Robert B. Murphy

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

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.

A Mixed Quantum Mechanics/Molecular Mechanics (qm/mm) Method for Large-Scale Modeling of Chemistry in Protein Environments

A QM–MM method, using our previously developed frozen orbital QM–MM interface methodolgy, is presented as a general, accurate, and computationally efficient model for studying chemical problems in a protein environment. The method, its parametrization, and a preliminary application to modeling cytochrome P‐450 chemistry are presented.

Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic‐size systems. Employing high‐level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas‐phase many‐body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di‐ and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS‐AA force field. 1 Finally, we have employed the newly developed first‐generation model in computing gas‐phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed‐charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second‐generation model.

Pseudospectral localized Mo/ller–Plesset methods: Theory and calculation of conformational energies

We have developed an algorithm based upon pseudospectral ab initio electronic structure methods for evaluating correlation energies via the localized Mo/ller–Plesset methodology of Pulay and Saebo. Even for small molecules (∼20 atoms) CPU times are diminished by a factor of ∼10 compared to canonical MP2 timings for Gaussian 92 and the scaling is reduced from N4−N5 in conventional methods to ∼N3. We have tested the accuracy of the method by calculating conformational energy differences for 36 small molecules for which experimental data exists, using the Dunning cc‐pVTZ correlation consistent basis set. After removing 6 test cases on the grounds of unreliability of the experimental data, an average deviation with experiment of 0.18 kcal/mol between theory and experiment is obtained, with a maximum deviation of ∼0.55 kcal/mol. This performance is significantly better than that obtained previously with a smaller basis set via canonical MP2; it is also superior to the results of gradient corrected density func...

Frozen orbital QM/MM methods for density functional theory

Abstract We have developed a density functional (DFT) version of our quantum chemistry/molecular mechanics (QM/MM) methodology based on using frozen molecular orbitals as the interface between the QM and MM regions. The methodology is distinguished from previous frozen orbital work by the availability of an accurate analytical gradient for ab initio methods and by the construction of a QM/MM interface capable of reproducing both deprotonation energies and conformational energetics around the frozen bond via fitting of interface parameters to a small model molecule. Results are presented for several test cases, including the alanine tetrapeptide and four amino acid side chains. Excellent agreement between fully QM DFT calculations and the QM/MM calculations is obtained for both conformational energetics and deprotonation energies in all cases.

Pseudospectral localized generalized Mo/ller–Plesset methods with a generalized valence bond reference wave function: Theory and calculation of conformational energies

We describe a new multireference perturbation algorithm for ab initio electronic structure calculations, based on a generalized valence bond (GVB) reference system, a local version of second-order Mo/ller–Plesset perturbation theory (LMP2), and pseudospectral (PS) numerical methods. This PS-GVB-LMP2 algorithm is shown to have a computational scaling of approximately N3 with basis set size N, and is readily applicable to medium to large size molecules using workstations with relatively modest memory and disk storage. Furthermore, the PS-GVB-LMP2 method is applicable to an arbitrary molecule in an automated fashion (although specific protocols for resonance interactions must be incorporated) and hence constitutes a well-defined model chemistry, in contrast to some alternative multireference methodologies. A calculation on the alanine dipeptide using the cc-pVTZ(−f) basis set (338 basis functions total) is presented as an example. We then apply the method to the calculation of 36 conformational energy differ...

AB INITIO QUANTUM CHEMICAL CALCULATION OF ELECTRON TRANSFER MATRIX ELEMENTS FOR LARGE MOLECULES

Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree–Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ∼14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

How iron-containing proteins control dioxygen chemistry: a detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations

Abstract Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C–H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

Pseudospectral contracted configuration interaction from a generalized valence bond reference

A multireference configuration interaction method is presented based upon pseudospectral integration and a novel generalized valence bond referenced contraction procedure. The combination of these approaches is shown to allow for unprecedented multiconfiguration self‐consistent‐field calculations on large molecules.

Accurate quantum chemical calculation of the relative energetics of C20 carbon clusters via localized multireference perturbation calculations

Abstract We present the first correlated ab initio calculations on isomers of C 20 clusters with accurate basis sets using pseudospectral methods. These calculations are in quantitative agreement with the quantum Monte Carlo results and disagree strongly with density functional results.