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

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Quantum mechanical continuum solvation models.

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

A new molecular mechanics force field, the Universal force field (UFF), is described wherein the force field parameters are estimated using general rules based only on the element, its hybridization, and its connectivity. The force field functional forms, parameters, and generating formulas for the full periodic table are presented

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org
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Open Babel: An open chemical toolbox

A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

The application of a Universal force field (UFF) to the treatment of organic molecules is described. The ability of the force field to predict the structures of a variety of organic molecules is examined, and the results are compared with the MM2 or MM3 force fields. UFF correctly predicts the structures of unstrained and uncongested hydrocarbons, silanes, alkenes, saturated amines, saturated ethers and phosphines, aromatic systems, and simple unconjugated multiple bond containing compounds such as nitriles, ketones, and imines well

Application of a universal force field to organic molecules

The ability of a universal force field (UFF) to reproduce the structures of a variety of metal-containing molecules is examined. M-C bond distances are well reproduced, and errors in M-Y polar covalent bond distances are generally less than 0.05 A. Use of half-integer bond orders to take into account π back-bonding and the trans influence leads to errors of less than 0.05 A in bond distances for these complexes. Errors on the order of 0.15 A remain for high-valent-metal to halogen bond distances

Application of a universal force field to metal complexes

The ability of a Universal force field (UFF) to reproduce the structures of a variety of main group molecules is examined. The magnitude of bond distance errors for main group compounds are somewhat larger than for organic compounds, though X-C bond distances are well reproduced. Bond distance errors for X-Y polar covalent bonds are generally less than 0.05 A. Comparable bond length errors are observed for hypervalent X-O and X-N bonds (errors on the order of 0.05 A) and dative bonds (errors as large as 0.04 A). The error in bond length for bonds involving centers with multiple electronegative substituents bound to an electropositive center approaches 0.1 A

K. S. Colwell

Papers

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

Application of a universal force field to organic molecules

Application of a universal force field to metal complexes

Application of a universal force field to main group compounds

Application of a Universal Force Field to Organic Molecules