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Journal ArticleDOI

Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model.

30 Apr 2003-Journal of Computational Chemistry (John Wiley & Sons, Ltd)-Vol. 24, Iss: 6, pp 669-681
TL;DR: The conductor‐like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo.
Abstract: The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute A number of test applications are presented to evaluate the performances of the method
Citations
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Journal ArticleDOI
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

13,286 citations

Journal ArticleDOI
TL;DR: The SMD model may be employed with other algorithms for solving the nonhomogeneous Poisson equation for continuum solvation calculations in which the solute is represented by its electron density in real space, including, for example, the conductor-like screening algorithm.
Abstract: We present a new continuum solvation model based on the quantum mechanical charge density of a solute molecule interacting with a continuum description of the solvent. The model is called SMD, where the “D” stands for “density” to denote that the full solute electron density is used without defining partial atomic charges. “Continuum” denotes that the solvent is not represented explicitly but rather as a dielectric medium with surface tension at the solute−solvent boundary. SMD is a universal solvation model, where “universal” denotes its applicability to any charged or uncharged solute in any solvent or liquid medium for which a few key descriptors are known (in particular, dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters). The model separates the observable solvation free energy into two main components. The first component is the bulk electrostatic contribution arising from a self-consistent reaction field treatment that involves the solution of the nonho...

10,945 citations

Journal ArticleDOI
TL;DR: The computed alignments of the molecular orbitals of the different complexes with the band edges of a model TiO(2) nanoparticle provide additional insights into the electronic factors governing the efficiency of dye-sensitized solar cell devices.
Abstract: We report a combined experimental and computational study of several ruthenium(II) sensitizers originated from the [Ru(dcbpyH2)2(NCS)2], N3, and [Ru(dcbpyH2)(tdbpy)(NCS)2], N621, (dcbpyH2 = 4,4‘-dicarboxy-2,2‘-bipyridine, tdbpy = 4,4‘-tridecyl-2,2‘-bipyridine) complexes. A purification procedure was developed to obtain pure N-bonded isomers of both types of sensitizers. The photovoltaic data of the purified N3 and N621 sensitizers adsorbed on TiO2 films in their monoprotonated and diprotonated state, exhibited remarkable power conversion efficiency at 1 sun, 11.18 and 9.57%, respectively. An extensive Density Functional Theory (DFT)−Time Dependent DFT study of these sensitizers in solution was performed, investigating the effect of protonation of the terminal carboxylic groups and of the counterions on the electronic structure and optical properties of the dyes. The calculated absorption spectra are in good agreement with the experiment, thus allowing a detailed assignment of the UV−vis spectral features ...

2,660 citations

Journal ArticleDOI
TL;DR: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided in this paper, covering approximately the last seven years, including developments in density functional theory and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces.
Abstract: A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller–Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr_2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

2,396 citations

Journal ArticleDOI
TL;DR: A continuous surface charge (CSC) approach is introduced that leads to a smooth and robust formalism for the PCM models and achieves a clear separation between "model" and "cavity" which, together with simple generalizations of modern integral codes, is all that is required for an extensible and efficient implementation of thePCM models.
Abstract: Continuum solvation models are appealing because of the simplified yet accurate description they provide of the solvent effect on a solute, described either by quantum mechanical or classical methods. The polarizable continuum model (PCM) family of solvation models is among the most widely used, although their application has been hampered by discontinuities and singularities arising from the discretization of the integral equations at the solute-solvent interface. In this contribution we introduce a continuous surface charge (CSC) approach that leads to a smooth and robust formalism for the PCM models. We start from the scheme proposed over ten years ago by York and Karplus and we generalize it in various ways, including the extension to analytic second derivatives with respect to atomic positions. We propose an optimal discrete representation of the integral operators required for the determination of the apparent surface charge. We achieve a clear separation between “model” and “cavity” which, together with simple generalizations of modern integral codes, is all that is required for an extensible and efficient implementation of the PCM models. Following this approach we are now able to introduce solvent effects on energies, structures, and vibrational frequencies (analytical first and second derivatives with respect to atomic coordinates), magnetic properties (derivatives with respect of magnetic field using GIAOs), and in the calculation more complex properties like frequency-dependent Raman activities, vibrational circular dichroism, and Raman optical activity.

2,033 citations

References
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MonographDOI
12 Dec 2002
TL;DR: In this article, Solvent effects on acid/base equilibria and Tautomeric Equilibria have been investigated in terms of acid-base behavior and specific Solute/Solvent interactions.
Abstract: INTRODUCTION SOLUTE-SOLVENT INTERACTIONS Solutions Intermolecular Forces Solvation Preferential Solvation Micellar Solvation (Solubilization) Ionization and Dissociation CLASSIFICATION OF SOLVENTS Classification of Solvents According to Chemical Constitution Classification of Solvents Using Physical Constants Classification of Solvents in Terms of Acid-Base Behaviour Classification of Solvents in Terms of Specific Solute/Solvent Interactions Classification of Solvents Using Multivariate Statistical Methods SOLVENT EFFECTS ON THE POSITION OF HOMOGENEOUS CHEMICAL EQUILIBRIA General Remarks Solvent Effects on Acid/Base Equilibria Solvent Effects on Tautomeric Equilibria Solvent Effects on other Equilibria SOLVENT EFFECTS ON THE RATES OF HOMOGENEOUS CHEMICAL REACTIONS General Remarks Gas-Phase Reactivities Qualitative Theory of Solvent Effects on Reaction Rates Quantitative Theories of Solvent Effects on Reaction Rates Specific Solvation Effects on Reaction Rates SOLVENT EFFECTS ON THE ABSORPTION SPECTRA OF ORGANIC COMPOUNDS General Remarks Solvent Effects on UV/Vis Spectra Solvent Effects on Infrared Spectra Solvent Effects on Electron Spin Resonance Spectra Solvent Effects on Nuclear Magnetic Resonance Spectra EMPIRICAL PARAMETERS OF SOLVENT POLARITY Linear Gibbs Energy Relationships Empirical Parameters of Solvent Polarity from Equilibrium Measurements Empirical Parameters of Solvent Polarity from Kinetic Measurements Empirical Parameters of Solvent Polarity from Spectroscopic Measurements Empirical Parameters of Solvent Polarity from Other Measurements Interrelation and Application of Solvent Polarity Parameters Multiparameter Approaches SOLVENTS AND GREEN CHEMISTRY Green Chemistry Reduction of Solvent Use Green Solvent Selection Non-Traditional Solvents Outlook APPENDIX: PROPERTIES, PURIFICATION, AND USE OF ORGANIC SOLVENTS Physical Properties Purification of Organic Solvents Spectroscopic Solvents Solvents as Reaction Media Solvents for Recrystallization Solvents for Extraction and Partitioning (Distribution) Solvents for Adsorption Chromatography Solvents for Acid/Base Titrations in Non-Aqueous Media Solvents for Electrochemistry Toxicity of Organic Solvents

5,515 citations


"Energies, structures, and electroni..." refers background in this paper

  • ...(1) means that in infinitely polar liquids, the Figure 1....

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BookDOI
01 Jan 2002
TL;DR: Theoretical basis for the treatment of Solvent Effects in the context of Density Functional Theory R. Bianco, J.T. Hynes and D. Truhlar as mentioned in this paper.
Abstract: Preface. Continuum Solvation Models C.J. Cramer, D.G. Truhlar. Theoretical Basis for the Treatment of Solvent Effects in the Context of Density Functional Theory R. Contreras, et al. Monte Carlo Simulations of Chemical Reactions in Solution A. Gonzalez-Lafont, et al. Computer Simulation for Chemical Systems: From Vacuum to Solution G. Corongiu, et al. Crossing the Transition State in Solution J.T. Hynes. Valence Bond Multistate Approach to Chemical Reactions in Solution R. Bianco, J.T. Hynes. Quantum Theory of Solvent Effects and Chemical Reactions O. Tapia, et al. Index.

177 citations


"Energies, structures, and electroni..." refers background in this paper

  • ...(3) one obtains q S (1)[Sq f( )V], so that...

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  • ...(3) for finite values of is an approximation....

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Book
05 Mar 2001
TL;DR: The structure and function of blue copper proteins, Myoglobin, and protein-DNA interactions in the initiation of transcription: the role of flexibility and dynamics of the TATA recognition sequence and the Tata box binding protein are studied.
Abstract: The structure and function of blue copper proteins, (U. Ryde et al.). Myoglobin (D. Karancsi-Menhard et al.). Mechanisms for enzymatic reaction involviing formation or cleavage of O-O bonds (P.E.M. Siegbahn et al.). Catalytic reactions of radical enzymes (F Himo, L.A. Eriksson). Theoretical studies of coenzyme B12-dependant carbon-skeleton rearrangements (D.M. Smith et al.). Simulations of enzymatic systems: perspectives form Car-Parinello molecular dynamics simulations(P. Carloni, U. Rothlisberger). Computational enzymology: protein tyrosine phospatase reactions (K. Kolmodoin et al.). Monte Carlo simulations of HIV-1 protease binding dynamics and thermodynamics with ensembles of protein conformations: incorporating protein flexibility in decipherine mechanisms of molecular recognition (G.M. Verkhivker et al.). Modelling G-protein coupled receptors (C. Higgs, C.A. Reynolds). Protein-DNA interactions in the initiation of transcription: the role of flexibility and dynamics of the TATA recognition sequence and the TATA box binding protein (N. Pastor, H. Weinstein). A multi-component model for radiation damage to DNA from its components (S.D. Wetmore et al..). New computational strategies for the quantum mechanical study of biological systems in condensed phases (C. Adamo et al.). Modelling enzyme-ligand interactions (M.J. Ramos et al.). The QM/CM approach to enzymatic reactions (A.J. Mulholland). Quinones and quinoidal radicals in photosynthesis (R.A. Wheeler). Author index. Subject index.

56 citations


"Energies, structures, and electroni..." refers background in this paper

  • ...(4)] as a test for the total computed solvation charge....

    [...]