Barry T. Pickup

Bio: Barry T. Pickup is an academic researcher from University of Sheffield. The author has contributed to research in topics: Propagator & Molecular graph. The author has an hindex of 26, co-authored 92 publications receiving 3517 citations. Previous affiliations of Barry T. Pickup include Uppsala University & AstraZeneca.

Direct calculation of ionization energies

Abstract: The advantages of the propagator formalism, as a direct method of calculating ionization energies, are stressed. The propagator equations are derived for closed-shell systems using an operator method instead of the usual diagrammatic derivations. The equations enable the development of an interpretation of the ionization energies in terms of conceptually simple quantities, such as pair correlation energies and associated relaxation effects, and retain the idea of orbital ionization. Infinite summations appearing in the self-energy terms are replaced by finite expressions involving functions satisfying uncoupled inhomogeneous differential equations. Certain high-order propagator equations are derived, and a connection with the Bethe-Goldstone formulation of pair correlation is made. Several computational procedures are advocated as forming the basis for balanced calculations of atomic and molecular ionization energies.

A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape

Abstract: A Gaussian description of molecular shape is used to compare the shapes of two molecules by analytically optimizing their volume intersection. The method is applied to predict the relative orientation of ligand series binding to the proteins, thrombin, HIV protease, and thermolysin. The method is also used to quantify the degree of chirality of asymmetric molecules and to investigate the chirality of biphenyl and the amino acids. The shape comparison method uses the newly described shape multipoles that can also be used to describe the inherent shape of molecules. Some results of calculated shape quadrupoles are given for the ligands used in this work. © 1996 by John Wiley & Sons, Inc.

A smooth permittivity function for Poisson–Boltzmann solvation methods

Abstract: This work introduces a continuous smooth permittivity function into Poisson–Boltzmann techniques for continuum approaches to modeling the solvation of small molecules and proteins. The permittivity function is derived using a Gaussian method to describe volume exclusion. The new method allows a rigorous determination of solvent forces within a grid-based technology. The generality of approach is demonstrated by considering a range of applications for small molecules and macromolecules. We also present a very complete statistical analysis of grid errors, and show that the accuracy of our Gaussian-based method is improved over standard techniques. The method has been implemented in a new code called ZAP, which is freely available to academic institutions.1 © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 608–640, 2001

Quantum theory of molecular electronic structure

Abstract: With the increasing availability of powerful computers, attempts to calculate the electronic structure and properties of molecules by the direct ab initio solution of a many-body Schrodinger equation have received a great stimulus. The authors review the mainstream developments in quantum chemistry and give a straightforward account of some of the many-body techniques borrowed, with appropriate modifications, from other areas of physics-field theory, nuclear theory and solid-state theory. After a historical introduction, the traditional approach based on the self-consistent field and the method of configuration interaction is developed in detail. This is followed by the introduction of the cluster expansion, various types of correlated electron-pair theory, and diagrammatic perturbation methods. Finally, propagator and Green function techniques are reviewed, not only as a means of calculating transition energies but also as an alternative approach to the determination of the electronic ground state.

PubChem Substance and Compound databases

Abstract: PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.

Role of Frontier Orbitals in Chemical Reactions

Abstract: Since the 3rd century for more than a thousand years chemistry has been thought of as a complicated, hard-to-predict science. Efforts to improve even a part of its unpredictable character are said to have born fruit first of all in the success of the \" electronic theory \". This was founded mainly by organic chemists , such as Fry, Stieglitz, Lucas, Lapworth and Sidgwick, brought to a completed form by Robinson and Ingold, and developed later by many other chemists. 1 In the electronic theory, the mode of migration of electrons in molecules is noted and is considered under various judgements. For that purpose, a criterion is necessary with respect to the number of electrons which should originally exist in an atom or a bond in a molecule. Therefore, it can be said to be the concept by Lewis of the sharing of electrons that has given a firm basis to the electronic theory. 2 In the organic electronic theory, the chemical concepts such as acid and base, oxidation and reduction and so on, have been conveniently utilized from a long time ago. Furthermore, there are terms centring closer around the electron concept, such as electrophilicity and nucleophilicity, and electron donor and acceptor both being pairs of relative concepts. One may be aware that these concepts can be connected qualitatively to the scale of electron density or electric charge. In the electronic theory, the static and dynamic behaviours of molecules are explained by the electronic effects which are based on nothing but the distribution of electrons in a molecule. The mode of charge distribution in a molecule can be sketched to some extent by the use of the electronegativity concept of atoms through organic chemical experience. At the same time, it is given foundation, made quantitative , and supported by physical measurements of electron distribution and theoretical calculations based on quantum theory. The distribution of electrons or electric charge-with either use the result is unchanged-in a molecule is usually represented by the total numbers (generally not integer) of electrons in each atom and each bond, and it was a concept easily acceptable even to empirical chemists as having a tolerably realistic meaning. Therefore, chemists employed the electron density as a fundamental concept to explain or to comprehend various phenomena. In particular, for the purpose of promoting chemical investigations, researchers usually rely upon the analogy through experience, and the electron density …

Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database

Abstract: Here, we present the algorithm and validation for OMEGA, a systematic, knowledge-based conformer generator. The algorithm consists of three phases: assembly of an initial 3D structure from a library of fragments; exhaustive enumeration of all rotatable torsions using values drawn from a knowledge-based list of angles, thereby generating a large set of conformations; and sampling of this set by geometric and energy criteria. Validation of conformer generators like OMEGA has often been undertaken by comparing computed conformer sets to experimental molecular conformations from crystallography, usually from the Protein Databank (PDB). Such an approach is fraught with difficulty due to the systematic problems with small molecule structures in the PDB. Methods are presented to identify a diverse set of small molecule structures from cocomplexes in the PDB that has maximal reliability. A challenging set of 197 high quality, carefully selected ligand structures from well-solved models was obtained using these methods. This set will provide a sound basis for comparison and validation of conformer generators in the future. Validation results from this set are compared to the results using structures of a set of druglike molecules extracted from the Cambridge Structural Database (CSD). OMEGA is found to perform very well in reproducing the crystallographic conformations from both these data sets using two complementary metrics of success.

Integrated Modeling Program, Applied Chemical Theory (IMPACT).

Abstract: We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.

Analysis of Past and Present Synthetic Methodologies on Medicinal Chemistry: Where Have All the New Reactions Gone?

Abstract: An analysis of chemical reactions used in current medicinal chemistry (2014), three decades ago (1984), and in natural product total synthesis has been conducted. The analysis revealed that of the current most frequently used synthetic reactions, none were discovered within the past 20 years and only two in the 1980s and 1990s (Suzuki–Miyaura and Buchwald–Hartwig). This suggests an inherent high bar of impact for new synthetic reactions in drug discovery. The most frequently used reactions were amide bond formation, Suzuki–Miyaura coupling, and SNAr reactions, most likely due to commercial availability of reagents, high chemoselectivity, and a pressure on delivery. We show that these practices result in overpopulation of certain types of molecular shapes to the exclusion of others using simple PMI plots. We hope that these results will help catalyze improvements in integration of new synthetic methodologies as well as new library design.