Daniel T. Mainz

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.

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

We have developed a polarizable force field for peptides, using all-atom OPLS (OPLS-AA) nonelectrostatic terms and electrostatics based on a fluctuating charge model and fit to ab initio calculations of polarization responses. We discuss the fitting procedure, and specific techniques we have developed that are necessary in order to obtain an accurate, stable model. Our model is comparable to the best existing molecular mechanics force fields in reproducing quantum-chemical peptide energetics. It also accurately reproduces many-body effects in many cases. We believe that straightforward extensions of our linear-response electrostatic model will significantly improve the accuracy for those cases that the present model does not adequately address.

New pseudospectral algorithms for electronic structure calculations: Length scale separation and analytical two‐electron integral corrections

We describe improved algorithms for carrying out pseudospectral Hartree–Fock calculations; these algorithms are applicable to other ab initio electronic structure methodologies as well. Absolute energies agree with conventional basis set codes to within 0.25 kcal/mol, and relative energies agree to better than 0.1 kcal/mol for a wide variety of test molecules. Accelerations of CPU times of as large as a factor of 6.5 are obtained as compared to GAUSSIAN 92, with the actual timing advantage increasing for larger basis sets and larger molecules. The method is shown to be highly reliable and capable of handling extended basis sets.

Multiscale modeling and simulation methods with applications to dendritic polymers

Abstract Dendrimers and hyperbranched polymers represent a novel class of structurally controlled macromolecules derived from a branches-upon-branches structural motif. The synthetic procedures developed for dendrimer preparation permit nearly complete control over the critical molecular design parameters, such as size, shape, surface/interior chemistry, flexibility, and topology. Dendrimers are well defined, highly branched macromolecules that radiate from a central core and are synthesized through a stepwise, repetitive reaction sequence that guarantees complete shells for each generation, leading to polymers that are mono-disperse. This property of dendrimers makes it particularly natural to coarsen interactions in order to simulate dynamic processes occurring at larger length and longer time scales. In this paper, we describe methods to construct 3-dimensional molecular structures of dendrimers (Continuous Configuration Boltzmann Biased direct Monte Carlo, CCBB MC) and methods towards coarse graining dendrimer interactions (NEIMO and hierarchical NEIMO methods) and representation of solvent dendrimer interactions through continuum solvation theories, Poisson–Boltzmann (PB) and Surface Generalized Born (SGB) methods. We will describe applications to PAMAM, stimuli response hybrid star-dendrimer polymers, and supra molecular assemblies crystallizing to A15 colloidal structure or Pm6m liquid crystals.

Extension of the PS-GVB electronic structure code to transition metal complexes

We have developed a parameterization enabling ab initio electronic structure calculation via the PS‐GVB program on transition‐metal‐containing systems using two standard effective core potential basis sets. Results are compared with Gaussian‐92 for a wide range of complexes, and superior performance is demonstrated with regard to computational efficiency for single‐point energies and geometry optimization. Additionally, the initial guess strategy in PS‐GVB is shown to provide considerably more reliable convergence to the ground state. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1863–1874, 1997

Recent Advances in Simulation of Dendritic Polymers

Dendrimers and hyperbranched polymers represent a revolution in methodology for directed synthesis of monodisperse polymers with enormous possibility of novel architectures. They demonstrate the ability to attain micelle-like structures with distinct internal and external character. Furthermore, the polyfunctional character of dendrimers allows varied response to environment and promise as selective sensors, carrier for drugs, encapsulation of toxic chemicals and metals. One of the key problems is the characterization of the structures. Theory and simulation can be essential to provide and predict structure and properties. We present some recent advances in theory, modeling and simulation of dendritic polymers.

Application of lightweight threading techniques to computational chemistry

The recent advent of inexpensive commodity multiprocessor computers with standardized operating system support for lightweight threads provides computational chemists and other scientists with an exciting opportunity to develop sophisticated new approaches to materials simulation. We contrast the flexible performance characteristics of lightweight threading with the restrictions of traditional scientific supercomputing, based on our experiences with multithreaded molecular dynamics simulation. Motivated by the results of our molecular dynamics experiments, we propose an approach to multi-scale materials simulation using highly dynamic thread creation and synchronization within and between concurrent simulations at many different scales. This approach will enable extremely realistic simulations, with computing resources dynamically directed to areas where they are needed. Multi-scale simulations of this kind require large amounts of processing power, but are too sophisticated to be expressed using traditional supercomputing programming models. As a result, we have developed a high-level programming system called Sthreads that allows highly dynamic, nested multithreaded algorithms to be expressed. Program development is simplified through the use of innovative synchronization operations that allow multithreaded programs to be tested and debugged using standard sequential methods and tools. For this reason, Sthreads is very well suited to the complex multi-scale simulation applications that we are developing.