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Solvation
Kinds of Solvation Terms modified by Solvation Selected AbstractsAzide,Tetrazole Ring-Chain Isomerism in Polyazido-1,3,5-triazines, Triazido- s -heptazine, and DiazidotetrazinesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2006Anton Hammerl Abstract The azide,tetrazole isomerism in several polyazido-1,3,5-triazines, triazido- sym -heptazine, and some diazido-1,2,4,5-tetrazines was investigated by ab initio quantum chemical methods in order to determine whether the polyazides are suitable starting materials for the synthesis of the isomeric tetrazoles. The effects of solvation in CCl4, DMSO and water on this isomerism were included using the self consistent reaction field (SCRF) method. The effect of amino- and nitrosubstituents on the azide,tetrazole isomerism was also examined. In the gas phase all investigated polyazidoheterocycles do not cyclize to form tetrazoles. An electron-donating amino group favors the ring closure to tetrazoles, whereas an electron-withdrawing nitro group favors the azides. Solvation in polar solvents favors the formation of a tetrazole ring system due to higher charge separation in the tetrazole ring system, but for all polyazido-1,3,5-triazines, including triazido- s -heptazine, the effects of solvation are not strong enough to shift the equilibrium to the tetrazole side, which explains why several attempts to detect these compounds have failed. The monotetetrazoles of diazidotetrazine and bis(azido)azo-1,2,4,5-tetrazine and the ditetrazole of bis(azido)hydrazo-1,2,4,5-tetrazine are the minimum energy species in DMSO and water. Thus we predict that the diazidoazo- and hydrazotetrazines will readily cyclize to the tetrazoles in polar solvents. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Solvation of acylium fragment ions in electrospray ionization quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 3 2001Ziqiang Guan Abstract In electrospray ionization (ESI) quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometry, certain fragment ions (e.g. acylium ions) generated either during the ion transportation process (in the source interface region) or in the ion trap are found to undergo ion,molecule reactions with ESI solvent molecules (water, acetonitrile and aliphatic alcohols) to form adduct species. These unexpected solvated fragment ions severely complicate the interpretation of mass spectrometic data. High-resolution accurate mass measurements are important in establishing the elemental compositions of these adduct species and preventing erroneous data interpretation. Copyright © 2001 John Wiley & Sons, Ltd. [source] Thermochemistry, bonding, and reactivity of Ni+ and Ni2+ in the gas phaseMASS SPECTROMETRY REVIEWS, Issue 4 2007Otilia Mó Abstract In this review, we present a general overview on the studies carried out on Ni+- - and Ni2+ -containing systems in the gas phase since 1996. We have focused our attention in the determination of binding energies in parallel with an analysis of the structure and bonding of the complexes formed by the interaction of Ni+ with one ligand, or in clusters where this metal ion binds several identical or different ligands. Solvation of Ni2+ by different ligands is also discussed, together with the theoretical information available of doubly charged Ni-containing species. The final section of this review is devoted to an analysis of the gas-phase uni- and bimolecular reactivity of Ni+ and Ni2+ complexes. © 2007 Wiley Periodicals, Inc., Mass Spectrom. Rev. [source] Controlled Hydrogen-Bond Breaking in a Rotaxane by Discrete Solvation,ANGEWANDTE CHEMIE, Issue 23 2010Anouk Molekulare Bremse: Die Wechselwirkungen zwischen Stab und Makrocyclus eines [2]Rotaxans können quasi stufenlos eingestellt werden, indem man H-Brücken bildende Lösungsmittelmoleküle einzeln zu einem isolierten [2]Rotaxan-Molekül gibt. So lassen sich gezielt Konformationsänderungen herbeiführen, die den Stab vom Makrocyclus freigeben , was dem kontrollierten Lösen der molekularen Bremse entspricht. [source] Solvent effects on coupling yields during rapid solid-phase synthesis of CGRP(8-37) employing in situ neutralization,CHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2005C.K. Taylor Abstract:, The success of solid-phase peptide synthesis is often dependent upon solvation of the resin and the growing resin-bound peptide chain. We investigated the relationship between solvent properties and solvation of the resin and peptide-resin in order to obtain satisfactory coupling yields for the rapid solid-phase peptide synthesis, using butyloxycarbonyl-(Boc)-amino acid derivatives, of human-,-calcitonin gene-related peptide(8-37) (CGRP(8-37)). Solvation of (p -methylbenzhydrylamine)copoly(styrene,1% divinylbenzene (DVB) (resin) and resin covalently bound to the fully protected amino acid sequence of CGRP(8-37) (peptide,resin) was correlated to solvent Hildebrand solubility (,) and hydrogen-bonding (,h) parameters. Contour solvation plots of ,h vs. , revealed maximum solvation regions of resin and peptide,resin. Maximum resin solvation occurred with N-methylpyrrolidinone (NMP), NMP : dimethylsulfoxide (DMSO) (8 : 2) and DMSO. Inefficient solvation of the peptide,resin occurred with these solvents and resulted in poor syntheses with average coupling yields of 78.1, 88.9 and 91.8%, respectively. Superior peptide,resin solvation was obtained using dimethylacetamide (DMA) and dimethylformamide (DMF), resulting in significantly higher average coupling yields of 98.0 and 99.5%, respectively. Thus, the region of maximum peptide,resin solvation shifts to solvents with higher ,h values. DMF provided the most effective peptide,resin solvation and was the only solvent from which CGRP(8-37) was obtained as a single major product in the crude cleaved material. [source] Electronic Structure and Solvation of Copper and Silver Ions: A Theoretical Picture of a Model Aqueous Redox ReactionCHEMINFORM, Issue 23 2004Jochen Blumberger Abstract For Abstract see ChemInform Abstract in Full Text. [source] Insight into the Solvation and Isomerization of 3-Halo-1-azaallylic Anions from Ab Initio Metadynamics Calculations and NMR ExperimentsCHEMISTRY - A EUROPEAN JOURNAL, Issue 3 2009Reinout Declerck Dr. Long live theZisomer! The solvation and isomerization properties of lithiated 3-chloro-1-azaallylic anions in tetrahydrofuran are revealed. Extensive and convincing evidence is obtained from state-of-the-art first-principle molecular dynamics and metadynamics simulations in an explicit periodic solvent model, together with detailed NMR experiments. [source] Solvation of Uranyl(II), Europium(III) and Europium(II) Cations in "Basic" Room-Temperature Ionic Liquids: A Theoretical StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 16 2004Alain Chaumont Abstract We report a molecular dynamics study of the solvation of UO22+, Eu3+ and Eu2+ ions in two "basic" (Lewis acidity) room-temperature ionic liquids (IL) composed of the 1-ethyl-3-methylimidazolium cation (EMI+) and a mixture of AlCl4, and Cl, anions, in which the Cl,/AlCl4, ratio is about 1 and 3, respectively. The study reveals the importance of the [UO2Cl4]2, species, which spontaneously form during most simulations, and that the first solvation shell of europium is filled with Cl, and AlCl4, ions embedded in a cationic EMI+ shell. The stability of the [UO2Cl4]2, and [EuIIICl6]3, complexes is supported by quantum mechanical calculations, according to which the uranyl and europium cations intrinsically prefer Cl, to the AlCl4, ion. In the gas phase, however, [EuIIICl6]3, and [EuIICl6]4, complexes are predicted to be metastable and to lose two to three Cl, ions. This contrasts with the results of simulations of complexes in ILs, in which the "solvation" of the europium complexes increases with the number of coordinated chlorides, leading to an equilibrium between different chloro species. The behavior of the hydrated [Eu(OH2)8]3+ complex is considered in the basic liquids; the complex exchanges H2O molecules with Cl, ions to form mixed [EuCl3(OH2)4] and [EuCl4(OH2)3], complexes. The results of the simulations allow us to better understand the microscopic nature and solvation of lanthanide and actinide complexes in "basic" ionic liquids. [source] Glycosylation Enhances Peptide Hydrophobic Collapse by Impairing SolvationCHEMPHYSCHEM, Issue 11 2010Shanmei Cheng Dr. Abstract Post-translational N-glycosylation of proteins is ubiquitous in eukaryotic cells, and has been shown to influence the thermodynamics of protein collapse and folding. However, the mechanism for this influence is not well understood. All-atom molecular dynamics simulations are carried out to study the collapse of a peptide linked to a single N-glycan. The glycan is shown to perturb the local water hydrogen-bonding network, rendering it less able to solvate the peptide and thus enhancing the hydrophobic contribution to the free energy of collapse. The enhancement of the hydrophobic collapse compensates for the weakened entropic coiling due to the bulky glycan chain and leads to a stronger burial of hydrophobic surface, presumably enhancing folding. This conclusion is reinforced by comparison with coarse-grained simulations, which contain no explicit solvent and correspondingly exhibit no significant thermodynamic changes on glycosylation. [source] Force Field Evaluation for Biomolecular Simulation: Free Enthalpies of Solvation of Polar and Apolar Compounds in Various SolventsCHEMPHYSCHEM, Issue 3 2006Daan P. Geerke Abstract Recently, the GROMOS biomolecular force field parameter set 53A6,which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexane of amino acid side-chain analogs,was presented. To investigate the transferability of the new parameter set, we calculated free enthalpies of solvation of a range of polar and apolar compounds in different solvents (methanol, dimethyl sulfoxide (DMSO), acetonitrile, and acetone) from molecular dynamics simulations using the GROMOS 53A6 force field. For methanol and DMSO, parameters were used that are available in the 53A6 parameter set. For acetonitrile, a recently developed model was taken and for acetone, two models available in literature were used. We found that trends in and values for the solvation free enthalpies are in satisfactory agreement with experiment, except for the solvation in acetone for which deviations from experiment can be explained in terms of the properties of the models used. [source] Pressure Perturbation Calorimetry: A New Technique Provides Surprising Results on the Effects of Co-solvents on Protein Solvation and Unfolding BehaviourCHEMPHYSCHEM, Issue 4 2004Revanur Ravindra Dr. Exquisitely sensitive, pressure perturbation calorimetry was used by the authors to study the solvation and volumetric properties of proteins in their native and unfolded states. The magnitude and even sign of the volume change on unfolding drastically depends on the co-solvent concentration (see graphic). [source] Azide,Tetrazole Ring-Chain Isomerism in Polyazido-1,3,5-triazines, Triazido- s -heptazine, and DiazidotetrazinesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11 2006Anton Hammerl Abstract The azide,tetrazole isomerism in several polyazido-1,3,5-triazines, triazido- sym -heptazine, and some diazido-1,2,4,5-tetrazines was investigated by ab initio quantum chemical methods in order to determine whether the polyazides are suitable starting materials for the synthesis of the isomeric tetrazoles. The effects of solvation in CCl4, DMSO and water on this isomerism were included using the self consistent reaction field (SCRF) method. The effect of amino- and nitrosubstituents on the azide,tetrazole isomerism was also examined. In the gas phase all investigated polyazidoheterocycles do not cyclize to form tetrazoles. An electron-donating amino group favors the ring closure to tetrazoles, whereas an electron-withdrawing nitro group favors the azides. Solvation in polar solvents favors the formation of a tetrazole ring system due to higher charge separation in the tetrazole ring system, but for all polyazido-1,3,5-triazines, including triazido- s -heptazine, the effects of solvation are not strong enough to shift the equilibrium to the tetrazole side, which explains why several attempts to detect these compounds have failed. The monotetetrazoles of diazidotetrazine and bis(azido)azo-1,2,4,5-tetrazine and the ditetrazole of bis(azido)hydrazo-1,2,4,5-tetrazine are the minimum energy species in DMSO and water. Thus we predict that the diazidoazo- and hydrazotetrazines will readily cyclize to the tetrazoles in polar solvents. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] N -Methylation Effects on the Coordination Chemistry of Cyclic Triamines with Divalent Transition Metals and Their CoII Dioxygen CarriersEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 2 2006Silvia Del Piero Abstract The thermodynamics of complex formation of CoII and CdII ions with the triaza macrocyclic ligand 1,4,7-triazacyclononane (tacn) and its N -methylated derivative 1,4,7-trimethyl-1,4,7-triazacyclononane (Me3tacn) has been studied in dimethyl sulfoxide (DMSO) at 298.1 K and in an ionic medium (0.1 M Et4NClO4) by means of potentiometric, UV/Vis, calorimetric and FT-IR techniques. The results are discussed by taking into account electronic and steric effects as well as solvation of the species concerned. Computational methods based on density functional theory (DFT) have been used to obtain structural information about the ligands and their complexes in order to provide further, independent insights into the effect of N -methylation on the coordination affinity of the ligands towards the metal ions. The computational suggestions are of great help to correlate steric effects and thermodynamic results. The kinetics of dioxygen uptake for the formation of the Co(tacn)2O2 superoxo adduct has also been studied by means of UV/Vis measurements. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source] Complexation and Dynamic Switching Properties of Fluorophore-Appended Resorcin[4]arene CavitandsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 5 2010Laura D. Shirtcliff Abstract Fluorophore-appended resorcin[4]arene-based cavitands having pyrene (2) and anthracene (3) moieties attached to the rims were prepared by short synthetic routes. Both undergo reversible temperature- and acid- (CF3COOD) induced vase,,,kite switching as evidenced by 1H NMR spectroscopy. The 1H NMR spectra also suggest that suitably sized solvents, such as [D8]toluene, efficiently solvate the cavity, reducing the conformational flexibility. In [D12]mesitylene, both cavitands undergo remarkably stable host-guest inclusion complexation with cycloalkanes. The larger cavity of 3 preferentially hosts cyclohexane, whereas the smaller cavity of 2 forms the most stable complex with cyclopentane. The propensity for the cavitands to facilitate ,,, stacking between the chromophores was confirmed by both 1H NMR and fluorescence spectroscopy. The interchromophoric interaction is strongly solvent-dependent: ,,, stacking between the pyrene moieties of 2 is not as efficient in [D8]toluene, as it solvates the inner cavity and prevents the two chromophores from approaching each other. Fluorescence studies revealed an unexpectedly large conformational flexibility of the cavitand structures both in the vase and kite forms, which was further confirmed by molecular dynamics simulations. Excimer formation is most preferred in [D12]mesitylene when the cavities are empty, whereas efficient solvation or guest binding in the interior spaces reduces the propensity for excimer formation. The observed high conformational flexibility of the cavitands in solution explains previous differences from the behavior of related systems in the solid state. This study shows that the rigid, perfect vase and kite geometries found for bridged resorcin[4]arene cavitands in the solid state are largely a result of crystal packing effects and that the conformational flexibility of the structures in solution is rather high. [source] Basicity of Guanidines with Heteroalkyl Side Chains in AcetonitrileEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 30 2008Mirjana Eckert-Maksi Abstract The pKa values of seven novel guanidine derivatives, six of them possessing heteroalkyl substituents capable of forming intramolecular hydrogen bonds, were determined in acetonitrile (MeCN) by using the UV/Vis spectrophotometric titration method. The obtained pKa values range from 24.7 to 27.2. The most basic among the studied guanidines was found to be by ca. 4 pKa units more basic than thewell-known superbase N1,N1,N3,N3 -tetramethylguanidine (TMG). The trends in the changes in the measured pKa values were compared with the experimental (determined by the extended kinetic method) and theoretical [B3LYP/6-311+G(2df,p)//B3LYP/6-31G(d)] gas-phase proton affinities. It was shown that basicity ordering of the bases with dimethylaminopropyl substituents in acetonitrile follows the trend encountered in the gas phase. However, this is not the case for the methoxypropyl-substituted guanidines indicating that in these molecules formation of the intramolecular hydrogen bonds is to large extent hindered due to solvation by acetonitrile.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Reactivity of (Mono- tert -butyloxiranyl)lithium: A Theoretical Ab Initio StudyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 26 2008Abdelatif Bouyacoub Abstract The reactivity of the lithiated tert -butyloxiranyl anion has been studied by means of ab initio calculations at the CCSD(T)//MP2 level of theory. Four reaction paths have been studied (three ring-opening reactions and one addition reaction). All extrema were located and characterised. The effects of solvation by one or two MeLi molecules were studied for each reaction path by reoptimising the various extrema. It was found that the addition reaction path becomes competitive when at least two MeLi molecules are taken into account. This shows the catalytic effect of alkyllithium on this reaction path. In no case could a free carbene be characterised as a reaction intermediate. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Radical Cation and Dication Derived from 4,8-Diethylbenzo[1,2- d:4,5- d,]bis[1,2,3]trithiole [DEBBT]: Change of Electronic State from Singlet-State Dication DEBBT(2+)- S to Triplet-State Dimer 2DEBBT(2+)- T in D2SO4 and CD3CN SolutionsEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 24 2003Takeshi Kimura Abstract 4,8-Diethylbenzo[1,2- d:4,5- d,]bis[1,2,3]trithiole [DEBBT] was oxidized using concentrated D2SO4, leading to the generation of the radical cation DEBBT(·+) which was verified by ESR spectroscopy. DEBBT(·+) in the solution was further oxidized to produce the dication DEBBT(2+), as determined by 1H and 13C NMR spectroscopy. DEBBT(2+) was also prepared by treating DEBBT 1-oxide [DEBBT 1-O] with concentrated D2SO4, and was verified by 1H and 13C NMR spectroscopy. The 13C NMR chemical shifts of DEBBT(2+), calculated by the density functional theoretical (DFT) method at the B3LYP6-31G** level, correlated well with those obtained experimentally. The ESR signal of DEBBT(2+) generated from DEBBT 1-O was observed in solution, which implies that the singlet-state dication DEBBT(2+)- S isomerizes to the triplet-state dication DEBBT(2+)- T, and that two molecules of DEBBT(2+)- T further form a spin pair at one trithiole ring with significant distance between the two radical centers. The oxidation of DEBBT with one or two equivalents of single-electron oxidizing reagents produced DEBBT(·+) and DEBBT(2+), and the salts were isolated in a stable form. However, the DEBBT(2+) that was prepared by oxidation with NOPF6 proved silent for NMR in CD3CN, while ESR was active. The stability, electronic state, and NMR and ESR spectroscopy of the dication are affected by solvation with D2SO4 and CD3CN. The optimized structures and the total energy of the singlet- and triplet-state dication were calculated using the DFT method at the B3LYP6-31G** level, which shows that the structures of the singlet- and triplet-state dications have a completely planar form with 1.7 kcal/mol as the total energy difference between them. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Computational NMR Spectroscopy of Transition-Metal/Nitroimidazole Complexes: Theoretical Investigation of Potential RadiosensitizersHELVETICA CHIMICA ACTA, Issue 10 2005Teodorico The computed chemical shifts of transition-metal complexes with dimetridazole (=,1,2-dimethyl-5-nitro-1H -imidazole; 1), a prototypical nitro-imidazole-based radiosensitizer, are reported at the GIAO-BP86 and -B3LYP levels for BP86/ECP1-optimized geometries. These complexes comprise [MCl2(1)2] (M,=,Zn, Pd, Pt), [RuCl2(DMSO)2(1)2], and [Rh2(O2CMe)4(1)2]. Available ,(1H) and ,(15N) values, and ,,(1H) and ,,(15N) coordination shifts are well-reproduced theoretically, provided solvation and relativistic effects are taken into account by means of a polarizable continuum model and suitable methods including spin,orbit (SO) coupling, respectively. These effects are particularly important for the metal-coordinated N-atom, where the contributions from solvation and relativity can affect ,(15N) and ,,(15N) values up to 10,20,ppm. The 195Pt chemical shifts of cis - and trans -[PtCl2(1)2] are well-reproduced using the zero-order regular approximation including SO coupling (ZORA-SO). Predictions are reported for 99Ru and 103Rh chemical shifts, which suggest that these metal centers could be used as additional, sensitive NMR probes in their complexes with nitro-imidazoles. [source] Chemo- and Enzyme-Catalyzed Reactions Revealing a Common Temperature-Dependent Dynamic Solvent Effect on EnantioselectivityHELVETICA CHIMICA ACTA, Issue 11 2003Gianfranco Cainelli The enantiomeric ratio E of enzyme-catalyzed (Candida antarctica lipase and lipase PS) and chemo-catalyzed (L -proline-based diamines) acylation reactions of 1-(naphthalen-2-yl)ethanol, 2-phenylpropanol, and 2-benzylpropane-1,3-diol is dependent on solvent and temperature. Plots of ln,E vs. 1/T showed the presence of inversion temperatures (Tinv). The Tinv values for the bio-catalyzed and the chemo-catalyzed reactions are fairly in agreement, and correspond as well to the TNMR values obtained by variable-temperature 13C-NMR experiments on the substrates in the same solvent of the resolution. This result demonstrates that clustering effects in the substrate solvation manage the chemical and the enzymatic enantioselectivity, and, moreover, that the solutesolvent cluster is always the real reacting species in solution for chemical as well as for enzymatic reactions. [source] Effect of the Media on the Quantum Yield of Singlet Oxygen (O2(1,g)) Production by 9H -Fluoren-9-one: Solvents and Solvent MixturesHELVETICA CHIMICA ACTA, Issue 2 2003Claudia We have investigated the effect of a series of 18 solvents and mixtures of solvents on the production of singlet molecular oxygen (O2(1,g), denoted as 1O2) by 9H -fluoren-9-one (FLU). The normalized empirical parameter E derived from ET(30) has been chosen as a measure of solvent polarity using Reichardt's betaine dyes. Quantum yields of 1O2 production (,,) decrease with increasing solvent polarity and protic character as a consequence of the decrease of the quantum yield of intersystem crossing (,ISC). Values of ,, of unity have been found in alkanes. In nonprotic solvents of increasing polarity, ,ISC and, therefore, ,, decrease due to solvent-induced changes in the energy levels of singlet and triplet excited states of FLU. This compound is a poor 1O2 sensitizer in protic solvents, because hydrogen bonding considerably increases the rate of internal conversion from the singlet excited state, thus diminishing ,, to values much lower than those in nonprotic solvents of similar polarity. In mixtures of cyclohexane and alcohols, preferential solvation of FLU by the protic solvent leads to a fast decrease of ,, upon addition of increasing amounts of the latter. [source] Kinetic and thermodynamic study of thiolato and sulfenato Co(III) complexes in water,acetonitrile mixturesINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 1 2004Monika Aranyosiová Rate constants are reported for peroxodisulfate as well as periodate oxidation of[Co(en)2{SCH2CH(COO)NH2}]+, [Co(en)2(SCH2CH2NH2)]2+, and [Co(en)2(SOCH2CH2NH2)]2+ in water,acetonitrile mixtures. The dependence of rate constants on the acetonitrile concentration is established and discussed. Ancillary information relevant to solvation of reactants has been obtained from solvatochromism and from Gibbs transfer functions. The solvent effect is discussed from the viewpoint of change in solvation of initial and transition state on going from water to water,acetonitrile mixtures. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 36: 34,40, 2004 [source] Nonequilibrium solvent polarization in kinetics of SN2 reactionsINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 2 2003J. S. JaworskiArticle first published online: 21 NOV 200 The solvent effect on the experimental activation barriers for the reactions of methyl iodide with chloride and thiocyanate ions was analyzed according to the Marcus and Shaik theories, considering SN2 mechanism in terms of a single electron shift. The linear increase in the solvent reorganization energy of the Marcus theory (after removing contributions from the specific solvation) with the solvent Pekar factor, describing the effect of the nonequilibrium solvent polarization, was observed for six aprotic solvents. The direct support of the title effect based on the Shaik theory was less evident; however, in general, the calculated activation barriers in 10 solvents change parallel with the experimental ones. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 35: 61,66, 2003 [source] Computational study of the solvation of protoporphyrin IX and its Fe2+ complexINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008Teobaldo Cuya Guizado Abstract Molecular dynamics (MD) simulations of a well known hydrophobic structure, the heme (ferroprotoporphyrin IX) and its precursor in the heme synthesis, protoporphyrin IX (PPIX) are presented. The objective of the present study is to determine the stability of both structures in an aqueous medium, as well as the structure-solvent relation, hydration shells, and discuss their implications for biological processes. The density functional theory (DFT) is used for the electronic and structural characterization of both PPIX and its Fe2+ complex. A classical approach based on the Gromacs package is used for the MD. The radial distribution function g(r) is used to examine the allocation of water molecules around different regions of the porphyrins. The calculations demonstrate the heterogeneous character of the porphyrins with respect to the affinity with water molecules, the general hydrophobic character of the porphyrin ring bonded or not to the ion Fe, the hydrophilic character of the carboxylic oxygen that is unchanged upon iron binding, and the low hydrophilicity of Fe2+ in the heme. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Theoretical study of the oxidative polymerization of aniline with peroxydisulfate: Tetramer formationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2008-Marjanovi, Gordana Abstract Semi-empirical quantum chemical study of the oxidative polymerization of aniline with ammonium peroxydisulfate, in aqueous solutions without added acid, has been based on the MNDO-PM3 computations of thermodynamic, redox, and acid,base properties of reactive species and the intermediates, combined with the MM2 molecular mechanics force-field method and conductor-like screening model of solvation. The main reaction routes of aniline tetramerization are proposed. The regioselectivity of the formation of aniline tetramers by redox and electrophilic aromatic substitution reactions is analyzed. It was proved that the linear NC4 coupled tetra-aniline is formed as a dominant product by three different pathways: comproportionation redox reaction between N -phenyl-1,4-benzoquinonediimine and 4-aminodiphenylamine, the one-electron oxidation of aniline with its half-oxidized NC4 coupled trimer, and the electrophilic aromatic substitution reaction of aniline with fully oxidized NC4 coupled trianiline nitrenium cation. The electrophilic aromatic substitution reaction of the NC4 coupled aniline trimer with aniline nitrenium cation, as well as the oxidation of aniline with half-oxidized branched trimer, lead to the branched aniline tetramers. The competing character of different tetramerization routes is highlighted. The oxidative intramolecular cyclization of branched oligoanilines and polyaniline, leading to the generation of substituted phenazine units, has been predicted to accompany the classical routes of the polymerization of aniline. Various molecular (branched vs. linear) oligomeric structures produced at different level of acidity during the course of polymerization and their impact on the formation of supramolecular structures of conducting polyaniline (nanorods and nanotubes vs. granular morphology), are discussed. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Explicitly correlated SCF study of anharmonic vibrations in (H2O)2INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2002Donald D. Shillady Abstract Modeling solvation in high-pressure liquid chromatography (HPLC) requires calculation of anharmonic vibrational frequencies of solvent clusters for a statistical partition function. An efficient computational method that includes electron correlation is highly desirable for large clusters. A modified version of the "soft Coulomb hole" method of Chakravorty and Clementi has recently been implemented in a Gaussian-lobe-orbital (GLO) program (PCLOBE) to include explicit electron,electron correlation in molecules. The soft Coulomb hole is based on a modified form of Coulomb's law: An algorithm has been developed to obtain the parameter "w" from a polynomial in the effective scaling of each primitive Gaussian orbital relative to the best single Gaussian of the H1s orbital. This method yields over 90% of the correlation energy for molecules of low symmetry for which the original formula of Chakravorty and Clementi does not apply. In this work, all the vibrations of the water dimer are treated anharmonically. A quartic perturbation of the harmonic vibrational modes is constrained to be equal to the exact Morse potential eigenvalue based on a three-point fit. This work evaluates the usefulness of fitting a Morse potential to a hydrogen bond vibrational mode and finds it to be slightly better than using MP2 vibrational analysis for this important dimer. A three-point estimate of the depth, De, of a Morse potential leads to a correction formula for anharmonicity in terms of the perturbed harmonic frequency: When scaled by 0.9141, the harmonic Morse method leads to essentially the same results as scaling the BPW91 local density method by 0.9827. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Femtosecond dynamics of electron transfer, localization, and solvation processes at the ice,metal interfaceISRAEL JOURNAL OF CHEMISTRY, Issue 1-2 2005Uwe Bovensiepen The ultrafast dynamics of excess electrons in amorphous ice layers on single-crystal metal surfaces are investigated by femtosecond time- and angle-resolved two-photon-photoemission spectroscopy. Photoexcited electrons are injected from the metal substrate into delocalized states of the conduction band of ice and localize in the ice layer within 100 fs. Subsequently, energetic stabilization of this localized species is observed on a time scale of ,1 ps, which is attributed to electron solvation by nonadiabatic coupling to nuclear degrees of freedom of the surrounding polar molecular environment. Concomitant with this stabilization process, residual wave function overlap of the solvated electron with the metal substrate results in back-transfer by tunneling through the solvation shell. At such interfaces the correlation of electronic and molecular structure with the resulting solvation dynamics can be explored using different substrates as a template. Here we compare data on molecularly thin D2O ice layers grown on Cu(111) and Ru(001). On Ru(001) both the stabilization and back-transfer proceed about three times faster compared to Cu(111), which is attributed to different interfacial structures and the role of d-states, and projected band gaps in the electron transfer process. [source] The analysis of solvation in ionic liquids and organic solvents using the Abraham linear free energy relationshipJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 10 2006William E Acree Jr The original article to which this Erratum refers was published in Journal of Chemical Technology and Biotechnology (81: 1441,1446). [source] Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweightingJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2010Hisashi Okumura Abstract The use of the replica exchange (RE) molecular dynamics (MD) method for the efficient estimation of conformational populations of ligand-sized molecules in solution is investigated. We compare the computational efficiency of the traditional constant temperature MD technique with that of the parallel RE molecular dynamics method for a series of alkanes and rilpivirine (TMC278), an inhibitor against HIV-1 reverse transcriptase, with implicit solvation. We show that conformational populations are accurately estimated by both methods; however, replica exchange estimates converge at a faster rate, especially for rilpivirine, which is characterized by multiple stable states separated by high-free energy barriers. Furthermore, convergence is enhanced when the weighted histogram analysis method (WHAM) is used to estimate populations from the data collected from multiple RE temperature replicas. For small drug-like molecules with energetic barriers separating the stable states, the use of RE with WHAM is an efficient computational approach for estimating the contribution of ligand conformational reorganization to binding affinities. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solventJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2007Anna Jagielska Abstract The influences of temperature, friction, and random forces on the folding of protein A have been analyzed. A series of all-atom molecular dynamics folding simulations with the Amber ff99 potential and Generalized Born solvation, starting from the fully extended chain, were carried out for temperatures from 300 to 500 K, using (a) the Berendsen thermostat (with no explicit friction or random forces) and (b) Langevin dynamics (with friction and stochastic forces explicitly present in the system). The simulation temperature influences the relative time scale of the major events on the folding pathways of protein A. At lower temperatures, helix 2 folds significantly later than helices 1 and 3. However, with increasing temperature, the folding time of helix 2 approaches the folding times of helices 1 and 3. At lower temperatures, the complete formation of secondary and tertiary structure is significantly separated in time whereas, at higher temperatures, they occur simultaneously. These results suggest that some earlier experimental and theoretical observations of folding events, e.g., the order of helix formation, could depend on the temperature used in those studies. Therefore, the differences in temperature used could be one of the reasons for the discrepancies among published experimental and computational studies of the folding of protein A. Friction and random forces do not change the folding pathway that was observed in the simulations with the Berendsen thermostat, but their explicit presence in the system extends the folding time of protein A. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007 [source] A Kirkwood-Buff derived force field for amidesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2006Myungshim Kang Abstract A force field for the computer simulation of aqueous solutions of amides is presented. The force field is designed to reproduce the experimentally observed density and Kirkwood,Buff integrals for N -methylacetamide (NMA), allowing for an accurate description of the NMA activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. The force field is then extended to include N,N,-dimethylacetamide and acetamide with good success. Analysis of the simulations of low concentrations of NMA in water indicates a high degree of solvation with only 15% of the NMA molecules involved in solute,solute hydrogen bonding. There is only a weak angular dependence of the solute,solute hydrogen bonding interaction with a minimum at an angle of 65° for the NH and CO dipole vectors. The models presented here provide a basis for an accurate force field for peptides and proteins. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1477,1485, 2006 [source] | |||||||||||||||||||||||||||||||||||||