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Jacopo Tomasi

Bio: Jacopo Tomasi is an academic researcher from University of Pisa. The author has contributed to research in topics: Polarizable continuum model & Ab initio. The author has an hindex of 73, co-authored 294 publications receiving 61051 citations. Previous affiliations of Jacopo Tomasi include University of Milan & École Normale Supérieure.


Papers
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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: In this article, a method is presented which utilizes the calculation of the molecular electrostatic potential or the electric field at a discrete number of preselected points to evaluate the environmental effects of a solvent on the properties of a molecular system.

7,618 citations

Journal ArticleDOI
TL;DR: In this paper, a new integral equation formulation of the polarizable continuum model (PCM) is presented, which allows one to treat in a single approach dielectrics of different nature: standard isotropic liquids, intrinsically anisotropic medialike liquid crystals and solid matrices, or ionic solutions.
Abstract: We present a new integral equation formulation of the polarizable continuum model (PCM) which allows one to treat in a single approach dielectrics of different nature: standard isotropic liquids, intrinsically anisotropic medialike liquid crystals and solid matrices, or ionic solutions. The present work shows that integral equation methods may be used with success also for the latter cases, which are usually studied with three-dimensional methods, by far less competitive in terms of computational effort. We present the theoretical bases which underlie the method and some numerical tests which show both a complete equivalence with standard PCM versions for isotropic solvents, and a good efficiency for calculations with anisotropic dielectrics.

5,760 citations

Journal ArticleDOI
TL;DR: In this article, an efficient version of the polarizable continuum solvation model was implemented in the GAUSSIAN94 package, which exploits a new definition of surface elements area, and a direct formulation of the electrostatic self-consistent problem.

2,978 citations


Cited by
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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 “Activation‐strain TS interaction” (ATS) model of chemical reactivity is reviewed as a conceptual framework for understanding how activation barriers of various types of reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis.
Abstract: We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001

8,490 citations

Journal ArticleDOI
TL;DR: A new method, based on chemical thermodynamics, is developed for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments, as found, biological units may be recovered at 80-90% success rate, which makesX-ray crystallography an important source of experimental data on macromolescular complexes and protein-protein interactions.

8,377 citations

Journal ArticleDOI
TL;DR: In this article, a method is presented which utilizes the calculation of the molecular electrostatic potential or the electric field at a discrete number of preselected points to evaluate the environmental effects of a solvent on the properties of a molecular system.

7,618 citations