Computational chemistry on a PC

We describe a package of some IBM PC programs that may find application in computer-aided molecular design. PCGEOM constructs and visualizes molecular models from bond lengths, bond angles, and dihedral angles, from Cartesian coordinates, or from stored fragments. It may prepare output files to be used as input for other programs, like CNDOB (conventional CNDO /2) or PCMEP using the bond increment (BI ) method for the calculation of molecular electrostatic potentials. PCPROT is in preparation and will use Protein Data Bank coordinates to visualize and manipulate protein molecular models. Starting from these, it will calculate electrostatic potentials using the BI method and/or monopoles adjusted to reproduce ab initio values for amino acid residues. FSCF is based on a CNDO -type approximation and uses strictly localized molecular orbitals in order to partition large molecules into a central fragment, a polarizable region, and a fully transferable environment. The partition allows one to handle relatively large systems with up to 200 atoms. To illustrate applications, we present estimation of relative inhibitory potencies of a series of substituted triazines on chicken liver dihydrofolate reductase.     

Computational chemistry at Janssen

Computer-aided drug discovery activities at Janssen are carried out by scientists in the Computational Chemistry group of the Discovery Sciences organization. This perspective gives an overview of the organizational and operational structure, the science, internal and external collaborations, and the impact of the group on Drug Discovery at Janssen.     

Quantum chemistry simulation on quantum computers: theories and experiments

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.     

Computational chemistry and cheminformatics: an essay on the future

Computers have changed the way we do science. Surrounded by a sea of data and with phenomenal computing capacity, the methodology and approach to scientific problems is evolving into a partnership between experiment, theory and data analysis. Given the pace of change of the last twenty-five years, it seems folly to speculate on the future, but along with unpredictable leaps of progress there will be a continuous evolution of capability, which points to opportunities and improvements that will certainly appear as our discipline matures.     

Recent applications of digital computers in analytical chemistry

Minicomputers are finding increasing use for the control and operation of analytical instruments. This role is likely to be shared in the near future with dedicated microcomputers. Applications of computers to electroanalytical chemistry, Fourier transform techniques, spectroscopy, rapid-reaction kinetics, equilibrium constants, studies of analytical methods and to literature searching, are also discussed.     

第十五华沙国际金属有机化学讨论会

本文从(一)金属有机化合物的合成、结构及反应性的研究、(二)新颖、独特和官能化配体的研究、(三)金属原子簇合物化学、(四)催化、(五)有机硅化学、(六)其他研究领域等六个方面做了阐述。本届讨论会较全面地体现了从上届会议以来国际金属有机化学的研究进展及发展趋势。这届会议的成功举行,不仅强化了各国金属有机化学家间的学术交流而且增进了各国人民之间的友好情谊。     

Computational enzymatic catalysis - clarifying enzymatic mechanisms with the help of computers

Enzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in life. However, despite their critical role in nature, attaining a clear understanding of the way an enzyme acts, i.e. its catalytic mechanism, is a cumbersome task that requires the cooperative efforts of a large number of different scientific techniques. Computational methods offer a particularly insightful way to study such mechanisms, always beautifully complementing the information arising from experimental techniques and working as an excellent alternative for assessing the viability of different mechanistic proposals. This review highlights two important computational strategies to study enzymatic catalysis - the cluster modeling approach and the hybrid quantum mechanical/molecular mechanical (QM/MM) method - complemented with a selection of hand-picked examples of our own work.     

Extracting more than a few eigenvectors from a dense real symmetric matrix: Optimal algorithms versus the architectural constraints of the FPS-X64

Ten widely available sets of routines, including HQRII, QCPE GIVENS and EISPACK 3, were evaluated for reliability, robustness, accuracy, speed, compactness, portability and simplicity. All were found lacking in one or more areas. Modified versions of the EISPACK routines TRED3, TQLRAT, TINVIT and TRBAK3 performed somewhat better. Changes to TINVIT were especially important for improved speed, accuracy and reliability. To achieve the maximum capabilities of the FPS-X64 series of computers access to table memory is required, but since the FORTRAN compiler does not allow this and there is no library support for the required operations, it was necessary to write three routines in APAL. The standard algorithm needs to be modified before full efficiency can be achieved for the back transformation.Operated for the US Department of Energy by Iowa State University under contract no. W-74-05-ENG-82. This work was supported by the Office of Basic Energy Sciences     

Computational study of the chemistry of 3-phenylpropyl radicals

Density functional theory (DFT) and G3-type (G3(MP2)-RAD) composite calculations were performed on a series of substituted 3-phenylpropyl radicals, to determine the relative importance of fragmentation and cyclization reactions in the chemistry of such species. Our studies indicate that cyclization is generally the more important of these reactions, with exceptions where fragmentation yields highly stabilized benzylic species. The energetic barriers for the cyclization reactions (enthalpies of activation) were found to be determined largely by the stability of the reactant radical and to a lesser but significant extent, by steric factors. Polarity effects in the transition state (modeled by SOMO-LUMO gaps of the products) appear to be less important. The data obtained indicated that the addition of benzyl radical to alkenes may be considered to be irreversible, but calculations for α-substituted styrenic systems indicate that reversibility of addition may become a factor in dilute polymerizing solutions for select systems.     

Computational insights into the acceptor chemistry of phosphenium cations

Phosphines are traditionally considered as Lewis bases or ligands in transition metal and main group complexes. Despite their electron-rich (lone pair-bearing) nature, an extensive coordination chemistry for Lewis acidic phosphorus centers is being developed; such chemistry provides a new synthetic approach for phosphorus-element bond formation, leading to new types of structures and modes of bonding. Complexes of Ph2P+ with a variety of donor elements (P, N, C) give experimentally short donor-acceptor bond lengths, when compared to other cationic phosphorus Lewis acid complexes. We have calculated that the energy of the lowest unoccupied molecular orbital (LUMO) in Ph2P+ is lower than that of (Me2N)2P+, which partially explains the greater exothermicity of reactions of donors with the diaryl acceptor. Furthermore, the energies required to distort the diphenylphosphenium cation from its ground-state geometry are significantly smaller than those of the diamido cations and, thus, enhance the exothermicity of donor coordination. These computational data, in conjunction with evidence from experimental solid-state structures, indicate that Ph2P+ is a significantly better Lewis acid relative to the more common diaminophosphenium analogues (R2N)2P+ and are used to elucidate the nature of the bonding in donor-phosphenium complexes.     

Computational chemistry in pharmaceutical research: at the crossroads

Computational approaches are an integral part of pharmaceutical research. However, there are many of unsolved key questions that limit the scientific progress in the still evolving computational field and its impact on drug discovery. Importantly, a number of these questions are not new but date back many years. Hence, it might be difficult to conclusively answer them in the foreseeable future. Moreover, the computational field as a whole is characterized by a high degree of heterogeneity and so is, unfortunately, the quality of its scientific output. In light of this situation, it is proposed that changes in scientific standards and culture should be seriously considered now in order to lay a foundation for future progress in computational research.     

Computational chemistry in drug lead discovery and design

The main contributions of our group during the last 15 years developing and using biomolecular simulation tools in drug lead discovery and design, in close collaboration with experimental researchers, are presented. Special emphasis has been given to methodological improvements in the following areas: (1) target homology modeling incorporating knowledge about known ligands to accurately characterize the binding site; (2) designing alternative strategies to account for protein flexibility in high-throughput docking; (3) development of stochastic- and normal-mode-based methods to de novo design structurally diverse protein conformers; (4) development and validation of quantum mechanical semi-empirical linear-scaling calculations to correctly estimate ligand binding free energy. Several successful cases of computer-aided drug discovery are also presented, especially our recent work on viral targets.     

Computational chemistry and molecular simulations of phosphoric acid

Quantum mechanics (QM) calculations, molecular dynamics (MD) simulations using the condensed‐phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field, and the atom‐centered density matrix propagation (ADMP) approach have been used to investigate properties of phosphoric acid (PA). QM using B3LYP/6‐31++G(d,p) density functional theory were used to calculate gas‐phase proton affinities and interaction energies of PA and its derivatives. Detailed single coordinate driving, followed by quadratic synchronous transit optimization was used to determine energy barriers for different proton transfer (PT) pathways. Determined energy barrier heights in ascending order are (unit: kJ/mol): H₃O⁺→H₃PO₄ (0); H₄P₂O₇→H₃PO₄ (2.61); H₃PO₄→H₂PO (5.31); H₄PO→H₃PO₄ (～7.33); H₃PO₄→H₄P₂O₇/H₃PO₄→H₃PO₄ (15.99); H₄P₂O₇→H₂O (28.61); H₃PO₄→H₂O (47.14). The COMPASS force field was used to study condensed‐phase properties of PA. Good agreement between experimental data and MD results including density, radial distribution functions, and self‐diffusion coefficient at different temperatures provides validation of the COMPASS force field for PA. Finally, preliminary ADMP studies on a cluster of three PA molecules shows that the ADMP approach can reasonably describe the PT and self‐dissociation processes in PA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011