A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.

General atomic and molecular electronic structure system

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com.

Multiwfn: a multifunctional wavefunction analyzer.

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

Chemistry with ADF

http://theory.cm.utexas.edu/henkelman/pubs/henkelman06_354.pdf

A fast and robust algorithm for Bader decomposition of charge density

The 11th edition of Harrison's Principles of Internal Medicine welcomes Anthony Fauci to its editorial staff, in addition to more than 85 new contributors. While the organization of the book is similar to previous editions, major emphasis has been placed on disorders that affect multiple organ systems. Important advances in genetics, immunology, and oncology are emphasized. Many chapters of the book have been rewritten and describe major advances in internal medicine. Subjects that received only a paragraph or two of attention in previous editions are now covered in entire chapters. Among the chapters that have been extensively revised are the chapters on infections in the compromised host, on skin rashes in infections, on many of the viral infections, including cytomegalovirus and Epstein-Barr virus, on sexually transmitted diseases, on diabetes mellitus, on disorders of bone and mineral metabolism, and on lymphadenopathy and splenomegaly. The major revisions in these chapters and many

Harrison's Principles of Internal Medicine

List of symbols 1. Atoms in chemistry 2. Atoms and the topology of the charge desnity 3. Molecular structure and its change 4. Mathematical models of structural change 5. The quantum atom 6. The mechanics of an atom in a molecule 7. Chemical models and the Laplacian of the charge density 8. The action principle for a quantunm subsystem Appendix - Tables of data Index

Atoms in molecules : a quantum theory

A quantum theory of molecular structure and its applications

Atoms in molecules

The quantum mechanics of proper open systems yields the physics that governs the local behavior of the electron density, ρ(r). The Ehrenfest force F(r) acting on an element of ρ(r) and the virial field ν(r) that determine its potential energy are obtained from equations of motion for the electronic momentum and virial operators, respectively. Each is represented by a “dressed” density, a distribution in real space that results from replacing the property in question for a single electron with a corresponding density that describes its average interaction with all of the remaining particles in the system. All bond paths, lines of maximum density linking neighboring nuclei in a system in stable electrostatic equilibrium, have a common physical origin in terms of F(r) and ν(r), regardless of the nature of the interaction. Each is homeomorphically mirrored by a virial path, a line of maximally negative potential energy density linking the same nuclei. The presence of a bond path and its associated virial path...

A Bond Path: A Universal Indicator of Bonded Interactions

This article describes an algorithm for the calculation of the average properties of an atom in a molecule. The atom is defined within the topological theory of molecular structure, a theory which defines atoms, bonds, structure, and structural stability in terms of the topological properties of a system's charge distribution. The average properties of the atom so defined are uniquely determined by quantum mechanics. Results for a number of hydrocarbon molecules, obtained by the program PROAIM (properties of atoms in molecules) which implements this algorithm, are given. In general, this program enables one to calculate the average energy of an atom in a molecule to an accuracy of ±1 kcal/mol.

Richard F. W. Bader

Papers

Atoms in molecules : a quantum theory

A quantum theory of molecular structure and its applications

Atoms in molecules

A Bond Path: A Universal Indicator of Bonded Interactions

Calculation of the average properties of atoms in molecules. II