kohn–Sham and these hybrid models) and the conservation of the PIMD–PCM Hamiltonian were accessed. We confirmed that solvent effects on nuclear quantum fluctuation are efficiently computed using our combined simulation of quantum solute in implicit solvent.     

Recent Progress in First Principles O(N) Methods

Abstract

We describe recent progress in developing practical first principles methods for which the computer effort is proportional to the number of atoms: linear scaling or O(N) methods. It is shown that the locality property of the density matrix gives a general framework for constructing such methods. We then outline some of the main technical problems which must be solved in order to develop a practical O(N) method based on density functional theory and the pseudopotential method. Recent progress in solving these problems is presented, and we show that the spatial cut-off distances needed to achieve good accuracy are small enough to make the calculations feasible. Parallel implementation of the O(N) methods in the CONQUEST code is outlined, and it is shown that the code exhibits excellent linear-scaling behaviour on test systems of several thousand atoms. It is pointed out that the most important remaining problem concerns the optimal strategy for seeking the ground state. It is argued that there are three different mechanisms of ill-conditioning which cause present search methods to be inefficient, and some partial solutions are suggested.     

A force field for naproxen

A united-atom potential model for naproxen suitable for molecular dynamics (MD) simulation has been developed. The charge distribution is approximated by point charges obtained from ab initio calculations using the CHELPG method. Also the intramolecular interactions such as bond and angle vibration, and the torsion potential are obtained from ab initio calculations. The dispersive interaction contribution is taken from the literature. By MD simulation using a naproxen film in slap geometry, the temperature dependence of the density, surface tension and self-diffusion coefficient as well as the melting temperature for the developed potential model are obtained.     

Glass Transition Temperatures Studied by MD Simulation of Some Alkali Metasilicates

Abstract

Molecular dynamics simulation of some alkali metasilicates (M₂SiO₃, M = Li, Na, K) was performed to compare glass transition temperatures, T_g , defined in various ways. The potential parameters derived from ab initio MO calculations were used and found to reproduce the inflection of V-T relation on cooling the system. The T_g defined by the inflection point corresponds well to that defined by geometrical changes of coordination polyhedra found in previous work. The self-diffusion coefficients of the alkali ions in higher temperature regions were shown to be related to the amount of free volume in these systems.     

Conformational behaviour of the architectural units of peptides and proteins. Assessment of current understanding by ab initio quantum mechanical methods and refinement of the dipeptide energy surface.

The conformational energy surfaces of analogues of the dipeptide unit of polypeptides and proteins are calculated by ab initio methods using extended basis sets.The calculations are not particularly sensitive to the choice of (extended) basis set.The calculations are shown to support a particular empirical method parameterized with respect to crystal data. Non-hydrogen bonded conformations agree to within 3 kcal mol^?1, even for conformations in which quite considerable degrees of atomic overlap occur.Hydrogen bonded conformations, are, however, in less satisfactory agreement and it is the ab initio calculations which appear to be at fault.A simple correction is applied to the ab initio energy for hydrogen bonded conformations, and with the use of the empirical energy surface a full quantum mechanical conformational energy map is interpolated for the alanyl dipeptide.The effect of flexibility in the peptide backbone is taken into account, and supports recent empirical findings that distortions in valence angles must be considered in calculations of the conformational behaviour of peptides.     

Modelling of Structural and Vibrational Properties of Poly(p-Phenylene) and Polypyrrole Using Molecular Orbital Methods

Abstract

This paper concentrates on two very important conducting polymers poly(p-phenylene) and polypyrrole. Detailed atomistic molecular models have been developed with the help of ab initio and semi-empirical quantum mechanical calculations using the Cerius² and WinMOPAC (version 6.0) programs.

Their optimised geometry had been calculated and compared with experimental X-ray diffraction data. The simulated and experimental vibrational spectra of biphenyl as well as isolated pyrrole monomers and oligomers from n = 1 and 2, where n is the number of structural repeat units used, have been computed using the ab initio 3–21G basis set. The results obtained are compared with experimental data for the case of biphenyl and for oligomers with n = 2 to 5 for both neutral benzenoid and quinonoid oligopyrroles, from semi-empirical predictions obtained by AM1 and PM3. The trends in the computed harmonic force fields, vibrational frequencies and intensities are monitored as a function of the chain length. The data are analyzed in conjunction with the trends in computed equilibrium geometries.     

Hydrogen Bonding and Stacking of DNA Bases: A Review of Quantum-chemical ab initio Studies

Abstract

Ab initio quantum-chemical calculations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971).), and the II-II interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry.