It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.

Effect of the damping function in dispersion corrected density functional theory

Describes and discusses the use of theoretical models as an alternative to experiment in making accurate predictions of chemical phenomena. Addresses the formulation of theoretical molecular orbital models starting from quantum mechanics, and compares them to experimental results. Draws on a series of models that have already received widespread application and are available for new applications. A new and powerful research tool for the practicing experimental chemist.

AB INITIO Molecular Orbital Theory

The interpretation of protein structures: estimation of static accessibility.

Encoding and decoding hydrogen-bond patterns of organic compounds

Before we start, we need a working definition for MOPAC. The following description has been used many times to describe MOPAC: MOPAC is a general-purpose, semiempirical molecular orbital program for the study of chemical reactions involving molecules, ions, and linear polymers. It implements the semiempirical Hamiltonians MNDO, AM 1, MINDO/3, and MNDOPM3, and combir_es the calculations of vibrational spectra, thermodynamic quantities, isotopic substitution effects, and force constants in a fully integrated program. Elements parameterized at the MNDO level include H, Li, Be, B, C, N, O, F, A1, Si, P, S, C1, Ge, Br, Sn, Hg, Pb, and I; at the PM3 level the elements H, C, N, O, F, A1, Si, P, S, C1, Br, and I are available. Within the electronic part of the calculation, molecular and localized orbitals, excited states up to sextets, chemical bond indices, charges, etc. are computed. Both intrinsic and dynamic reaction coordinates can be calculated. A transition-state location routine and two transition-state optimizing routines are available for studying chemical reactions.

MOPAC: A semiempirical molecular orbital program

The Structures of the Elements

Base pairing in DNA.

Publisher Summary This chapter discusses the crystal structure studies of amino acids and peptides. It describes the structures, as elucidated by single-crystal X-ray investigations, of the crystalline amino acids and peptides. The chapter also deals with the powers and limitations of present-day X-ray diffraction techniques. This chapter illustrates that in earlier times only two amino acids and DL-alanine, one Dipeptide, and one cyclic dipeptide has been investigated, and these by X-ray diffraction techniques that were crude by present-day standards. Moreover, the conclusions drawn from these early investigations—that resulted in the formulation of the stable configurations of polypeptide chains—including the a-helix and the pleated sheet and in the derivation of detailed structures for many fibrous proteins are valid. Moreover, the advent of high-speed digital computers has been responsible for a tremendous improvement in the accuracy of crystal-structure investigations; moreover, it has resulted in a parallel increase in the complexity of the molecules.

Jerry Donohue

Papers

The Structures of the Elements

Base pairing in DNA.

Crystal structure studies of amino acids and peptides.

A three-dimensional refinement of the crystal structure of 4-nitroaniline

Critical evaluation of chemical and physical structural information.