From Molecular Electrostatic Potentials to Solvation Models and Ending with Biomolecular Photophysical Processes

[1]  F. Javier Luque,et al.  Extension of the MST model to the IEF formalism: HF and B3LYP parametrizations , 2005 .

[2]  Rudolph A. Marcus,et al.  Electrostatic Free Energy and Other Properties of States Having Nonequilibrium Polarization. I , 1956 .

[3]  R. S. Mulliken Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[4]  R. Bonaccorsi,et al.  An approximate expression of the electrostatic molecular potential for benzenic compounds , 1979 .

[5]  Jacopo Tomasi,et al.  A polarizable continuum model for molecules at diffuse interfaces. , 2004, The Journal of chemical physics.

[6]  C. Cramer,et al.  General parameterized SCF model for free energies of solvation in aqueous solution , 1991 .

[7]  J. Tomasi,et al.  Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .

[8]  S. Monti,et al.  Environmental effects on the spectroscopic properties of gallic acid: a combined classical and quantum mechanical study. , 2005, The journal of physical chemistry. A.

[9]  A. Tkatchenko,et al.  On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters. II. The water hexamer and van der Waals interactions. , 2008, The Journal of chemical physics.

[10]  Benedetta Mennucci,et al.  Self-Consistent-Field Calculation of Pauli Repulsion and Dispersion Contributions to the Solvation Free Energy in the Polarizable Continuum Model , 1997 .

[11]  Herbert van Amerongen,et al.  Refractive index dependence of the förster resonance excitation transfer rate , 2002 .

[12]  Jacopo Tomasi,et al.  Molecular SCF Calculations for the Ground State of Some Three‐Membered Ring Molecules: (CH2)3, (CH2)2NH, (CH2)2NH2+, (CH2)2O, (CH2)2S, (CH)2CH2, and N2CH2 , 1970 .

[13]  Roberto Cammi,et al.  Quantum mechanical polarizable continuum model approach to the Kerr effect of pure liquids. , 2005, The journal of physical chemistry. B.

[14]  K. Mikkelsen,et al.  Solvent effects on the n-->pi* electronic transition in formaldehyde: a combined coupled cluster/molecular dynamics study. , 2004, The Journal of chemical physics.

[15]  Chérif F. Matta,et al.  Atomic Charges Are Measurable Quantum Expectation Values: A Rebuttal of Criticisms of QTAIM Charges , 2004 .

[16]  Th. Förster Zwischenmolekulare Energiewanderung und Fluoreszenz , 1948 .

[17]  C. Cramer,et al.  Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. , 1999, Chemical reviews.

[18]  H. Ågren,et al.  Density-functional-theory study of the electric-field-induced second harmonic generation (EFISHG) of push–pull phenylpolyenes in solution , 2006 .

[19]  R. Bonaccorsi,et al.  An approximate expression of the electrostatic molecular potential in terms of completely transferable group contributions , 1977 .

[20]  Luca Frediani,et al.  Solvent effects on Raman optical activity spectra calculated using the polarizable continuum model. , 2006, The journal of physical chemistry. A.

[21]  C. Cramer,et al.  Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges. , 2007, Journal of chemical theory and computation.

[22]  J. Tomasi,et al.  Importance of water in aldol condensation reactions of acetaldehyde , 1994 .

[23]  M. Cho,et al.  Structure of N-acetylproline amide in liquid water: experimentally measured and numerically simulated infrared and vibrational circular dichroism spectra. , 2006, The journal of physical chemistry. B.

[24]  M. Tissandier,et al.  The Proton's Absolute Aqueous Enthalpy and Gibbs Free Energy of Solvation from Cluster-Ion Solvation Data , 1998 .

[25]  Jacopo Tomasi,et al.  Excitation energy transfer (EET) between molecules in condensed matter: a novel application of the polarizable continuum model (PCM). , 2004, Journal of Chemical Physics.

[26]  V. Barone,et al.  Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model , 1998 .

[27]  Jacopo Tomasi,et al.  Theoretical Approach to the Calculation of Vibrational Raman Spectra in Solution within the Polarizable Continuum Model , 2001 .

[28]  S. Xantheas,et al.  Development of transferable interaction models for water. I. Prominent features of the water dimer potential energy surface , 2002 .

[29]  A. Klamt,et al.  COSMO : a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient , 1993 .

[30]  B. Mennucci,et al.  STRUCTURE AND PROPERTIES OF MOLECULAR SOLUTES IN ELECTRONIC EXCITED STATES: A POLARIZABLE CONTINUUM MODEL APPROACH BASED ON THE TIME-DEPENDENT DENSITY FUNCTIONAL THEORY , 2008 .

[31]  J. Tomasi,et al.  Polarizable Continuum Model (PCM) Calculations of Solvent Effects on Optical Rotations of Chiral Molecules , 2002 .

[32]  S. Monti,et al.  Computational study of conformational and chiroptical properties of (2R,3S,4R)-(+)-3,3',4,4',7-flavanpentol. , 2005, Chirality.

[33]  Robert J. Harrison,et al.  Development of transferable interaction models for water. II. Accurate energetics of the first few water clusters from first principles , 2002 .

[34]  J. R. Pliego Thermodynamic cycles and the calculation of pKa , 2003 .

[35]  J. Tomasi,et al.  Modern Theories of Continuum Models , 2007 .

[36]  Kurt V. Mikkelsen,et al.  A multiconfiguration self‐consistent reaction field response method , 1994 .

[37]  J. Tomasi,et al.  Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation , 1991 .

[38]  Mark S. Gordon,et al.  The Effective Fragment Potential Method: A QM-Based MM Approach to Modeling Environmental Effects in Chemistry , 2001 .

[39]  D. L. Dexter A Theory of Sensitized Luminescence in Solids , 1953 .

[40]  Roberto Improta,et al.  Quantum mechanical computations and spectroscopy: from small rigid molecules in the gas phase to large flexible molecules in solution. , 2008, Accounts of chemical research.

[41]  Car,et al.  Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.

[42]  Robert J. Cave,et al.  Generalization of the Mulliken-Hush treatment for the calculation of electron transfer matrix elements , 1996 .

[43]  Rudolph A. Marcus,et al.  On the Theory of Oxidation‐Reduction Reactions Involving Electron Transfer. I , 1956 .

[44]  Jacopo Tomasi,et al.  The ONIOM-PCM method: Combining the hybrid molecular orbital method and the polarizable continuum model for solvation. Application to the geometry and properties of a merocyanine in solution , 2001 .

[45]  Jacopo Tomasi,et al.  Evaluation of the dispersion contribution to the solvation energy. A simple computational model in the continuum approximation , 1989 .

[46]  B. Mennucci,et al.  Ab initio model to predict NMR shielding tensors for solutes in liquid crystals , 2003 .

[47]  Jacopo Tomasi,et al.  Excited states and solvatochromic shifts within a nonequilibrium solvation approach: A new formulation of the integral equation formalism method at the self-consistent field, configuration interaction, and multiconfiguration self-consistent field level , 1998 .

[48]  F. J. Luque,et al.  On the performance of continuum solvation methods. A comment on "Universal approaches to solvation modeling". , 2009, Accounts of chemical research.

[49]  D. Chipman Energy correction to simulation of volume polarization in reaction field theory , 2002 .

[50]  L. Onsager Electric Moments of Molecules in Liquids , 1936 .

[51]  R. Pierotti,et al.  A scaled particle theory of aqueous and nonaqueous solutions , 1976 .

[52]  C. Ghio,et al.  On the acidic properties of compounds with CC or NN electrophilic double bonds , 1986 .

[53]  Jean-Louis Rivail,et al.  A quantum chemical approach to dielectric solvent effects in molecular liquids , 1976 .

[54]  D. Andrews,et al.  A QED theory of intermolecular energy transfer in dielectric media , 1994 .

[55]  J. Tomasi,et al.  Time‐dependent variational principle for nonlinear Hamiltonians and its application to molecules in the liquid phase , 1996 .

[56]  S. Mukamel,et al.  Bacteriochlorophyll and Carotenoid Excitonic Couplings in the LH2 System of Purple Bacteria , 2000 .

[57]  Gregory D Scholes,et al.  Long-range resonance energy transfer in molecular systems. , 2003, Annual review of physical chemistry.

[58]  C. Ghio,et al.  A Reappraisal of the Hydrogen Bonding Interaction Obtained by Combining Energy Decomposition Analyses and Counterpoise Corrections , 1988 .

[59]  Kazuo Kitaura,et al.  A new energy decomposition scheme for molecular interactions within the Hartree‐Fock approximation , 1976 .

[60]  Jacopo Tomasi,et al.  Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent , 1994 .

[61]  Robert Moszynski,et al.  Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes , 1994 .

[62]  C. Curutchet,et al.  Towards a molecular scale interpretation of excitation energy transfer in solvated bichromophoric systems. II. The through-bond contribution. , 2007, The journal of physical chemistry. B.

[63]  B. Mennucci Hydrogen bond versus polar effects: an ab initio analysis on n --> pi* absorption spectra and N nuclear shieldings of diazines in solution. , 2002, Journal of the American Chemical Society.

[64]  C. Cramer,et al.  Reply to Comment on “A Universal Approach to Solvation Modeling” , 2009 .

[65]  C. O. D. Silva,et al.  Ab Initio Calculations of Absolute pKa Values in Aqueous Solution I. Carboxylic Acids , 1999 .

[66]  M. Newton,et al.  Solvent Reorganization and Donor/Acceptor Coupling in Electron-Transfer Processes: Self-Consistent Reaction Field Theory and ab Initio Applications , 1995 .

[67]  Roberto Cammi,et al.  Continuum Solvation Models in Chemical Physics , 2007 .

[68]  Johannes Neugebauer,et al.  Comparison of frozen-density embedding and discrete reaction field solvent models for molecular properties. , 2006, Physical chemistry chemical physics : PCCP.

[69]  J. Tomasi,et al.  Towards the elaboration of a QM method to describe molecular solutes under the effect of a very high pressure , 2008 .

[70]  M. Newton,et al.  The multi-configurational adiabatic electron transfer theory and its invariance under transformations of charge density basis functions , 1994 .

[71]  Thanh N. Truong,et al.  Optimized atomic radii for quantum dielectric continuum solvation models , 1995 .

[72]  Richard A. Friesner,et al.  Constructing ab initio force fields for molecular dynamics simulations , 1998 .

[73]  Richard A. Friesner,et al.  Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method , 1996 .

[74]  J. Tomasi,et al.  Refinements on solvation continuum models: Hydrogen-bond effects on the OH stretch in liquid water and methanol , 2000 .

[75]  Ji-Min Yan,et al.  Point-Charge Models for Molecules Derived from Least-Squares Fitting of the Electric Potential , 1988 .

[76]  Graham R. Fleming,et al.  Excitation energy transfer in condensed media , 2001 .

[77]  G. Karlström,et al.  A theoretical study of the solvent shift to the transition in formaldehyde with an effective discrete quantum chemical solvent model including non-electrostatic perturbation , 2006 .

[78]  Yang Song,et al.  Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method. , 2008, The Journal of chemical physics.

[79]  F. Weinhold,et al.  Natural population analysis , 1985 .

[80]  Jacopo Tomasi,et al.  Dispersion and repulsion contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches in the polarizable continuum model , 2006, J. Comput. Chem..

[81]  T. Vreven,et al.  Density functional study of the optical rotation of glucose in aqueous solution. , 2004, The Journal of organic chemistry.

[82]  Jacopo Tomasi,et al.  How solvent controls electronic energy transfer and light harvesting. , 2007, The journal of physical chemistry. B.

[83]  Jacopo Tomasi,et al.  An Integrated Effective Fragment—Polarizable Continuum Approach to Solvation: Theory and Application to Glycine , 2002 .

[84]  J. Tomasi,et al.  Nonequilibrium formulation of infrared frequencies and intensities in solution: Analytical evaluation within the polarizable continuum model , 2000 .

[85]  Jacopo Tomasi,et al.  On the Calculation of Infrared Intensities in Solution within the Polarizable Continuum Model , 2000 .

[86]  Donald Bashford,et al.  An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules , 1997, ISCOPE.

[87]  Jacopo Tomasi,et al.  MEP: a tool for interpretation and prediction. From molecular structure to solvation effects , 1996 .

[88]  M. V. Basilevsky,et al.  Quantum-chemical evaluation of energy quantities governing electron transfer kinetics: applications to intramolecular processes , 1996 .

[89]  Jiali Gao,et al.  Solvatochromic Shifts of the n → π* Transition of Acetone from Steam Vapor to Ambient Aqueous Solution:  A Combined Configuration Interaction QM/MM Simulation Study Incorporating Solvent Polarization. , 2007, Journal of chemical theory and computation.

[90]  Feliu Maseras,et al.  IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states , 1995, J. Comput. Chem..

[91]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[92]  C. Curutchet,et al.  Self-consistent quantum mechanical model for the description of excitation energy transfers in molecules at interfaces. , 2006, The Journal of chemical physics.

[93]  B. Mennucci,et al.  Modeling the solvation of peptides. The case of (s)-N-acetylproline amide in liquid water. , 2008, The journal of physical chemistry. B.

[94]  Frank A. Momany,et al.  Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid , 1978 .

[95]  M. Vener,et al.  An advanced dielectric continuum approach for treating solvation effects: Time correlation functions. I. Local treatment , 1998 .

[96]  B. Honig,et al.  New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects , 1996 .

[97]  C. Curutchet,et al.  Toward a molecular scale interpretation of excitation energy transfer in solvated bichromophoric systems. , 2005, Journal of the American Chemical Society.

[98]  R. Taft,et al.  The solvatochromic comparison method. 6. The .pi.* scale of solvent polarities , 1977 .

[99]  J. Tomasi,et al.  Quantum mechanical continuum solvation models. , 2005, Chemical reviews.

[100]  M. Newton,et al.  Quantum chemical probes of electron-transfer kinetics: the nature of donor-acceptor interactions , 1991 .

[101]  J. Tomasi,et al.  Electronic and vibrational dynamic solvent effects on Raman spectra , 2001 .

[102]  Andrews,et al.  Quantum electrodynamics of resonant energy transfer in condensed matter. , 1994, Physical review. B, Condensed matter.

[103]  Harold L. Friedman,et al.  Green function theory of charge transfer processes in solution , 1988 .

[104]  S. Monti,et al.  Effect of the environment on vibrational infrared and circular dichroism spectra of (s)‐proline , 2005 .

[105]  M. Rostkowski,et al.  Influence of the solvent description on the predicted mechanism of SN2 reactions. , 2008, The journal of physical chemistry. B.

[106]  M. Nascimento,et al.  Ab Initio Calculations of Absolute pKa Values in Aqueous Solution II. Aliphatic Alcohols, Thiols, and Halogenated Carboxylic Acids , 2000 .

[107]  Jan H. Jensen,et al.  Continuum solvation of large molecules described by QM/MM: a semi-iterative implementation of the PCM/EFP interface , 2003 .

[108]  Jan H. Jensen,et al.  Prediction and rationalization of protein pKa values using QM and QM/MM methods. , 2005, The journal of physical chemistry. A.

[109]  J. Tomasi,et al.  Ab initio study of ionic solutions by a polarizable continuum dielectric model , 1998 .

[110]  Jacopo Tomasi,et al.  Vibrational circular dichroism within the polarizable continuum model: a theoretical evidence of conformation effects and hydrogen bonding for (S)-(-)-3-butyn-2-ol in CCl4 solution , 2002 .

[111]  Jacopo Tomasi,et al.  A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics , 1997 .

[112]  C. Cramer,et al.  A universal approach to solvation modeling. , 2008, Accounts of chemical research.

[113]  Chérif F Matta,et al.  An experimentalist's reply to "What is an atom in a molecule?". , 2006, The journal of physical chemistry. A.

[114]  Roberto Cammi,et al.  How solvent controls electronic energy transfer and light harvesting: toward a quantum-mechanical description of reaction field and screening effects. , 2007, The journal of physical chemistry. B.