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Modesto Orozco - One of the best experts on this subject based on the ideXlab platform.
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Misincorporation of 2'-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations.
Nucleic Acids Research, 2000Co-Authors: Begoña Hernández, Robert Soliva, F. Javier Luque, Modesto OrozcoAbstract:A wide range of theoretical methods, including high level ab initio, density functional, Self-Consistent Reaction Field, molecular dynamics and thermodynamic integration calculations, have been used to analyze the mutagenic properties of oxanosine. The major tautomeric forms in the gas phase and aqueous solution have been determined. The ability of oxanosine to recognize thymine and cytosine in the gas phase and in the DNA environment has been compared with that of guanine. A physicochemical explanation for the mutagenic properties of oxanosine is suggested.
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Simplified descriptions of the topological distribution of hydrophilic/hydrophobic characteristics of molecules
Physical Chemistry Chemical Physics, 2000Co-Authors: Xavier Barril, Jordi Muñoz, F. Javier Luque, Modesto OrozcoAbstract:Based on the fractional approach previously developed by our group in the framework of the Miertus–Scrocco–Tomasi Self-Consistent Reaction Field method, we explore here the suitability of ‘solvation’ and ‘transfer’ dipoles to describe the topological distribution of hydrophilic/hydrophobic properties of molecules. Both descriptors provide a simplified but yet accurate representation of the 3D distribution of hydrophilic and hydrophobic areas in molecules, which can be valuable in structure–activity relationship and molecular-Field alignment studies.
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Fractional description of free energies of solvation
Journal of Computer-Aided Molecular Design, 1999Co-Authors: F. Javier Luque, Xavier Barril, Modesto OrozcoAbstract:A new and rigorous method for the fractional description of solvation and transfer free energies is presented. The method is based on the use of the Miertus-Scrocco-Tomasi Self-Consistent Reaction Field method (MST-SCRF), and allows for a rigorous partition of the total solvation free energy into surface elements. The method gives a complete picture of the hydrophobicity/hydrophilicity of molecules. Present results allow us to expect that the method might provide useful information in drug design and molecular modeling studies.
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Helical preferences of alanine, glycine, and aminoisobutyric homopeptides
Proteins, 1997Co-Authors: Carlos Alemán, F. Javier Luque, Ramón Roca, Modesto OrozcoAbstract:: The stability between helical conformations of homopeptides of alanine, glycine, and aminoisobutyric acid has been studied by means of quantum-mechanical methods. The influence of peptide length on the relative stability between helical conformations has also been analyzed by means of systematic studies for peptides of size up to 11 residues. Finally, the influence of the solvent has been examined by using Self-Consistent Reaction Field methods. The results provide a detailed picture of the modulation exerted by these factors on the helical preferences of these peptides.
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New strategies to incorporate the solvent polarization in self‐consistent Reaction Field and free‐energy perturbation simulations
Journal of Chemical Physics, 1995Co-Authors: Francisco J. Luque, Josep Maria Bofill, Modesto OrozcoAbstract:A first‐order perturbation treatment of the polarization contribution to the free energy of hydration is presented. Very simple expressions for the computation of the total electrostatic free energy of solvation, the polarization contribution, and its components (distortion and stabilization) are derived. These equations can be used with either continuum (quantum and classical) or discrete approaches. The reliability of these equations is examined by comparison with rigorous expressions derived previously within the framework of the self‐consistent Reaction Field theory. Indeed, the suitability of the classical expressions for the distortion and stabilization terms used in the context of discrete strategies has been explored by comparison between self‐consistent Reaction Field and molecular dynamics–free‐energy perturbation results. The excellent agreement found between the two techniques allows us to envisage a procedure to account for the polarization in force Field‐derived methods.
Francisco J. Luque - One of the best experts on this subject based on the ideXlab platform.
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Misincorporation of 2^{\prime}-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations
Nucleic acids research, 2000Co-Authors: Begoña Hernández, Robert Soliva, Francisco J. Luque, Manuel OrozcoAbstract:A wide range of theoretical methods, including high level ab initio,\ndensity functional, Self-Consistent Reaction Field, molecular dynamics\nand thermodynamic integration calculations, have been used to analyze\nthe mutagenic properties of oxanosine...
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New strategies to incorporate the solvent polarization in self‐consistent Reaction Field and free‐energy perturbation simulations
Journal of Chemical Physics, 1995Co-Authors: Francisco J. Luque, Josep Maria Bofill, Modesto OrozcoAbstract:A first‐order perturbation treatment of the polarization contribution to the free energy of hydration is presented. Very simple expressions for the computation of the total electrostatic free energy of solvation, the polarization contribution, and its components (distortion and stabilization) are derived. These equations can be used with either continuum (quantum and classical) or discrete approaches. The reliability of these equations is examined by comparison with rigorous expressions derived previously within the framework of the self‐consistent Reaction Field theory. Indeed, the suitability of the classical expressions for the distortion and stabilization terms used in the context of discrete strategies has been explored by comparison between self‐consistent Reaction Field and molecular dynamics–free‐energy perturbation results. The excellent agreement found between the two techniques allows us to envisage a procedure to account for the polarization in force Field‐derived methods.
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The effect of hydration on the molecular charge distribution of cations. An ab initio SCRF study
Chemical Physics Letters, 1995Co-Authors: Francisco J. Luque, Pravin K. Bhadane, Shridhar R. Gadre, Modesto OrozcoAbstract:A theoretical study of the changes in the charge distribution of a series of small cations due to the polarization effect of water is presented. The results, which are obtained from high-level ab initio Self-Consistent Reaction Field calculations, show the complexity of the solvent effect on the electron distribution of cations. The polarization effect of water on the charge redistribution for cations is smaller than that for anions and neutral molecules, but it is still significant for some systems.
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Effect of solvation on the shapes, sizes, and anisotropies of polyatomic anions via molecular electrostatic potential topography: An ab initio self‐consistent Reaction Field approach
Journal of Chemical Physics, 1994Co-Authors: Francisco J. Luque, Modesto Orozco, Pravin K. Bhadane, Shridhar R. GadreAbstract:The effect of solvation, as studied by the self‐consistent Reaction Field procedure, on the shapes, sizes, and anisotropies of eight small prototypical anions (OH−, NH−2, CH−3, CN−, SH−, N−3, NO−2, and NO−3) has been studied at the ab initio 6–31++G(d) level. Both the general molecular electrostatic potential distribution and the molecular electrostatic potential topography have been used for examining the effect of solvation. The results demonstrate both the complexity and specificity of the hydration effect on the solute charge distribution. It is observed that in general anions tend to shrink upon solvation. The molecular electrostatic potential, in general, becomes more negative and the electron density is increased upon solvation. The effect of the solvation on the chemical reactivity and anisotropy of the anions in aqueous environment is discussed.
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Self‐consistent Reaction Field computation of the reactive characteristics of DNA bases in water
Biopolymers, 1993Co-Authors: Modesto Orozco, Francisco J. LuqueAbstract:The effect of the solvent in the molecular properties of DNA bases has been explored by using a Self-Consistent Reaction Field (SCRF) method based on the AM1 (Austin Model 1) Hamiltonian and a modified version of the high level Miertus–Scrocco–Tomasi (MST) algorithm. MST/AM1 estimates of free energies of hydration compare qualitatively well with the available experimental data, as well as with the results obtained from molecular dynamic simulations. Furthermore, the changes in the dipole predicted by the MST/AM1 method are in good agreement with Monte Carlo/quantum mechanical data, as well as with AM1-SM2 (Soluation Model 2) estimates. AM1/MST calculations of Mulliken, and electrostatic charges, dipoles, molecular electrostatic potentials and molecular interaction potentials in both vacuum and solution allowed us to quantify the effect of the water on the reactive characteristics of the DNA bases. This effect is large and complex, and cannot be neglected in theoretical calculations where an accurate representation of the DNA bases is needed. The possibility of including the polarization effect of the water into force-Field simulations of DNA structures is discussed. © 1993 John Wiley & Sons, Inc.
Louis Noodleman - One of the best experts on this subject based on the ideXlab platform.
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Density Functional Vertical Self-Consistent Reaction Field Theory for Solvatochromism Studies of Solvent-Sensitive Dyes
Journal of Physical Chemistry A, 2004Co-Authors: Fahmi Himo, G. Matthias Ullmann, Donald Bashford, Alexei Toutchkine, Klaus M. Hahn, Louis NoodlemanAbstract:On the basis of the Franck-Condon principle, a density functional vertical Self-Consistent Reaction Field (VSCRF) solvation model for vertical excitation and emission processes is established. The principles and implementation of the VSCRF model are presented. The predicted blue shifts of the vertical excitation energies of diazines in different solvents from n-heptane to water solutions are compared with the corresponding time dependent density functional calculations and are in very good agreement with experiment. We have also applied this method to predict the blue shifts and the vertical excitation and emission energies of Brooker’s merocyanine dye with increasing solvent polarities from CHCl3 to H2O solutions. Overall, our calculations predicted the relative excitation and emission energy orderings for Brooker’s merocyanine in different solvents with different polarities. Also, the calculated Stokes shift is fairly well represented for different solvents, and the calculations correctly show that the absorption energies have a much stronger solvent dependence than the emission energies. The importance of both relaxation of the molecular structures and consideration of explicit H-bonding H2O and CH3OH molecules in water and methanol solvents in predicting the solvatochromic shifts is also discussed.
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A theoretical study of the UV/visible absorption and emission solvatochromic properties of solvent-sensitive dyes.
ChemPhysChem, 2003Co-Authors: Fahmi Himo, Donald Bashford, Alexei Toutchkine, Klaus M. Hahn, Louis NoodlemanAbstract:: 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 amino-coumarin 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. Explict 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.
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Incorporating Protein Environments in Density Functional Theory: A Self-Consistent Reaction Field Calculation of Redox Potentials of [2Fe2S] Clusters in Ferredoxin and Phthalate Dioxygenase Reductase
Journal of Physical Chemistry A, 1998Co-Authors: Jian Li, Donald Bashford, Melanie R. Nelson, Chun Y. Peng, Louis NoodlemanAbstract:An approach to calculating molecular electronic structures of active-site clusters in the presence of protein environments has been developed. The active-site cluster is treated by density functional theory. The protein Field, together with the Reaction Field arising mainly from solvent, is obtained from a finite-difference solution to the Poisson−Boltzmann equation with three dielectric regions, and then these are coupled to the density functional calculation by a Self-Consistent iterative procedure. The method is applied to compute redox potentials of ferredoxin from Anabaena 7120 and phthalate dioxygenase reductase (PDR) from Pseudomonas cepacia, both having similar [Fe2S2(SR)4] active-site clusters. The calculated redox potentials, −1.007 V and −0.812 V in 0.05 M ionic strength for ferredoxin and PDR, respectively, deviate significantly from experimental values of −0.440 and −0.174 V. However, the calculated data reproduce the experimental trend fairly well. The calculated redox potential for PDR is 1...
Manuel F. Ruiz-lópez - One of the best experts on this subject based on the ideXlab platform.
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Study of some hydrogen bonded complexes in polar media using density functional theory and SCRF calculations
AIP Conference Proceedings, 2008Co-Authors: Y. Jeanvoine, Frédéric Bohr, Manuel F. Ruiz-lópezAbstract:The effect of electrostatic interactions on the structure of a series of hydrogen bonded complexes in polar environment is discussed using Density Functional methods and a Self‐Consistent Reaction Field model. Co‐operative effects are analyzed. Comparison with accurate ab initio results show that Density Functional calculations with density gradient corrected exchange‐correlation potentials are very promising to study processes in solution.
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Self-Consistent Reaction Field Calculations of Nonequilibrium Solvent Effects on Proton Transfer Processes through Low-Barrier Hydrogen Bonds
Journal of Physical Chemistry A, 1998Co-Authors: Manuel F. Ruiz-lópez, Antoni Oliva, And I. Tuñón, Juan BertránAbstract:We investigate dynamic solvent effects on proton transfer Reactions in the strongly hydrogen-bonded hydroxyl−water model system by using a Self-Consistent nonequilibrium Reaction Field method. The initial motivation for the present work lies in the results of a recently reported molecular dynamics simulation for the same system in aqueous solution, carried out through combined density functional and molecular mechanics potentials. Such a study has confirmed that proton transfer occurs in an essentially frozen environment and that solvent fluctuations may play a crucial role in the Reaction dynamics. Nevertheless, owing to the use of effective charge water models in molecular dynamics simulations, the effect of solvent electronic polarization, which can be assumed to respond instantaneously to solute charge modifications, cannot be accounted for explicitly. Our main goal in the present study is to analyze such an effect in the effective energy profile instantaneously experienced by the proton, using for th...
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Nonequilibrium solvent effects on the SN2 Reaction using a self‐consistent Reaction Field continuum model based on multipole expansions
Journal of Chemical Physics, 1995Co-Authors: Manuel F. Ruiz-lópez, Daniel Rinaldi, Juan BertránAbstract:A simple model has been developed that allows analysis of nonequilibrium solvent effects on chemical processes. It is based on the use of a self‐consistent Reaction Field approach using a multipole development of the solvation energy and on the separation of the inertial and noninertial polarization of the solvent. The solute’s wave function is computed at the ab initio level. The main advantage with respect to previously reported models is that the inclusion of nonequilibrium or dynamic solvent effects are introduced through the definition of a single solvent coordinate which is related to the chemical system coordinates. Besides, inclusion of polarization effects is straightforward. Results are presented for the SN2 Reaction F−+CH3F→FCH3+F−. The frozen‐solvent hypothesis and the role of solvent fluctuations are discussed. It is shown that the climb to the transition barrier must be preceded by a convenient fluctuation of the solvent so that its inertial polarization component is suitable to solvate the ...
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Importance of electronic and nuclear polarization energy on diastereofacial selectivity of Diels–Alder Reactions in aqueous solution
Journal of The Chemical Society Chemical Communications, 1995Co-Authors: Xavier Assfeld, Manuel F. Ruiz-lópez, J. I. Garcia, Joséa. Mayoral, Luis SalvatellaAbstract:Ab initio calculations at the 6-31G** level using a Self-Consistent Reaction Field continuum model show that electronic and nuclear polarization effects in solution are crucial to explain the stereoselectivity of asymmetric Diels–Alder Reactions.
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Electrostatic solvent effect on the ketene-imine cycloaddition Reaction
Journal of Molecular Structure-theochem, 1993Co-Authors: Xavier Assfeld, Manuel F. Ruiz-lópez, J.a. Sordo, Javier González, Tomás L. SordoAbstract:Abstract The ketene + formaldimine cycloaddition Reaction to give 2-azetidinone has been studied as a model of one of the most interesting methods for the synthesis of β-lactams. The role of the solvent has been analyzed using a Self-Consistent Reaction Field method in which the solvation energy is obtained using a multipole expansion of the molecular charge distribution. Substantial solvent effects are predicted both for the Reaction mechanism and for the Reaction rate. Zero-point energy corrections have been shown to also be important.
Kurt V. Mikkelsen - One of the best experts on this subject based on the ideXlab platform.
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The iterative Self-Consistent Reaction-Field method: The refractive index of pure water
International Journal of Quantum Chemistry, 2010Co-Authors: Kristian O. Sylvester-hvid, Kurt V. Mikkelsen, Mark A. RatnerAbstract:We present different microscopic models for describing electromagnetic properties of condensed phases and the models involve iterative Self-Consistent procedures for calculating the properties. We report calculations of the frequency-dependent refractive index of pure water. We investigate the importance of the first solvation shell and nonequilibrium solvent configurations, and present a procedure for estimating appropriate cavity sizes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 904-913, 2011
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Heterogeneous solvation: An ab initio approach
Journal of Chemical Physics, 2001Co-Authors: Solvejg Jørgensen, Mark A. Ratner, Kurt V. MikkelsenAbstract:A multiconfigurational Self-Consistent Reaction Field (MCSCRF) method is presented for solvation of a molecule on a metal surface. We assume that the molecular system is enclosed in a half-spherical cavity and adsorbed on the surface of a perfect conductor. The half-spherical cavity is embedded in a linear, homogeneous, isotropic dielectric medium. A multiconfigurational Self-Consistent Reaction Field linear response method is presented for calculating frequency dependent polarizabilities as well as electronic excitation energies and transition moments of a solvated molecule on a metal surface.
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Excited state polarizabilities in solution obtained by cubic response theory : Calculations on para-, ortho-, and meta-nitroaniline
Journal of Chemical Physics, 1998Co-Authors: Dan Jonsson, Kristian O. Sylvester-hvid, Hans Ågren, Patrick Norman, Kurt V. MikkelsenAbstract:We show that response theory implemented with a Self-Consistent Reaction Field theory model is a viable approach to simulate excited state polarizabilities of molecules in solution. The excited sta ...
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Theory of hyperfine coupling constants of solvated molecules: Applications involving methyl and ClO2 radicals in different solvents
Journal of Chemical Physics, 1996Co-Authors: Berta Fernández, Rgensen, Ota Bludský, Poul Jo, Ove Christiansen, Kurt V. MikkelsenAbstract:A multiconfiguration self‐consistent Reaction Field method is presented for calculating isotropic hyperfine coupling constants of solvated molecules. The solvent model is based on generalizations of Kirkwood’s model for describing solvation effects. Isotropic hyperfine coupling constants are calculated for the methyl and ClO2 radicals in different solvents.
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Multiconfigurational Self-Consistent Reaction Field theory for nonequilibrium solvation
Journal of Chemical Physics, 1995Co-Authors: Kurt V. Mikkelsen, Hans Ågren, Amary Cesar, Hans Joørgen Aa JensenAbstract:We present multiconfigurational self‐consistent Reaction Field theory and implementation for solvent effects on a solute molecular system that is not in equilibrium with the outer solvent. The approach incorporates two different polarization vectors for studying the influence of the solvent. The solute, an atom, a molecule or a supermolecule, is assumed to be surrounded by a linear, homogeneous medium described by two polarization vector Fields, the optical polarization vector and the inertial polarization vector Fields. The optical polarization vector is always in equilibrium with the actual electronic structure whereas the inertial polarization vector is not necessarily in equilibrium with the actual electronic structure. The electronic structure of the compound is described by a correlated electronic wave function—a multiconfigurational self‐consistent Field (MCSCF) wave function. This wave function is fully optimized with respect to all variational parameters in the presence of the surrounding polariz...