Showing papers by "Richard A. Friesner published in 1997"

Accurate ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields

Abstract: Correlated ab initio calculations have been carried out with a parallel version of the PSGVB electronic structure code to obtain relative energetics of a number of conformations of the alanine tetrapeptide. The highest level of theory utilized, local MP2 with the cc-pVTZ(−f) correlation-consistent basis set, has previously been shown to provide accurate conformational energies in comparison with experiment for a data set of small molecules. Comparisons with published and new canonical MP2 calculations on the alanine dipeptide are made. Results for ten gas-phase tetrapeptide conformations and a β-sheet dipeptide dimer are compared with 20 different molecular mechanics force field parametrizations, providing the first assessment of the reliability of these models for systems larger than a dipeptide. Comparisons are made with the LMP2/cc-pVTZ(−f) results, which are taken as a benchmark for the tetrapeptides. Statistical summaries with regard to energetics and structure are produced for each force field, and ...

Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation

Abstract: We have compared solvation free energies obtained from a number of approximate solvation models with an accurate solution of the Poisson−Boltzmann equation for a large data set of peptide structure...

Numerical solution of the Poisson–Boltzmann equation using tetrahedral finite-element meshes

Abstract: The automatic three-dimensional mesh generation system for molecular geometries developed in our laboratory is used to solve the Poisson–Boltzmann equation numerically using a finite element method. For a number of different systems, the results are found to be in good agreement with those obtained in finite difference calculations using the DelPhi program as well as with those from boundary element calculations using our triangulated molecular surface. The overall scaling of the method is found to be approximately linear in the number of atoms in the system. The finite element mesh structure can be exploited to compute the gradient of the polarization energy in 10–20% of the time required to solve the equation itself. The resulting timings for the larger systems considered indicate that energies and gradients can be obtained in about half the time required for a finite difference solution to the equation. The development of a multilevel version of the algorithm as well as future applications to structure optimization using molecular mechanics force fields are also discussed. © 1997 John Wiley & Sons, Inc. J Comput Chem18: 1591–1608, 1997

An automatic three-dimensional finite element mesh generation system for the poisson-boltzmann equation

Abstract: We present an automatic three-dimensional mesh generation system for the solution of the Poisson–Boltzmann equation using a finite element discretization. The different algorithms presented allow the construction of a tetrahedral mesh using a predetermined spatial distribution of vertices adapted to the geometry of the dielectric continuum solvent model. A constrained mesh generation strategy, based on Bowyer's algorithm, is used to construct the tetrahedral elements incrementally and embed the Richards surface of the molecule into the mesh as a set of triangular faces. A direct mesh construction algorithm is then used to refine the existing mesh in the neighborhood of the dielectric interface. This will allow an accurate calculation of the induced polarization charge to be carried out while maintaining a sparse grid structure in the rest of the computational space. The inclusion of an ionic boundary at some finite distance from the dielectric interface can be automatically achieved as the grid point distribution outside the solute molecule is constructed using a set of surfaces topologically equivalent to this boundary. The meshes obtained by applying the algorithm to real molecular geometries are described. © 1997 John Wiley & Sons, Inc. J Comput Chem18: 1570–1590, 1997

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

Abstract: 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

Abstract: 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.

A three-dimensional reduction of the ornstein-zernicke equation for molecular liquids

Abstract: The derivation of a three-dimensional integral equation for solute molecule-solvent site correlation functions is presented. The equation is obtained by averaging the Ornstein–Zernicke equation for molecular liquids over orientations of the solvent molecule consistent with one site of the solvent remaining at a fixed distance from a solute-based origin. The approach is similar to that adopted in the reduction leading to the reference interaction site model (RISM) equations but retains full three-dimensional information regarding the structure of the reference solute molecule. The proposed equation can be solved using three-dimensional HNC-like closures, of which three different forms are discussed. A formulation which allows the introduction of long range interactions through a renormalization of the equation is also presented. Applications to various molecular liquids indicate that the proposed theory provides pair correlation functions that are in better agreement with molecular dynamics simulations than those obtained using the extended RISM formulation. Furthermore, qualitative errors in the correlation functions, frequently seen in results from RISM calculations are completely eliminated through geometrical averaging of the Mayer function in the 3D HNC closure. Prospects for the development of a novel mean field theory of solvation are also discussed.

Hydrogen Bonding between Amino Acid Backbone and Side Chain Analogues: A High-Level ab Initio Study

Abstract: We have carried out calculations of hydrogen-bonding structures and energies, using the pseudospectral local MP2 methodology and a high-quality triple ζ basis set for a large set of amino acid side chain analogues. Both neutral and charged amino acid analogues are examined, and interactions between donors and the π electron acceptor moiety in a benzene ring are considered. A total of >140 structures have been studied, representing all possible hydrogen-bonding interactions between a set of 11 amino acid side chain analogues. The effects of electron correlation, basis set size, and basis set superposition error are analyzed in detail for this data set. A particular focus of the paper in terms of chemically interesting effects is the influence of resonance interactions upon hydrogen-bonding strength, which is elucidated quantitatively for a significant number of donor−acceptor pairs. Finally, it is observed that donors and acceptors fall into “strong” and “weak” categories, with the weak species severely da...

Extension of the ps-gvb electronic structure code to transition metal complexes

Abstract: 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 Chem18: 1863–1874, 1997