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Solvation Effects (solvation + effects)
Selected AbstractsGianfranco Cainelli, Paola Galletti, Silvia Pieraccini, Arianna Quintavalla, Daria Giacomini, Gian Piero Spada, "Chiral aldehydes in hydrocarbons: Diastereoselective nucleophilic addition, NMR, and CD spectroscopy reveal dynamic solvation effects,"Chirality(2004) 16(1) 50,56CHIRALITY, Issue 4 2004Article first published online: 16 MAR 200 The original article to which this Erratum refers was published in Chirality (2004) 16(1) 50,56 Correction to the article: "Chiral Aldehydes in Hydrocarbons: Diastereoselective Nucleophilic Addition, NMR, and CD Spectroscopy Reveal Dynamic Solvation Effects" by Gianfranco Cainelli, Paola Galletti, Silvia Pieraccini, Arianna Quintavalla, Daria Giacomini, and Gian Piero Spada, Chirality 16:50,56, 2004. [source] Activation barriers for DNA alkylation by carcinogenic methane diazonium ionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 3 2006Kaushalya S. Ekanayake Abstract Methylation reactions of the DNA bases with the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, were examined. The SN2 transition states of the methylation reactions at N7, N3, and O6 of guanine; N7, N3, and N1 of adenine; N3 and O2 of cytosine; and O2 and O4 of thymine were calculated using the B3LYP density functional method. Solvation effects were examined using the conductor-like polarizable continuum method and the combined discrete/SCRF method. The transition states for reactions at guanine N3, adenine N7, and adenine N1 are influenced by steric interactions between the methane diazonium ion and exocyclic amino groups. Both in the gas phase and in aqueous solution, the methylation reactions at N atoms have transition states that are looser, and generally occur earlier along the reaction pathways than reactions at O atoms. The forming bonds in the transition states in water are 0.03 to 0.13 Å shorter than those observed in the gas phase, and the activation energies are 13 to 35 kcal/mol higher. The combined discrete/SCRF solvation energy calculations using base-water complexes with three water molecules yield base solvation energies that are larger than those obtained from the CPCM continuum method, especially for cytosine. Reactivities calculated using barriers obtained with the discrete/SCRF method are consistent with the experimentally observed high reactivity at N7 of guanine. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 277,286, 2006 [source] Solvation effects of H2O and DMSO on the O,H bond dissociation energies of substituted phenolsJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 4 2004Yao Fu Abstract Solvation effects on the O,H homolytic bond dissociation energies (BDEs) of substituted phenols were studied. It was demonstrated that the BDEs measured in solution in general do not equal the BDEs in the gas phase. Detailed theoretical analyses indicated that a long-range solvation effect (i.e. the interaction between the solvent and the overall dipole moment of the solute) and a short-range solvation effect (i.e. the hydrogen bonding between the solute and solvent) were both important for the O,H BDEs in water and in DMSO. Neither one of these two factors by itself could fully explain the experimentally observed solvation effect. However, a combination of these two factors, estimated through a semi-continuum solvation model, was shown to be reasonably successful in explaining the experimental results. Copyright © 2004 John Wiley & Sons, Ltd. [source] Solvation effects in calculated electrostatic association free energies for the C3d-CR2 complex and comparison with experimental dataBIOPOLYMERS, Issue 6 2010Alexander S. Cheung Abstract The complement system is an integral part of the innate immune system that participates in the clearance of pathogens from the body. The association between complement protein fragment C3d and B or T cell-receptor complement receptor (CR) 2 represents a crucial link between innate and adaptive immunities. The goal of this study is to predict association abilities of C3d and CR2 mutants by theoretically calculating electrostatic free energies of association and to assess the importance of solvation effects in the calculations. We demonstrate that calculated solvation free energy differences and Coulombic free energies of association are more sensitive than electrostatic free energies of association in solution and, thus, more accurate in predicting previously published experimental data for the association abilities (relative to the parent proteins) of specific C3d and CR2 mutants. We show that a proportional relationship exists between the predicted solvation free energy differences and the experimental data, while an inversely proportional relationship exists between the predicted Coulombic free energies of association and the experimental data. Our results yield new insights into the physicochemical properties underlying C3d-CR2 association. We discuss the predictive validity of Coulombic, solvation, and solution electrostatic free energies of association and the generalization of our method for theoretical mutagenesis studies of other systems. This is a basic study, aimed toward improving our understanding of the theoretical basis of immune system regulation at the molecular level. Such insight can serve as the groundwork for the design of regulators with tailored properties, vaccines, and other biotechnology products. © 2010 Wiley Periodicals, Inc. Biopolymers 93:509,519, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Enhanced electrophoretic resolution of monosulfate glycosaminoglycan disaccharide isomers on poly(methyl methacrylate) chipsELECTROPHORESIS, Issue 3 2007Yong Zhang Abstract To improve the separation of monosulfate glycosaminoglycan disaccharide isomers by microchip electrophoresis, we found that addition of 1,4-dioxane,(DO) dramatically improved analyte resolution, probably due to solvation effects. Methylcellulose,(MC) was tested for the ability to suppress EOF and analyte adsorption to the chip. To improve analyte resolution, buffer pH, ,-CD, and DO were systematically investigated. Fast separation was achieved by increasing the electric field strength, and field-amplified sample stacking occurred with increasing buffer concentrations. Therefore, based on our findings, we describe an efficient method for the separation of monosulfate and trisulfate unsaturated disaccharides (,Di-UA2S, ,Di-4S, ,Di-6S, and ,Di-triS) derivatized with 2-aminoacridone hydrochloride. A mixture of monosulfate disaccharide isomers (,Di-UA2S, ,Di-4S, and ,Di-6S) was baseline-separated within 75,s on a poly(methyl methacrylate) chip using a mixed buffer (DO/running buffer 57:43,v:v), 0.5% MC, pH,6.81, with an Esep of 558,V/cm. The theoretical plate was in the range of 5×105 to 1×106,m,1. [source] MP2, DFT-D, and PCM study of the HMB,TCNE complex: Thermodynamics, electric properties, and solvent effects,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 9 2008Ondrej Kysel Abstract Geometry, thermodynamic, and electric properties of the ,-EDA complex between hexamethylbenzene (HMB) and tetracyanoethylene (TCNE) are investigated at the MP2/6-31G* and, partly, DFT-D/6-31G* levels. Solvent effects on the properties are evaluated using the PCM model. Fully optimized HMB,TCNE geometry in gas phase is a stacking complex with an interplanar distance 2.87 × 10,10 m and the corresponding BSSE corrected interaction energy is ,51.3 kJ mol,1. As expected, the interplanar distance is much shorter in comparison with HF and DFT results. However the crystal structures of both (HMB)2,TCNE and HMB,TCNE complexes have interplanar distances somewhat larger (3.18 and 3.28 × 10,10 m, respectively) than our MP2 gas phase value. Our estimate of the distance in CCl4 on the basis of PCM solvent effect study is also larger (3.06,3.16 × 10,10 m). The calculated enthalpy, entropy, Gibbs energy, and equilibrium constant of HMB,TCNE complex formation in gas phase are: ,H0 = ,61.59 kJ mol,1, ,S = ,143 J mol,1 K,1, ,G0 = ,18.97 kJ mol,1, and K = 2,100 dm3 mol,1. Experimental data, however, measured in CCl4 are significantly lower: ,H0 = ,34 kJ mol,1, ,S = ,70.4 J mol,1 K,1, ,G0 = ,13.01 kJ mol,1, and K = 190 dm3 mol,1. The differences are caused by solvation effects which stabilize more the isolated components than the complex. The total solvent destabilization of Gibbs energy of the complex relatively to that of components is equal to 5.9 kJ mol,1 which is very close to our PCM value 6.5 kJ mol,1. MP2/6-31G* dipole moment and polarizabilities are in reasonable agreement with experiment (3.56 D versus 2.8 D for dipole moment). The difference here is due to solvent effect which enlarges interplanar distance and thus decreases dipole moment value. The MP2/6-31G* study supplemented by DFT-D parameterization for enthalpy calculation, and by the PCM approach to include solvent effect seems to be proper tools to elucidate the properties of ,-EDA complexes. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Theoretical electronic spectra of 2-aminopurine in vapor and in waterINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2006Antonio Carlos Borin Abstract The accurate quantum chemical CASSCF and CASPT2 methods combined with a Monte Carlo procedure to mimic solvation effects have been used in the calculation of the spectroscopic properties of two tautomers of 2-aminopurine (2AP). Absorption and emission spectra have been simulated both in vacuum and in aqueous environment. State and transition energies and properties have been obtained with high accuracy, leading to the assignment of the most important spectroscopic features. The lowest-lying 1(,,,*) (1La) state has been determined as responsible for the first band in the absorption spectrum and also for the strong fluorescence observed for the system in water. The combined approach used in the present work gives quantitatively accurate results. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Conceptual, Qualitative, and Quantitative Theories of 1,3-Dipolar and Diels,Alder Cycloadditions Used in SynthesisADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 16-17 2006Daniel Abstract The application and performance of conceptual and qualitative theories and quantitative quantum mechanical methods to the study of mechanism, reactivity, and selectivity of 1,3-dipolar and Diels,Alder cycloadditions are reviewed. This review emphasizes the application of conceptual density functional theory (DFT) for predicting reactivity and regioselectivity, and highly accurate quantum mechanical methods for predicting barrier heights and reaction energetics. Applications of computations to solvation effects, metal and organocatalysis, are also described. [source] Comparison of implicit solvent models for the simulation of protein,surface interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2006Yu Sun Abstract Empirical force field-based molecular simulations can provide valuable atomistic-level insights into protein,surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface,separation distance for peptide,surface interactions using different empirical force field-based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self-consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source] Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2002Sonja M. Schwarzl Abstract The prediction of a ligand binding constant requires generating three-dimensional structures of the complex concerned and reliably scoring these structures. Here, the scoring problem is investigated by examining benzamidine-like inhibitors of trypsin, a system for which errors in the structures are small. Precise and consistent binding free energies for the inhibitors are determined experimentally for this test system. To examine possible improvement of scoring methods, we test the suitability of continuum electrostatics to account for solvation effects and use an ideal-gas entropy correction to account for the changes in the degrees of freedom of the ligand. The small observed root-mean-square deviation of 0.55 kcal/mol of the calculated relative to the experimental values indicates that the essentials of the binding process have been captured. Even though all six ligands make the same salt bridge and H-bonds to the protein, the electrostatic contribution varies among the ligands by as much as 2 kcal/mol. Moreover, although the ligands are rigid and similar in size, the entropic terms also significantly affect the relative binding affinities (by up to 2.7 kcal/mol). The present approach to solvation and entropy may allow the ranking of the ligands to be considerably improved at a cost that makes the method applicable to the optimization of lead compounds or to the screening of small collections of ligands. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1143,1149, 2002 [source] Cycloadditions in mixed aqueous solvents: the role of the water concentration,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 8 2005Theo Rispens Abstract We examined the kinetics of a series of cycloaddition reactions in mixtures of water with methanol, acetonitrile and poly(ethylene glycol) (MW 1000). The reactions include the Diels,Alder (DA) reaction between cyclopentadiene and N - n -butylmaleimide or acridizinium bromide, the retro-Diels-Alder (RDA) reaction of 1,4,4a,9a-tetrahydro-4a-methyl-(1,,4,,4a,,9a,)-1,4-methaneanthracene-9,10-dione and the 1,3-dipolar cycloaddition of benzonitrile oxide with N - n -butylmaleimide. Plots of logk vs the molar concentration or volume fraction of water are approximately linear, but with a characteristic break around 40,M water. This break, absent for the RDA reaction, is ascribed to hydrophobic effects. Comparison with aqueous mixtures of the more hydrophobic 1-propanol shows that these mixtures induce qualitatively similar effects on the rate, but that preferential solvation effects cause the mixtures of 1-propanol to exhibit a more complex behavior of logk on composition. The results are analyzed using the Abraham,Kamlett,Taft model. The solvent effects in aqueous mixtures are not satisfactorily described by this model. For some cycloadditions, small maxima in rate are observed in highly aqueous mixtures of alcohols. The origin of these maxima and the aforementioned breaks is most likely the same. Copyright © 2005 John Wiley & Sons, Ltd. [source] Specific and non-specific solvent effects on aromatic nucleophilic substitution.JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 5 20026-dinitrobenzene, Kinetics of the reaction of 1-fluoro-, homopiperidine in binary solvent mixtures Abstract This paper presents a comparative study of the solvent effects on the kinetics of the reactions between 1-fluoro-2,6-dinitrobenzene and hexahydro-1H -azepine in ethyl acetate,+,chloroform or acetonitrile and acetonitrile,+,chloroform binary solvent mixtures. The purpose was to asses the contribution of each molecular-microscopic solvent property to the overall solvation effect of the reaction critical state. The influence of the dipolarity/polarizability, hydrogen-bond donor acidity and hydrogen-bond acceptor basicity of the solvent mixtures on the reaction rate was analyzed by the application of the multiparametric approach of Kamlet, Abboud and Taft. The evaluation of the correlation coefficients shows that the solvation effects are dominated by the non-specific interactions. Moreover, the incidence of the hydrogen-bond acceptor solvent ability is more important than that corresponding to the hydrogen-bond donor character, except for the reactions that manifest kinetic retarding effects. The influence of the solvation effects on the base catalysis was analyzed, describing the response patterns of the partial rate coefficients to the mixture composition and also to each solvent property. The application of a preferential solvation model to the kinetic results yields information on the preferential solvation of the reaction critical state by any of the pure solvents, or by the hydrogen-bonded complexed media. Copyright © 2002 John Wiley & Sons, Ltd. [source] Computational chemistry study of the environmentally important acid-catalyzed hydrolysis of atrazine and related 2-chloro- s -triazinesPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 8 2002Phillip Sawunyama Abstract Many chlorine-containing pesticides, for example 2-chloro- s -triazines, are of great concern both environmentally and toxicologically. As a result, ascertaining or predicting the fate and transport of these compounds in soils and water is of current interest. Transformation pathways for 2-chloro- s -triazines in the environment include dealkylation, dechlorination (hydrolysis), and ring cleavage. This study explored the feasibility of using computational chemistry, specifically the hybrid density functional theory method, B3LYP, to predict hydrolysis trends of atrazine (2-chloro- N4 -ethyl- N6 -isopropyl-1,3,5-triazine-2,4-diamine) and related 2-chloro- s -triazines to the corresponding 2-hydroxy- s -triazines. Gas-phase energetics are described on the basis of calculations performed at the B3LYP/6-311++G(d,p)//B3LYP/6-31G* level of theory. Calculated free energies of hydrolysis (,hG298) are nearly the same for simazine (2-chloro- N4,N6 -diethyl-1,3,5-triazine-2,4-diamine), atrazine, and propazine (2-chloro- N4,N6 -di-isopropyl-1,3,5-triazine-2,4-diamine), suggesting that hydrolysis is not significantly affected by the side-chain amine-nitrogen alkyl substituents. High-energy barriers also suggest that the reactions are not likely to be observed in the gas phase. Aqueous solvation effects were examined by means of self-consistent reaction field methods (SCRF). Molecular structures were optimized at the B3LYP/6-31G* level using the Onsager model, and solvation energies were calculated at the B3LYP/6-311++G(d,p) level using the isodensity surface polarizable continuum model (IPCM). Although the extent of solvent stabilization was greater for cationic species than neutral ones, the full extent of solvation is underestimated, especially for the transition state structures. As a consequence, the calculated hydrolysis barrier for protonated atrazine is exaggerated compared with the experimentally determined one. Overall, the hydrolysis reactions follow a concerted nucleophilic aromatic substitution (SNAr) pathway. Published in 2002 for SCI by John Wiley & Sons, Ltd [source] Solvation effects in calculated electrostatic association free energies for the C3d-CR2 complex and comparison with experimental dataBIOPOLYMERS, Issue 6 2010Alexander S. Cheung Abstract The complement system is an integral part of the innate immune system that participates in the clearance of pathogens from the body. The association between complement protein fragment C3d and B or T cell-receptor complement receptor (CR) 2 represents a crucial link between innate and adaptive immunities. The goal of this study is to predict association abilities of C3d and CR2 mutants by theoretically calculating electrostatic free energies of association and to assess the importance of solvation effects in the calculations. We demonstrate that calculated solvation free energy differences and Coulombic free energies of association are more sensitive than electrostatic free energies of association in solution and, thus, more accurate in predicting previously published experimental data for the association abilities (relative to the parent proteins) of specific C3d and CR2 mutants. We show that a proportional relationship exists between the predicted solvation free energy differences and the experimental data, while an inversely proportional relationship exists between the predicted Coulombic free energies of association and the experimental data. Our results yield new insights into the physicochemical properties underlying C3d-CR2 association. We discuss the predictive validity of Coulombic, solvation, and solution electrostatic free energies of association and the generalization of our method for theoretical mutagenesis studies of other systems. This is a basic study, aimed toward improving our understanding of the theoretical basis of immune system regulation at the molecular level. Such insight can serve as the groundwork for the design of regulators with tailored properties, vaccines, and other biotechnology products. © 2010 Wiley Periodicals, Inc. Biopolymers 93:509,519, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCKBIOPOLYMERS, Issue 2 2004Xinshan Kang Abstract The calculation of ligand-nucleic acid binding free energies is investigated by including solvation effects computed with the generalized-Born model. Modifications of the solvation module in DOCK, including introduction of all-atom parameters and revision of coefficients in front of different terms, are shown to improve calculations involving nucleic acids. This computing scheme is capable of calculating binding energies, with reasonable accuracy, for a wide variety of DNA-ligand complexes, RNA-ligand complexes, and even for the formation of double-stranded DNA. This implementation of GB/SA is also shown to be capable of discriminating strong ligands from poor ligands for a series of RNA aptamers without sacrificing the high efficiency of the previous implementation. These results validate this approach to screening large databases against nucleic acid targets. © 2003 Wiley Periodicals, Inc. Biopolymers 73:192,204, 2004 [source] Solvent Effect on Optical Rotation: A Case Study of Methyloxirane in WaterCHEMPHYSCHEM, Issue 12 2006Parag Mukhopadhyay Explicit solute,solvent interactions: MD simulations and TD-DFT are used to determine the solvent dependence of the optical rotatory dispersion (ORD) for methyloxirane in water (see figure). The inclusion of explicit solute,solvent interactions is essential to describe the influence of the solvent on the OR of the system and the MD simulations provide a suitable means to analyze and predict chiroptical solvation effects. [source] The effects of conformation and solvation on optical rotation: Substituted epoxides,CHIRALITY, Issue 3-4 2008Shaun M. Wilson Abstract The vapor-phase optical rotation (or circular birefringence) of (S)-1,2-epoxybutane, (S)-epichlorohydrin, and (S)-epifluorohydrin has been measured at the nonresonant excitation wavelengths of 355 nm and 633 nm by means of Cavity Ring-Down Polarimetry (CRDP). Complementary solution-phase studies were performed in a wide variety of dilute solvent media to highlight the pronounced influence of solute,solvent interactions. Density functional theory calculations of optical activity have been enlisted to unravel the structural and electronic provenance of experimental observations. Three stable, low-lying conformers have been identified and characterized for each of the targeted chiral species, with thermal (relative population weighted) averaging of their antagonistic chiroptical properties allowing specific rotation values to be predicted under both isolated and solvated conditions. For (S)-epichlorohydrin and (S)-epifluorohydrin, a self-consistent isodensity polarizable continuum model (SCI-PCM) has been exploited to gain further insight into the underlying nature of solvation effects. Chirality, 2008. © 2007 Wiley-Liss, Inc. [source] Gianfranco Cainelli, Paola Galletti, Silvia Pieraccini, Arianna Quintavalla, Daria Giacomini, Gian Piero Spada, "Chiral aldehydes in hydrocarbons: Diastereoselective nucleophilic addition, NMR, and CD spectroscopy reveal dynamic solvation effects,"Chirality(2004) 16(1) 50,56CHIRALITY, Issue 4 2004Article first published online: 16 MAR 200 The original article to which this Erratum refers was published in Chirality (2004) 16(1) 50,56 Correction to the article: "Chiral Aldehydes in Hydrocarbons: Diastereoselective Nucleophilic Addition, NMR, and CD Spectroscopy Reveal Dynamic Solvation Effects" by Gianfranco Cainelli, Paola Galletti, Silvia Pieraccini, Arianna Quintavalla, Daria Giacomini, and Gian Piero Spada, Chirality 16:50,56, 2004. [source] | ||||||||||||||||||||||