Theoretical study of p‐methacryloyl‐aminophenylarsonic acid

Conformations of p‐methacryloylaminophenylarsonic acid (p‐MAPHA) are determined through molecular mechanics and DFT/B3LYP calculations. Solvation effects are studied within the self‐consistent isodensity continuum model (SCI‐PCM). The stationary points were found to correspond to minima as verified by the analysis of vibrational frequencies in the molecule. The molecular optical absorption was obtained by using different solvent environments. The present results are in good agreement with the available experimental data. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

A Theoretical Study of the UV/Visible Absorption and Emission Solvatochromic Properties of Solvent‐Sensitive Dyes

Using the density‐functional vertical self‐consistent reaction field (VSCRF) solvation model, incorporated with the conductor‐like screening model (COSMO) and the self‐consistent reaction field (SCRF) methods, we have studied the solvatochromic shifts of both the absorption and emission bands of four solvent‐sensitive dyes in different solutions. The dye molecules studied here are: S‐TBA merocyanine, Abdel‐Halim's merocyanine, the rigidified aminocoumarin C153, and Nile red. These dyes were selected because they exemplify different structural features likely to impact the solvent‐sensitive fluorescence of “push‐pull”, or merocyanine, fluorophores. All trends of the blue or red shifts were correctly predicted, comparing with the experimental observations. Explicit H‐bonding interactions were also considered in several protic solutions like H₂O, methanol and ethanol, showing that including explicit H‐bonding solvent molecule(s) in the calculations is important to obtain the correct order of the excitation and emission energies. The geometries, electronic structures, dipole moments, and intra‐ and intermolecular charge transfers of the dyes in different solvents are also discussed.     

Conformational and electronic study of N‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

A conformational and electronic study on N‐acetyl‐L ‐isoleucine‐N‐methylamide was carried out. All side‐chain as well as backbone conformations were explored for this compound. Multidimensional conformational analysis predicts 81 structures in the case of N‐acetyl‐L ‐isoleucine‐N‐methylamide, 53 relaxed structures were determined at the DFT (B3LYP/6‐31G(d)) level of theory. An exhaustive electronic study employing the atoms‐in‐molecules (AIM) method was carried out. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) method. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Conformational analysis,tautomeric preference,intramolecular hydrogen bonding,and solvent effect on dinitrosamine: A quantum chemical study

HF, B3LYP, and MP2 methods with the standard basis set, 6‐311++G(d,p), were used to study various aspects of dinitrosamine. These results were compared with the outcomes of G2 and CBS‐QB3 methods. First, the conformational analysis and characterization of equilibrium conformations, especially global minima, were performed. On the basis of relative energies, we found that the dinitroso tautomers are more stable than the nitroso‐hydroxy (NH) ones. This preference is well‐interpreted in terms of tautomerization process and nitrosamine resonance. Furthermore, the nature of O? H···O intramolecular hydrogen bond (IMHB), in chelated forms of NH (NH‐11 and NH‐13) was comprehensively studied to evaluate the effect of hetero atoms (N) on the characteristic of IMHB systems. According to the results of isodesmic reaction method, the hydrogen bond energy of NH‐11 is greater than the malonaldehyde (MA) and NH‐13, whereas the electron density analysis and energy‐geometry correlation methods clearly predict that the hydrogen bond of NH‐11 is weaker than the MA. Additionally, the geometrical, atoms in molecules (AIM) and natural bond orbital's (NBO) parameters also emphasize on the MA as a chelated form with the strongest hydrogen bond. Finally, the solvent effects on the relative stability of selected dinitrosamine conformers are evaluated by different continuum (polarizable‐continuum model, isodensity polarizable continuum model, and self‐consistent isodensity polarizable continuum model), discrete and mixed solvent models. Theoretical results readily show that the potential energy surface of dinitrosamine, especially global minima, is strongly affected by the solvent. © 2012 Wiley Periodicals, Inc.     

溶液环境中水对甲酰胺质子迁移影响的密度泛函研究

甲酰胺酮式和烯醇式的互变异构(FM→FA)可被视为DNA中生物碱基点突变的一个模型. 使用B3LYP密度范函的计算方法, 在B3LYP/6-311++G**的基组条件下运用SCRF溶液模型研究了溶液环境对甲酰胺互变异构的影响. 研究表明, 从水分子对甲酰胺异构的作用进行划分, 分子的周围有三个不同的区域, 和气态计算结果一致, 在一些区域中, 水对异构起到了催化的作用; 而在其它区域中, 水分子却能阻碍反应的进行,保护酮式, 同时溶液环境的存在也使两种作用得到了加强和削弱. 溶液状态下的质子转移研究将会对水分子对中心分子的异构化研究提供参考, 同时也部分解释了试验中酮式比例高于烯醇式的现象.     

Electronic g-tensors of solvated molecules using the polarizable continuum model

We present the implementation of density functional response theory combined with the polarizable continuum model (PCM), enabling first principles calculations of molecular g-tensors of solvated molecules. The calculated g-tensor shifts are compared with experimental g-tensor shifts obtained from electron paramagnetic resonance spectra for a few solvated species. The results indicate qualitative agreement between the calculations and the experimental data for aprotic solvents, whereas PCM fails to reproduce the electronic g-tensor behavior for protic solvents. This failure of PCM for protic solvents can be resolved by including into the model those solvent molecules which are involved in hydrogen bonding with the solute. The results for the protic solvents show that the explicit inclusion of the solvent molecules of the first solvation sphere is not sufficient in order to reproduce the behavior of the electronic g-tensor in protic solvents, and that better agreement with experimental data can be obtained by including the long-range electrostatic effects accounted for by the PCM approach on top of the explicit hydrogen-bonded complexes.     

Optimized parameters for continuum solvation calculations with carbohydrates

Continuum solvent models have been shown to be an efficient method for the calculation of the energetics of biomolecules in solution. However, for these methods to produce accurate results, an appropriate set of atomic radii or volumes is needed. While these have been developed for proteins and nucleic acids, the same is not true of carbohydrates. Here, a set of optimized parameters for continuum solvation calculations of carbohydrates in conjunction with the Carbohydrate Solution Force Field are presented. Explicit solvent free-energy perturbation simulations were performed on a set of hexapyranose sugars and used to fit atomic radii for Poisson-Boltzmann and generalized-Born calculations, and to fit atomic volumes for use with the analytical continuum electrostatics model. The solvation energetics computed with the optimized radii and a Poisson-Boltzmann model show remarkable agreement with explicit solvent simulation, with a root-mean-square error of 1.19 kcal/mol over a large test set of sugars in many conformations. The generalized-Born model gives slightly poorer agreement, but still correlates very strongly, with an error of 1.69 kcal/mol. The analytical continuum electrostatics model correlates well with the explicit solvent results, but gives a larger error of 4.71 kcal/mol. The remarkable agreement between the solvation free energies computed in explicit and implicit solvent provides strong motivation for the use of implicit solvent models in the simulation of carbohydrate-containing systems.     

UV-vis spectra of <Emphasis Type="Italic">p</Emphasis>-benzoquinone anion radical in solution by a TD-DFT/PCM approach

Excited electronic states of the anion radical of para-benzoquinone were studied by time dependent density functional theory (TD-DFT) including bulk solvent effects by the polarizable continuum model (PCM). The computed vertical excitation energies for the first four low-lying doublet states are in good agreement with previous post-Hartree–Fock computations. Geometry optimization of excited states and inclusion of solvent effects lead to a remarkable agreement between computed adiabatic transition energies and experimental band maxima. Together with their specific interest, the results point out the reliability of TD-DFT/PCM approach for valence excitations and the need to take geometry relaxation and solvent effects into the proper account for a meaningful comparison between computed and experimental absorption spectra.     

Determination of aqueous acid‐dissociation constants of aspartic acid using PCM/DFT method

Determination of acid‐dissociation constants, pK_a, of aspartic acid in aqueous solution, using density functional theory calculations combined with the conductor‐like polarizable continuum model (CPCM) and with integral‐equation‐formalism polarizable continuum model (IEFPCM) based on the UAKS and UAHF radii, was carried out. The computed pK_a values derived from the CPCM and IEFPCM with UAKS cavity model of bare structures of the B3LYP/6‐31+G(d,p)‐optimized tetrahydrated structures of aspartic acid species are mostly close to the experimental pK_a values. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Electronic confinement effects on the reaction field type calculations of solvent effects

We analyze some procedures to introduce the effect of confining the electrons of the hydrogen atoms in cavitation spheres like those used in the self‐consistent reaction field models for studying the solvent influence on molecular properties [as polarizable continuum model (PCM), or conductor screening model (COSMO)]. We have found that the boundary conditions to be applied have an important effect on the system energy that by no means should be neglected in this type of calculations. We have found as well that “‐nG” expansion technique could be applicable in this kind of calculations (even at the very simple “‐3G” level) and lead us to a relatively simple form of applying the theory. Moreover, we have found a way to define the cavitation radius of PCM calculations, by minimizing the system energy with respect to this parameter, which could be a more satisfactory procedure—at least from a theoretical point of view—than the use of empirical values characteristic of most of the PCM or COSMO standard calculations. © 2013 Wiley Periodicals, Inc.     

Density Functional Theory Study of Solvent Effects on the Structure and Vibrational Frequencies of Tetranitrotetraazabicyclooctane “bicyclo‐HMX”

Density Functional Theory (DFT) calculations have been performed on the high explosive compound tetranitrotetraazabicyclooctane (bicyclo‐HMX) in gas phase employing the self‐consistent field (SCF) theory and in different solvents, i.e. cyclohexane, dichloroethane, ethylalcohol, acetonitrile, and water, utilizing the self‐consistent reaction field (SCRF) theory at a B3LYP/6–31 1G** level of theory. Reasonable agreement has been found between the computed and the available experimental data. The effects of different solvents on the geometry, electronic structure, and vibrational frequencies are discussed. Various solvents under consideration are found to have similar effects on the above properties. But some properties change regularly with the increasing polarity of the solvents, and the stronger the solvent polarity is, the larger the change is. In addition, based on the vibrational analysis, standard thermodynamic properties of bicyclo‐HMX in gas phase are also computed by using the statistical thermodynamic principle.     

Combined experimental and computational modeling studies on 4‐[(2‐hydroxy‐3‐methylbenzylidene) amino]‐1,5‐dimethyl‐2‐phenyl‐1,2‐dihydro‐3H‐pyrazol‐3‐one

The Schiff base compound, 4‐[(2‐hydroxy‐3‐methylbenzylidene)amino]‐1,5‐dimethyl‐2‐phenyl‐1,2‐dihydro‐3H‐pyrazol‐3‐one, has been synthesized and characterized by IR, UV–vis, and X‐ray single‐crystal determination. Molecular geometry from X‐ray experiment of the title compound in the ground state have been compared using the density functional method (B3LYP) with 6‐31G(d,p) basis set. Calculated results show that density functional theory (DFT) can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6‐31G(d,p) basis set by applying the Onsager and the polarizable continuum model (PCM). The results obtained with these methods reveal that the PCM method provided more stable structure than Onsager's method. By using TD‐DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD‐DFT method and the experimental one is determined. The predicted nonlinear optical properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential and NBO analysis were performed at B3LYP/6‐31G(d,p) level of theory. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A comprehensive study of the solvent effects on the cycloaddition reaction of diethyl azodicarboxylate and ethyl vinyl ether: Efficient implementation of QM and TD‐DFT study

In this work, quantum chemistry calculations performed to study the kinetics and thermodynamic parameters of [2+2] cycloaddition reaction of diethyl azodicarboxylate and ethyl vinyl ether in eighty‐three solvents and gas phase. The solvent effect on the reaction path and electron density of the C2? N6 critical bond as the reaction coordinate at the TS was investigated. Calculated rate constants in various solvents showed that increase in the activation dipole moment accelerates the reaction. Based on the time‐dependent studies, using a conductor like polarizable continuum model solvation model, the solvent effects on the excitation energies of the reactants and transition states (TSs) and the corresponding chemical shifts were analyzed. Finally, some correlations between the rate constant and quantum reactivity indices such as electrophilicity index, chemical hardness, and electronic chemical potential were investigated. © 2014 Wiley Periodicals, Inc.     

Comparison of radii sets,entropy, QM methods,and sampling on MM‐PBSA,MM‐GBSA,and QM/MM‐GBSA ligand binding energies of F. tularensis enoyl‐ACP reductase (FabI)

To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM‐PBSA, MM‐GBSA, and QM/MM‐GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM‐GBSA using 6 ns MD simulation trajectories together with GB^neck2, PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r² = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called “multiple independent sampling”), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB^HCT and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r² = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive “multiple independent sampling method” may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM‐P(G)BSA were limited to inhibitors’ relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program. © 2015 Wiley Periodicals, Inc.     

Theoretical study of the excited states and the redox potentials of unusually distorted ��-trifluoromethylporphycene

Quantum chemical calculations were performed to analyze the excited states and the redox potentials of a recently synthesised fluorine-containing porphycene, 2,7,12,17-tetraethyl-3,6,13,16-tetrakis(trifluoromethyl) porphycene. The reduction and oxidation potentials of the porphycenes measured by cyclic voltammetry were semiquantitatively reproduced using density-functional theory (DFT) and polarizable continuum model calculations, in which solvent effect and basis-sets extension effect were indispensable. Symmetry-adapted cluster configuration interaction and time-dependent (TD) DFT calculations were performed to analyze the visible region of the absorption spectra, and the results were in good agreement with the experimental data. The results of the calculations showed that both structural distortion and electronic effects cause specifically large stabilization of the LUMO level and become the origin of the particularly large positive-side shift of the reduction potential and the red-shift in the Q band absorption.     

Ab initio and semiempirical computational studies on 1‐{(2E)‐2‐[(aminocarbonothioyl)hydrazono]‐2‐(3‐mesityl‐3‐methylcyclobutyl)ethyl}‐pyrrolidine‐2,5‐dione

The molecular geometry, vibrational frequencies, and gauge including atomic orbital (GIAO) ¹H‐ and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated using the Hartree‐Fock (HF) and density functional theory (DFT) methods with 6‐31G(d) basis sets, and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters and the theoretical vibrational frequencies, and ¹H‐ and ¹³C NMR chemical shift values show good agreement with experimental data. To determine conformational flexibility, the molecular energy profile of the title compound was obtained by semiempirical (AM1) calculations with respect to the selected torsion angle, which was varied from ?180° to +180° in steps of 10°. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6‐31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). The results obtained with these methods reveal that the PCM method provided more stable structure than Qnsager's method. By using TD‐DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD‐DFT method and the experimental one is determined. The predicted nonlinear optical properties of the title compound are much greater than ones of urea. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, NBO analysis and thermodynamic properties of the title compound were investigated using theoretical calculations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Time‐dependent density functional theory study on the absorption spectrum of Coumarin 102 and its hydrogen‐bonded complexes

The effect of both solvent polarity and hydrogen bonding (HB) on the electronic transition energy of Coumarin 102 (C102) has been examined using the time‐dependent density functional theory (TDDFT). Solvent effect on both geometry and electronic transition energy is evaluated using the polarizable continuum model (PCM). A linear relation of the absorption maximum of C102 with the solvent polarity function Δf is found using the TDDFT‐PCM method for all solvents except dimethyl sulfoxide. The solvent polarity and the type B HB between the carbonyl oxygen and solvent hydrogen atom make the absorption wavelength redshift, whereas the type A HB between the amino nitrogen atom and solvent hydrogen atom has an opposite effect on the absorption wavelength. The calculated absorption wavelengths of C102 with two type B HB between the carbonyl oxygen and solvent hydrogen atom are in excellent agreement with experimental measurements. The solvatochromism of C102 is analyzed in terms of the Kamlet–Taft equation and the parameters s and a are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011.     

Absorption Spectrum of A–T DNA Unraveled by Quantum Mechanical Calculations in Solution on the (dA)2⋅(dT)2 Tetramer

The absorption spectrum of A–T DNA is computed for the first time in aqueous solution by means of quantum mechanical calculations performed on realistic models, thereby accounting for both stacking and base pairing interactions and including solvent effects through the polarizable continuum model. The computed and experimental spectra are in close agreement. Our analysis allows the identification of all the electronic transitions hidden in the broad absorption spectrum of A–T DNA, thus determining their most relevant properties and providing an explanation for the most significant experimental features, such as the small blue shift of the band maximum and the appearance of a shoulder on the red wing of the absorption band. The lowest‐energy dark excited state corresponds to a charge‐transfer state between two stacked adenine bases.