Peter J. Knowles

Bio: Peter J. Knowles is an academic researcher from Cardiff University. The author has contributed to research in topics: Configuration interaction & Coupled cluster. The author has an hindex of 48, co-authored 144 publications receiving 23977 citations. Previous affiliations of Peter J. Knowles include University of Sussex & University of Western Ontario.

An efficient internally contracted multiconfiguration–reference configuration interaction method

Abstract: A new internally contracted direct multiconfiguration–reference configuration interaction (MRCI) method is described which allows the use of much larger reference spaces than any previous MRCI method. The configurations with two electrons in the external orbital space are generated by applying pair excitation operators to the reference wave function as a whole, while the singly external and internal configurations are standard uncontracted spin eigenfunctions. A new efficient and simple method for the calculation of the coupling coefficients is used, which is well suited for vector machines, and allows the recalculation of all coupling coefficients each time they are needed. The vector H⋅c is computed partly in a nonorthogonal configuration basis. In order to test the accuracy of the internally contracted wave functions, benchmark calculations have been performed for F−, H2O, NH2, CH2, CH3, OH, NO, N2, and O2 at various geometries. The deviations of the energies obtained with internally contracted and uncontracted MRCI wave functions are mostly smaller than 1 mH and typically 3–5 times smaller than the deviations between the uncontracted MRCI and the full CI. Dipole moments, electric dipole polarizabilities, and electronic dipole transition moments calculated with uncontracted and contracted MRCI wave functions also are found to be in close agreement. The efficiency of the method is demonstrated in large scale calculations for the CN, NH3, CO2, and Cr2 molecules. In these calculations up to 3088 reference configurations and up to 154 orbitals were employed. The biggest calculation is equivalent to an uncontracted MRCI with more than 78 million configurations.

Molpro: a general-purpose quantum chemistry program package

Abstract: Molpro (available at http://www.molpro.net) is a general-purpose quantum chemical program. The original focus was on high-accuracy wave function calculations for small molecules, but using local approximations combined with explicit correlation treatments, highly accurate coupled-cluster calculations are now possible for molecules with up to approximately 100 atoms. Recently, multireference correlation treatments were also made applicable to larger molecules. Furthermore, an efficient implementation of density functional theory is available.

A second order multiconfiguration SCF procedure with optimum convergence

Abstract: An MCSCF procedure is described which is based on the direct minimization of an approximate energy expression which is periodic and correct to second order in the changes in the orthonormal orbitals Within this approximation, the CI coefficients are fully optimized, thereby accounting for the coupling between orbital rotations and CI coefficients to higher order than in previous treatments Additional transformations among the internal orbitals and their associated one‐ and two‐electron integrals are performed which amounts to treating the rotations among internal orbitals to higher than second order These extra steps are cheap compared to the four index transformation performed in each iteration, but lead to a remarkable enhancement of convergence and overall efficiency In all calculations attempted to date, convergence has been achieved in at most three iterations The energy has been observed to converge better than quadratically from the first iteration even when the initial Hessian matrix has many negative eigenvalues

General atomic and molecular electronic structure system

Abstract: 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.

The HITRAN 2008 molecular spectroscopic database

Abstract: This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Abstract: The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net .

Accurate Coulomb-fitting basis sets for H to Rn

Abstract: A series of auxiliary basis sets to fit Coulomb potentials for the elements H to Rn (except lanthanides) is presented. For each element only one auxiliary basis set is needed to approximate Coulomb energies in conjunction with orbital basis sets of split valence, triple zeta valence and quadruple zeta valence quality with errors of typically below ca. 0.15 kJ mol−1 per atom; this was demonstrated in conjunction with the recently developed orbital basis sets of types def2-SV(P), def2-TZVP and def2-QZVPP for a large set of small molecules representing (nearly) each element in all of its common oxidation states. These auxiliary bases are slightly more than three times larger than orbital bases of split valence quality. Compared to non-approximated treatments, computation times for the Coulomb part are reduced by a factor of ca. 8 for def2-SV(P) orbital bases, ca. 25 for def2-TZVP and ca. 100 for def2-QZVPP orbital bases.

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

Abstract: Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side-chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha-helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side-chain torsion potentials of these residues to match new, high-level quantum-mechanical calculations. Finally, we used microsecond-timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side-chain conformations. The new force field, which we have termed Amber ff99SB-ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley-Liss, Inc.