Theory Of Solvent Effects Research Articles

Unraveling chemical glycosylation: DFT insights into factors imparting stereoselectivity

Stereoselective chemical glycosylation reactions are pivotal for preparing manifold biologically and medically important compounds, while mechanisms of chemical glycosylation reactions remain obscure and largely speculative. Herein, we performed DFT calculations to delve into the multifaceted mechanistic details of glycosylation reactions, including the equilibria among reactive glycosyl triflate intermediates in solution, the stereoselectivity imparting protecting groups, solvent effects, base, and the anomeric effect. Our results provided theoretical corroboration to 2-OAc neighbouring group participation (NGP), the arming/disarming effect, the coordination theory of solvent effect on glycosylation stereochemistry, and the influence of solvent polarity on the reaction kinetics spanning the SN1-SN2 continuum. For the first time, the existence of putative contact-ion-pairs (CIP) of glycosyl oxocarbenium and triflate anion in organic solutions was theoretically confirmed with the identification of multiple ground state structures employing an implicit Solvation Model based on Density (SMD). Kinetics of nucleophilic attack of model glucosyl triflates by simple alcohol acceptors ethanol (EtOH) and trifluoroethanol (TFE), complexed with 2,4,6-tri-tert-butylpyrimidine (TTBP) were explored, revealing the essential role of the close accompanying base for rendering glycosidic bond formation thermodynamically favourable. Our work deepens the comprehension of the glycosylation mechanism, paving the way for the rational design and future advancement of efficient and environmentally friendly stereoselective glycosylation reactions.

A quick selection of natural deep eutectic solvents for the extraction of chlorogenic acid from herba artemisiae scopariae.

Natural deep eutectic solvents (NADES) were successfully employed as green alternatives to the traditional ones for the extraction of chlorogenic acid from herba artemisiae scopariae. Significantly, the method of solvent effect theory chemical calculation assistance to guide the NADES selection for the extraction was proposed. Proline–malic acid was successfully screened as the suitable solvent using the calculation results and it gave the best chlorogenic acid yield of 3.77 mg g−1 among the NADES tested with a solvation free energy of −5.86 × 106 kJ mol−1 from the calculation. The calculation-assisted method saves costs and material resources for the applications of the green alternative NADES and provides a research route that can be used for the extraction of target active molecules in the traditional Chinese medicine and food industry.

Theoretical Calculations and Modeling for the Molecular Polarization of Furan and Thiophene under the Action of an Electric Field Using Quantum Similarity

A theoretical study on the molecular polarization of thiophene and furan under the action of an electric field using Local Quantum Similarity Indexes (LQSI) was performed. This model is based on Hirshfeld partitioning of electron density within the framework of Density Functional Theory (DFT). Six local similarity indexes were used: overlap, overlap-interaction, coulomb, coulomb-interaction, Euclidian distances of overlap, and Euclidean distances of coulomb. In addition Topo-Geometrical Superposition Algorithm (TGSA) was used as a method of alignment. This method provides a straightforward procedure to solve the problem of molecular relative orientation. It provides a tool to evaluate molecular quantum similarity, enabling the study of structural systems, which differ in only one atom such as thiophene and furan (point groupC2v) and cyclopentadienyl molecule (point groupD5h). Additionally, this model can contribute to the interpretation of chemical bonds, and molecular interactions in the framework of the solvent effect theory.

A theoretical thermochemical study of solute-solvent dielectric effects in the displacement of codon-anticodon base pairs

Quantum-chemical solvent effect theories describe the electronic structure of a molecular subsystem embedded in a solvent or other molecular environment. The solvation of biomolecules is important in molecular biology, since numerous processes involve proteins interacting in changing solvent-solute systems. In this theoretical study, we focus on mRNA-tRNA base pairs as a fundamental step in protein synthesis influenced by hydrogen bonding between two antiparallel trinucleotides, namely, the mRNA codon and tRNA anticodon. We use the mean reaction field theories, which describe electrostatic and polarization interactions between solute and solvent in the AAA, UUU, AAG, and UUC triplex sequences optimized in various solvent media such as water, dimethylsulfoxide, methanol, ethanol, and cyclopean using the self-consistent reaction field model. This process depends on either the reaction potential function of the solvent or charge transfer operators that appear in solute-solvent interaction. Because of codon and anticodon biological criteria, we performed nonempirical quantum-mechanical calculations at the BLYP and B3LYP/3-21G, 6-31G, and 6-31G* levels of theory in the gas phase and five solvents at three temperatures. Finally, to obtain more information, we calculated thermochemical parameters to find that the dielectric constant of solvents plays an important role in the displacement of amino acid sequences on codon-anticodon residues in proteins, which can cause some mutations in humans.

Rayleigh-Schrödinger many-body perturbation theory for density functionals: A unified treatment of one- and two-electron perturbations

A time-independent many-body Rayleigh-Schr\"odinger perturbation theory is developed for total energy functionals, which depend simultaneously on a wave function and on the associated electron density. The most prominent example of such functionals is the Kohn-Sham energy functional, but similar situations occur as well in quantum chemical solvent effect theories. In contrast to previous density-functional perturbation theories, formulated in terms of one-electron orbitals, the present approach provides energy and eigenvector corrections for a many-electron wave function that satisfies a nonlinear effective Schr\"odinger equation. While the perturbed eigenvalues of order $n$ depend on the eigenvector corrections up to the $n\text{th}$ order, perturbational corrections of the total energy functional satisfy Wigner's $(2n+1)$ rule by virtue of nontrivial cancelations between eigenvalue and double count corrections up to order $n$. As a direct consequence of the nonlinearity of the effective Schr\"odinger equation, the wave-function corrections of any order are obtained by the solution of a self-consistent equation involving the second functional derivative of the density functional. Explicit total energy corrections are elaborated up to the fourth order. It is shown that the present approach reproduces standard results of the density-functional perturbation theory for static one-electron perturbations. Furthermore, two variants of the long-range M\o{}ller-Plesset correlation energy corrections in the range-separated hybrid density-functional framework are derived and discussed.

Simulation study of N2 overtone solvent shifts using improved potentials

The solvent shifts of vibrational overtone spectra are predicted by Buckingham's theory of solvent effects on Raman and infrared spectra to be linear with the overtone number. We test this prediction for liquid N2 and dilute N2 in liquid Ar by extending the theory and by implementing the predictions using molecular dynamics simulations. Changes are made to the representations of both the intermolecular and the intramolecular parts of the total Hamiltonian. The representation of the intermolecular part is extended by including two additional terms of a Taylor series expansion in the vibrational coordinate of the intermolecular energy. We find, however, that their inclusion does not contribute significantly to the predicted overtone shifts for the systems studied here. The intramolecular potential is represented by a Morse potential in contrast to Buckingham's harmonic oscillator plus a cubic perturbation term. In our calculation the only perturbation terms of the Morse oscillator Hamiltonian are four expansion terms of the intermolecular potential in terms of the vibrational coordinate. Accordingly, the basis functions used to calculate the perturbed energy levels are Morse eigenfunctions. The simulations show that Buckingham's prediction is rather accurate for liquid N2 and dilute N2 in liquid Ar, at standard state conditions, and for liquid N2 at high-pressure high-temperature conditions. We find that for N2 there is a small negative contribution due to quantum anharmonic corrections to Buckingham's harmonic solvent induced vibrational frequency shift. We also show how equivalent theoretical results are obtained when the intramolecular potential is represented as harmonic plus anharmonic terms up to the fifth power of the vibrational coordinate (i.e. a Dunham potential), instead of a Morse potential.

Polarizable Continuum Model (PCM) Calculations of Solvent Effects on Optical Rotations of Chiral Molecules

A new theory of solvent effects on the optical rotations of chiral molecules is presented. The frequency-dependent electric dipole−magnetic dipole polarizability, βαβ(ν), is calculated using density functional theory (DFT). Solvent effects are included using the polarizable continuum model (PCM). DFT/PCM calculations of sodium D line specific rotations, [α]D, have been carried out for seven conformationally rigid chiral organic molecules (fenchone, camphor, α-pinene, β-pinene, camphorquinone, verbenone, and methyloxirane) for a diverse set of seven solvents (cyclohexane, carbon tetrachloride, benzene, chloroform, acetone, methanol, and acetonitrile). The predicted variation in [α]D for the solvents cyclohexane, acetone, methanol, and acetonitrile are in excellent agreement with experiment for all seven molecules. For the solvents carbon tetrachloride, benzene, and chloroform, agreement is much poorer. Since only electrostatic solute−solvent interactions are included in the PCM, our results lead to the conclusion that, for the seven molecules studied, in cyclohexane, acetone, methanol, and acetonitrile electrostatic effects are dominant while in carbon tetrachloride, benzene, and chloroform other nonelectrostatic effects are more important. The observed variations in [α]D with solvent are inconsistent, both qualitatively and quantitatively, with the variations predicted by the equation [α]D(solvent) = {[α]D(gas)}(nD2 + 2)/3.

Nonlocal dielectric functions of molecular liquids from computer simulations

The longitudinal dielectric function, χ( k)=1−1/ ε L( k), of both polar and nonpolar liquid environments is a key ingredient to modern theories of solvent effects upon charge transfer reactions in solution and solvation dynamics processes in general. In this work, we present a molecular dynamics simulation study of the dielectric function of several molecular liquids ranging from associating (H 2O, CH 3OH) and nonassociating ((CH 3) 2SO, CH 3CN) polar liquids to nondipolar ones (C 6H 6, CCl 4 and CO 2) aiming to better understand the relationships between the structure of the χ( k) functions to the charge–charge spatial correlations in each liquid. We show that the characteristic main peak of χ( k), located at some wave vector k ∗ , whose value depends on the liquid, arises from spatial charge density fluctuations of wavelength 2 π/k ∗ for all liquids considered, with the exception of CO 2. Further details about the shape of the χ( k) functions for the simulated liquids are discussed in terms of intra and intermolecular charge–charge correlations.

Theory of solvent effects on electronic absorption spectra of rodlike or disklike solute molecules: Frequency shifts

A theory, which has been advanced by the author and his co-workers, for frequency shifts of electronic absorption spectra of a nonpolar rodlike molecule in dilute nonpolar and polar solutions is extended so that it is applicable to a polar rodlike solute molecule and a nonpolar or polar disklike solute molecule. The theory takes into account higher-order multipole moments (in addition to a dipole) of the solute molecule, and its solution-phase polarizabilities are properly taken into account. Furthermore, it explains how the dispersive interaction is altered by the presence of permanent dipoles of the solvent.

Solvent Effects on Chemical Processes. 11. Solvent Effects on the Kinetics of Decarboxylative Dechlorination of N-Chloro Amino Acids in Binary Aqueous—Organic Solvents

The phenomenological theory of solvent effects is extended to chemical reaction rates and is tested against experimental data on the decarboxylative dechlorination of N-chloroalanine and N-chloroleucine at 25°C in binary aqueous–organic solvent mixtures. The organic cosolvents studied were methanol, ethanol, l-propanol, 2-propanol, ethylene glycol, propylene glycol, acetonitrile, and dioxane. Reaction rates increased in all cosolvent systems. The kinetic solvent effects could be quantitatively described by the theory, and the parameters of the theory (solvation exchange constants K1 and K2 and cavity surface area parameter ΔgA‡) were found to possess magnitudes reasonable for the physical significance assigned to them. In particular, the ΔgA‡ value is consistent with a recent measurement of the volume of activation ΔV‡ of the reaction.

Self consistent reaction field theory of solvent effects in the framework of Gaussian density functional method

AbstractElectrostatic and dispersion contributions of solute‐solvent interactions have been considered in the self‐consistent reaction field scheme and implemented in the LCGTO‐DF (linear combination of Gaussian‐type orbitals‐density functional) method. Results for the tautomeric equilibrium of formamide‐formamidic acid, for the cis‐trans energy difference in dichlorodiammineplatinum(II), and for H2OHF hydrogen‐bond systems are in agreement with the available experimental and previous high‐level ab initio data. The role of the dispersion energy is discussed for the different studied systems. © 1995 John Wiley & Sons, Inc.

Choosing between alternative MP2 algorithms in the self-consistent reaction field theory of solvent effects

The MP2 energy and electronic density can be obtained in the framework of the self-consistent reaction field theory of solvent effects by the simple application of the usual MP2 formulae using SCF orbitals which have been optimized in the self-consistent reaction field of the SCF density. Iterative schemes which apply an MP2-corrected density to achieve self-consistency of the reaction field are not only computationally much longer, but inconsistent, since they involve higher (fourth) order corrections in the electron correlation.

Solvent effects on chemical processes. 9. Energetic contributions to the complexation of 4-nitroaniline with α-cyclodextrin in water and in binary aqueous-organic solvents

Abstract The phenomenological theory of solvent effects partitions the free energy change of a process into contributions from solvent-solvent interactions (the general medium or solvophobic effect), solvent-solute interactions (the solvation effect), and solute-solute interactions (the intersolute or intrasolute effect). This approach is applied to complex formation between α-cyclodextrin and 4-nitroaniline in water and many aqueous-organic solvent mixtures; the organic solvents were methanol, ethanol, 2-propanol, ethylene glycol, dimethylsulfoxide, acetonitrile, and acetone. Complex stability constants were measured spectrophotometrically. The parameters of the phenomenological model were extracted by nonlinear regression or by graphical analysis. It is observed that there are two classes of cosolvents, distinguished by their polarity. If the pure solvent has log P < −0.3 (where P is the 1-octanol/water partition coefficient), the system behaves “normally,” with parameter values typical of nonelectrolyt...

OSIPE — a tool for scientific programming in FORTRAN

FORTRAN tools have been designed to support well-structures, modular, route-independent and easily interfaceable programming. This set of tools, which creates a kind of low-level object-oriented programming environment, is refered to as OSIPE (Open Structured Interfaceable Programming Environment). Its main role is to transform meaningful FORTRAN variables into Objects which are linked via “created-by” relationships. Two programs, written in the OSIPE environment, an ab initio electronic structure code, MUNGAUSS, and a novel implementation of a quantum chemical solvent effect theory, SOLVENT, are briefly described. Efficient tools are provided to restructure existing FORTRAN codes and make them compatible with the OSIPE environment.

Solvent effects on chemical processes. Part 6. The phenomenological model applied to the solubility of naphthalene and 4-nitroaniline in binary aqueous–organic solvent mixtures

The phenomenological theory of solvent effects on solubility partitions the free energy of solution into contributions from solvent–solvent interactions (the general medium or solvophobic effect), solvent–solute interactions (the solvation effect), and solute–solute interactions (the intersolute effect). The theory relates the solvent effect on solubility to the mole fractions of the solvent components and the model parameters K1 and K2(which are stepwise solvation exchange constants) and gA(the general medium parameter, where g is a curvature correction factor to the surface tension, and A is the nonpolar surface area of the solute). Solubility data for naphthalene and 4-nitroaniline are given over the entire composition range in aqueous–organic mixtures, the organic cosolvents being methanol, ethanol, propan-2-ol, propane-1, 2-diol, ethylene glycol, acetone, dimethyl sulfoxide and acetonitrile. The data are quantitatively described by the model. Cosolvents are classified, on the basis of their polarities (as measured by their octan-1-ol–water partition coefficient P), into a less polar class whose solvation exchange constants increase with log P, and a more hydrophilic class with the opposite tendency. The gA parameter can be reasonably predicted with the empirical relationship gA=–33.4 log PM+ 13.4 log PR(A2 mol–1), where M and R refer to the organic cosolvent and the solute, respectively. The product g(γ2–γ1), where γ2 and γ1 are the surface tensions of pure cosolvent and water, respectively, is close to the dispersion surface energy component of water and many other solvents.

Conformational energetics and excited state level ordering in 11-cis retinal.

Semiempirical molecular orbital theory and semiclassical solvent effect theory are used to analyze the conformational and electronic properties of the 12-s-cis and 12-s-trans conformers of 11-cis retinal. The goal is to examine the influence of solvent environment on the equilibrium geometries of these conformers as well as to provide a perspective on the electronic transitions that contribute to the four band systems that are observed in the 200-500 nm region of the optical spectrum. We conclude that the 12-s-cis isomer is more stable in vacuum, but that the 12-s-trans conformer is preferentially stabilized in both polar and nonpolar solvent environment due to dispersive as well as electrostatic interactions. This observation is in substantial agreement with previous literature results. In contrast, our analysis of the excited state manifold indicates that the spectral features observed in the absorption spectrum are associated with a complex set of overlapping transitions. A total of 18 pi*<--pi transitions contribute to the four bands, and in some cases, conformation changes the relative contribution of the individual transitions that define the overall band shape. This study provides the first definitive assignments for all four band systems.

Heterogenized homogeneous catalyst. 5. The theory of solvent effect and the effect of solvent on adsorption and diffusivity

The effects of solvent on the adsorption and diffusivity of benzaldehyde on the support of heterogenized homogeneous catalyst were studied. The theory of solvent effect on this reaction system was analyzed. Aprotic and protic solvents such as carbon tetrachloride, ethyl acetate, acetone, acetonitrile, propionic acid, and acetic acid were used. On the basis of both theoretical analysis and experimental results, the equations of solvent effects in terms of main properties of solvent on the adsorption and diffusivity, respectively, of the aldehyde were obtained

Solvent effect theories: Quantum and classical formalisms and their applications in chemistry and biochemistry

The quantum chemical and mathematical background and some new approaches to the modeling of solvent effects are described.

Common theoretical framework for quantum chemical solvent effect theories

Quantum chemical solvent effect theories deal with the description of the electronic structure of a molecular subsystem embedded in a solvent or other molecular environment. The average reaction field theories, which describe electrostatic and polarization interactions between solute and solvent, can be formulated in terms of a nonlinear reaction potential operator. This operator depends on the one hand on the reaction potential function of the solvent, and on the other hand on the charge density operators, which appear in the solute-solvent interaction. The former quantity is determined by the physical model of the solvent (e.g. dielectric continuum, discrete model, crystal lattice, etc.). The charge density operator can be approximated at different levels, like exact, one-centered and multicentered multipolar forms. These two ingredients of the theory, the reaction potential response function and the specific charge density operator, define unequivocally different solvent effect models. Various versions of average reaction field models are critically reviewed on the basis of this common theoretical framework.

Optically detected triplet-state magnetic resonance studies of the DNA complexes of the bisquinoline analog of echinomycin

The polymeric DNA and model duplex oligonucleotide complexes of the bisquinoline analogue of echinomycin (2QN) have been studied by optical detection of triplet-state magnetic resonance (ODMR) spectroscopy, with the quinoline chromophores of the drug used as intrinsic probes. Plots of ODMR transition frequencies versus monitored wavelength revealed heterogeneity in the phosphorescence emission of 2QN which was ascribed to the presence of a major and minor conformation of the drug in aqueous solutions (referred to as the red and blue forms of 2QN, respectively, in this report). ODMR results, in conjunction with findings from low-temperature phosphorescence investigations, indicate that the quinoline chromophores of the major (red) form of 2QN are involved in aromatic stacking interactions in complexes with the natural DNAs from Escherichia coli, Micrococcus lysodeikticus, Clostridium perfringens, and calf thymus as evidenced by red shifts in the phosphorescence 0,0-band of the drug, reductions in the phosphorescence lifetime and zero-field splitting (zfs) D and E parameters, and polarity reversals of the ODMR slow passage signals upon complex formation between the analogue and DNA. The polarity reversals, which reflect shifts in the triplet-state sublevel populations induced by complex formation, apparently result from changes in the triplet sublevel decay constants upon binding to the natural DNAs. The 2QN complexes of the double-stranded alternating copolymers poly(dG-dC).poly(dG-dC) [abbreviated as poly[d(G-C)2]] and poly(dA-dT).poly(dA-dT) [abbreviated as poly(dA-dT).poly(dA-dT) [abbreviated as poly[d(A-T)2], the homopolymer duplexes poly(dG).poly(dC) [abbreviated as poly(dG.dC)] and poly(dA).poly(dT) [abbreviated as poly(dA.dT)], and the self-complementary oligonucleotides d(ACGT)2, d(TCGA)2, and d(ACGTACGT)2 were also investigated. The extent of reduction of the zfs D parameter (delta D) for the major form of 2QN upon complex formation with the polymeric DNAs was found to scale linearly with the standard free energy of the drug-DNA interaction (delta G degrees) calculated from previously reported binding studies for these targets [Fox, K. R., et al. (1980) Biochem. J. 191, 729-740]. This relationship between spectroscopic and thermodynamic properties of the 2QN-polynucleotide complexes is a consequence of the effects of base stacking interactions on the electronic states of the intercalator, which were postulated to arise from second-order shifts of the ground-state and the triplet-state energies of the complex on the basis of a modification of the solvent effect theory of van Egmond et al. [(1975) Chem. Phys. Lett. 34, 423-426].