Journal of Computational Chemistry Volume 15 / Number 1 / January 1994 CONTENTS ============================================================== Updated Hessian Matrix and the Restricted Step Method for Locating Transition Structures Josep Maria Bofill 1 ABSTRACT A family of the updated Hessian matrices for locating transition structures is presented. An analysis and improvement of the restricted step algorithm described by Culot et al. is proposed. The efficiency of the latter method is compared with other well-established methods for locating transition structures. ============================================================== Comparison of NDDO and Quasi-Ab Initio Approaches to Compute Semiempirical Molecular Electrostatic Potentials C. Alhambra, F. J. Luque, and Modesto Orozco 12 ABSTRACT The suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. ============================================================== Hydrating Peptides Using a Sprouting Technique Carl W. David 23 ABSTRACT A scheme for generating water coordinates, whose proton orientations are random, and simultaneously generating side chain coordinates of peptides, preparatory to studying solvation of peptides using molecular dynamics schemes is presented in an X-PLOR context. Examples from the Integrin and Tropomyosin systems are used to illustrate the procedure. ============================================================== Performance of Fast Multipole Methods for Calculating Electrostatic Interactions in Biomacromolecular Simulations Jiro Shimada, Hiroki Kaneko, and Toshikazu Takada 28 ABSTRACT The fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher-order multipole moments. The second is an acceleration of the calculations by the particle-particle and particle-mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1-1 kcal/mol, much smaller than the 30-kcal/mol error involved in conventional simple truncations. ============================================================== Implementation of a Data Parallel, Logical Domain Decomposition Method for Interparticle Interactions in Molecular Dynamics of Structured Molecular Fluids William S. Young and Charles L. Brooks III 44 ABSTRACT In this article, we describe a domain decomposition method for the efficient parallel computation of nonbonded forces and energies in condensed-phase molecular systems. This decomposition is based upon the monotonic logical grid (MLG) approach of Boris [J. Boris, J. Comp. Phys., 66, 1 (1986)] and yields an efficient, scalable algorithm for interparticle interaction computation on private-memory, single-instruction multiple-data (SIMD) parallel computers. We illustrate the application of this technique in a molecular dynamics kernel for rigid molecular solvents by simulating the structural and thermodynamic properties of water and methanol. The performance of this algorithm on the Thinking Machines' CM-2, private-memory SIMD computer, is demonstrated to be good compared to conventional vector/parallel supercomputers. However, as the fluid becomes less structured performance slightly degrades. ============================================================== Newton-Raphson Optimization of the Explicitly Correlated Gaussian Functions for Calculations of the Ground State of the Helium Atom Zhenghong Zhang, Pawel M. Kozlowski, and Ludwik Adamowicz 54 ABSTRACT Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. ============================================================== Simulations of the Solution Structure of HIV-1 Protease in the Presence and Absence of Bound Zinc D. M. York, L. J. Bartolotti, T. A. Darden, L. G. Pedersen, and M. W. Anderson 61 ABSTRACT Zinc ions have been shown to inhibit human immunodeficiency virus type 1 (HIV-1) protease in vitro at neutral pH [Zhang et al. Biochemistry, 36, 8717 (1991)]. Kinetic data from this study support a reversible binding mechanism of zinc in the active site. Preliminary calculations of the ion-protein potential energy based on the geometry of the crystallographic structure [Wlodawer et al. Science, 245, 616 (1989)] are consistent with this proposed mechanism. To examine the structure of HIV-1 protease with zinc bound in the active site, molecular dynamics simulations in the presence and absence of zinc at this site have been carried out to 200 ps. These simulations suggest zinc remains stably bound to the catalytic aspartate residues without disruption of the dimer or significant alteration of the active site structure. These data are consistent with those observed by Zhang et al. (1991), and together give strong evidence that this is the binding site that leads to inactivation. A proposed model of zinc binding at the active site based on quantum mechanical calculations indicates Zn;sp2 coordination is monodentate with each catalytic aspartate, leaving at least two ligand positions potentially free (occupied by water molecules in the calculations). ============================================================== Canonical Numerical Methods for Molecular Dynamics Simulations Daniel I. Okunbor and Robert D. Skeel 72 ABSTRACT We consider the application of canonical numerical integrators to molecular dynamics simulations. Computer experiments are done to analyze the relative merits of using canonical integrators against their noncanonical counterparts. These experiments involve the study of the properties of liquid argon utilizing the Lennard-Jones interaction potential. To accomplish this comparative study of canonical and noncanonical integrators, we computed thermodynamic and structural quantities. Our results indicate that noncanonical methods, with one exception, fail miserably to conserve energy and as a consequence give poor estimates of the other quantities. Also, higher-order canonical methods may offer an advantage over the Stoermer/Verlet method. ============================================================== Display of the Flow of Energy in Molecules Charles D. Schwieters and Herschel Rabitz 80 ABSTRACT In this article, we develop a method to graphically display the flow of energy within molecules. An energy continuity equation is derived leading to a molecular energy flux vector field. Computation of the flux calls for the intramolecular potential, any external interactions, and the phase space trajectories of the molecular motion. The flux provides a means to display energy flow in still frames and as a tool to visualize hitherto undiscovered dynamic pathways in molecules. Examples are presented that show energy flow in three molecular systems and illustrate the point that depiction of energy flux patterns has increasing utility and meaning as one moves to larger molecules. Simple extensions to this work would also allow visualization of the flux of such quantities as linear and angular momentum. ============================================================== General Parameterization of a Reaction Field Theory Combined with the Boundary Element Method Takao Furuki, Akihiro Umeda, Minoru Sakurai, Yoshio Inoue, Riichiro Chujo, and Kazuaki Harata 90 ABSTRACT We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent- dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. ============================================================== Free Energy Derivatives: A New Method for Probing the Convergence Problem in Free Energy Calculations David A. Pearlman 105 ABSTRACT To test the applicability of the WKB semiclassical approximation to correctly describe the tunneling frequencies and energy levels in asymmetric double wells, we have considered the cases where the asymmetry comes from the nondegeneracy of the two minima and when it comes from the asymmetry in the shape of the barrier between both minima. To do this, we compare the tunneling frequencies and energy levels obtained through the WKB method for symmetric and asymmetric cases with exact results obtained by a basis set procedure. Our results show that the semiclassical WKB approximation has to be used with caution for asymmetric double wells. ========================================================================== Diskette Submission Instructions 124 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Journal of Computational Chemistry Volume 15 / Number 2 / February 1994 CONTENTS ================================================================ Applicability of the WKB Method in Asymmetric Double Wells with Degenerate and Nondegenerate Minima Ricard Gelabert, Miquel Moreno, and Jose M. Lluch 125 To test the applicability of the WKB semiclassical approximation to correctly describe the tunneling frequencies and energy levels in asymmetric double wells, we have considered the cases where the asymmetry comes from the nondegeneracy of the two minima and when it comes from the asymmetry in the shape of the barrier between both minima. To do this, we compare the tunneling frequencies and energy levels obtained through the WKB method for symmetric and asymmetric cases with exact results obtained by a basis set procedure. Our results show that the semiclassical WKB approximation has to be used with caution for asymmetric double wells. ================================================================ Conformation and Reactivity of alpha-Oxo-Ketenes: Ab Initio and Semiempirical (AM1, PM3) Calculations Rudolf Janoschek, Walter M. F. Fabian, Gert Kollenz, and C. Oliver Kappe 132 Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted alpha-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal alpha-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. ================================================================ Parallel Algorithm for Calculating Ro-Vibrational States of Diatomic Molecules J. J. Soares Neto 144 ABSTRACT In this article, we develop and implement an algorithm for calculating the ro- vibrational states of diatomic molecules optimized for multiple instructions multiple data computers of distributed memory. The method is based upon the p- version of the finite element method and has been implemented on an INTEL iPSC/2 machine with 16 processors. This article studies the representation of protein backbone conformations using a finite number of values for the backbone dihedral angles. We develop a combinatorial search algorithm that guarantees finding the global minima of functions over the configuration space of discrete protein conformations, and use this procedure to fit finite-state models to the backbones of globular proteins. It is demonstrated that a finite-state representation with a reasonably small number of states yields either a small root-mean-square error or a small dihedral angle deviation from the native structure, but not both at the same time. The problem can be resolved by introducing limited local optimization in each step of the combinatorial search. In addition, it is shown that acceptable approximation is achieved using a single dihedral angle as an independent variable in local optimization. Results for 11 proteins demonstrate the advantages and shortcomings of both the finite-state and reduced-parameter approximations of protein backbone conformations. ================================================================ Free Energy of Solvation of a Small Lennard-Jones Particle Ching-Lung Lin and Robert H. Wood 149 In molecular dynamics (MD) and Monte Carlo (MC) free energy calculations, the choices of the thermodynamic paths from state a to state b affect the accuracy of the result and the efficiency of the programs. Most of the problems occur at the initial stages of growing in a new particle into a solvent. Based on statistical mechanical perturbation theory, an accurate and efficient direct calculation of inserting a small Lennard=nJones particle into solvent is derived. This eliminates the need for calculation of the initial stages of growing in a new particle by MD or MC simulation. Examples are given to show the utility of direct calculation. The recommended procedure is to use direct calculation for a small Lennard=nJones particle and then use MD or MC simulations to calculate the DELTA G of changing the small Lennard=nJones particle into the target molecule. ================================================================ Rationalizing Nuclear Overhauser Effect Data for Compounds Adopting Multiple- Solution Conformations Mark J. Forster and Barbara Mulloy 155 An algorithm is described for refining the populations of a set of multiple- solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least-squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1- O-methyl-alpha-l-iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C;i4, ;s4C;i1, and 2S;i0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton-proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. ================================================================ Derivation of Class II Force Fields. I. Methodology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules J. R. Maple, M.-J. Hwang, T. P. Stockfisch, U. Dinur, M. Waldman, C. S. Ewig, and A. T. Hagler 162 A new method for deriving force fields for molecular simulations has been developed. It is based on the derivation and parameterization of analytic representations of the ab initio potential energy surfaces. The general method is presented here and used to derive a quantum mechanical force field (QMFF) for alkanes. It is based on sampling the energy surfaces of 16 representative alkane species. For hydrocarbons, this force field contains 66 force constants and reference values. These were fit to 128,376 quantum mechanical energies and energy derivatives describing the energy surface. The detailed form of the analytic force field expression and the values of all resulting parameters are given. A series of computations is then performed to test the ability of this force field to reproduce the features of the ab initio energy surface in terms of energies as well as the first and second derivatives of the energies with respect to molecular deformations. The fit is shown to be good, with rms energy deviations of less than 7% for all molecules. Also, although only two atom types are employed, the force field accounts for the properties of both highly strained species, such as cyclopropane and methylcyclopropanes, as well as unstrained systems. The information contained in the quantum energy surface indicates that it is significantly anharmonic and that important intramolecular coupling interactions exist between internals. The representation of the nature of these interactions, not present in diagonal, quadratic force fields (Class I force fields), is shown to be important in accounting accurately for molecular energy surfaces. The Class II force field derived from the quantum energy surface is characterized by accounting for these important intramolecular forces. The importance of each of the interaction terms of the potential energy function has also been assessed. Bond anharmonicity, angle anharmonicity, and bond/angle, bond/torsion, and angle/angle/torsion cross-term interactions result in the most significant overall improvement in distorted structure energies and energy derivatives. The implications of each energy term for the development of advanced force fields is discussed. Finally, it is shown that the techniques introduced here for exploring the quantum energy surface can be used to determine the extent of transferability and range of validity of the force field. The latter is of crucial importance in meeting the objective of deriving a force field for use in molecular mechanics and dynamics calculations of a wide range of molecules often containing functional groups in novel environments. ================================================================ Semiempirical Study of Compounds with Intramolecular O-H...O Hydrogen Bonds. II: Further Verification of a Modified MNDO Method Jesus Rodriguez 183 In the forerunner of this article, we described a MNDO modification designed for studies of compounds with intramolecular O-H...O hydrogen bonds. Here, we report the further verification of the modification by means of its application to 14 compounds not considered in its development. Comparison of the calculated structural parameters and proton transfer characteristics with available experimental or ab initio results, and with those obtained using MNDO, AM1, MNDO/H, MNDO/M, and PM3, supports the validity of the new modification for prediction of hydrogen bond characteristics. ================================================================ Utilization of Shape Data in Molecular Mechanics Using a Potential Based on Spherical Harmonic Surfaces Arun Malhotra, Robert K.-Z. Tan, and Stephen C. Harvey 190 This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron-microscopy-based three- dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff =+=+21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.2;s7 Implementation details and results of several test cases are discussed here. ================================================================ Atomic Charges Derived from a Fast and Accurate Method for Electrostatic Potentials Based on Modified AM1 Calculations Bingze Wang and George P. Ford 200 Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. ================================================================ Conformational Sampling of Hydrocarbon and Lipid Chains in an Orienting Potential Barry J. Hardy and Richard W. Pastor 208 A Distribution Biased Monte Carlo (DBMC) sampling procedure is developed for the efficient generation of chain conformations in the oriented environment of lipid membranes and other liquid crystalline systems. Conformations of the sn-1 chain of dipalmitoyl phosphatidylcholine (DPPC) were generated by independently sampling torsion angles from continuous distributions in an orienting potential based on a Marcelja mean field; depending on the chain position, the convergence in the deuterium order parameters (S;zC;zD) was 100 to 3000 times more efficient with DBMC than with Brownian dynamics. Optimization using joint distribution and torsional potentials of mean force yielded a further threefold increase in sampling efficiency. Overall chain tilt was included using Euler angle rotations and a separate field strength for the anchor. A segmental DBMC procedure was used to generate a set of complete DPPC conformations with well- converged conformationally averaged S;zC;zD consistent with experimental values. These conformations show considerable flexibility, not only in the hydrocarbon tails, but additionally in both the glycerol and head-group portions of the lipid. An appendix compares DBMC with a number of other Monte Carlo and stochastic dynamics algorithms using the example of a bistable oscillator, and illustrates the tuning of parameters for optimal convergence. ================================================================ Preconditioners for Distance Matrix Algorithms W. Glunt, T. L. Hayden, and M. Raydan 227 A recent gradient algorithm in nonlinear optimization uses a novel idea that avoids line searches. This so-called spectral gradient algorithm works well when the spectrum of the Hessian of the function to be minimized has a small range or is clustered. In this article, we find a general preconditioning method for this algorithm. The preconditioning method is applied to the stress function, which arises in many applications of distance geometry, from statistics to finding molecular conformations. The Hessian of stress is shown to have a nice block structure. This structure yields a preconditioner which decreases the amount of computation needed to minimize stress by the spectral gradient algorithm. ================================================================ A Ring-Bracing Approach to Computer-Assisted Ligand Design Andrew R. Leach and Richard A. Lewis 233 Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be `braced' using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. ================================================================ Computational Study of the Hydrolysis of Degradable Polysaccharide Biomaterials: Substituent Effects on the Hydrolytic Mechanism Lawrence M. Pratt and C. C. Chu 241 Hyaluronic acid and its derivatives are absorbable polysaccharides which are used extensively in cosmetics and as biomaterials. Two possible mechanisms of degradation, involving an oxocarbenium ion and the corresponding radical cation, are examined by modeling of the saccharide ring and the effects of various ring substituents on the two possible mechanisms. ======================================================================== Announcement 249 Diskette Submission Instructions 250 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Journal of Computational Chemistry Volume 15 / Number 3 / March 1994 CONTENTS Force Field Calculations (MM3) on Glyoxal, Quinones, and Related Compounds Norman L. Allinger and Yi Fan 251 Quantum Mechanical Computations on Very Large Molecular Systems: The Local Self-Consistent Field Method Vincent Thery, Daniel Rinaldi, Jean-Louis Rivail, Bernard Maigret, and Gyoergy G. Ferenczy 269 Molecular Mechanics (MM3) Calculations on Alkyl Radicals Ruifeng Liu and Norman L. Allinger 283 Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations Ljubomir J. Buturovi;aac, Temple F. Smith, and Sandor Vajda 300 A Comparative Study of Effective Core Potential and Full-Electron Calculations in Mo Compounds. I. An Analysis of Topological Properties of Bond Charge Distribution Anibal Sierraalta and Fernando Ruette 313 The Structures of LiNC, NaNC, and KNC: Potential Energy Surface for the Orbiting Motion of the Metal Cation around the CN Group Andrea Dorigo, Paul von Rague Schleyer, and Pavel Hobza 322 Molecular Simulation of Alkyl Boronic Acids: Molecular Mechanics and Solvation Free Energy Calculations Xiannong Chen, Libero Bartolotti, Khalid Ishaq, and Alexander Tropsha 333 Ab Initio Study of Low-Lying Electronic States of the PF;i2 Radical Z.-L. Cai 346 Free Energy Perturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup Stephen E. DeBolt, David A. Pearlman, and Peter A. Kollman 351 Diskette Submission Instructions 375 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Volume 15 / Number 4 / April 1994 CONTENTS Normal Coordinates-Finite Elements Calculation of 3D Vibrational Energy Levels: Henon-Heiles and Eckart Potentials, [diH[es;pl[rb[ei3[rb[ee Molecule J. R. Alvarez-Collado 377 Ab Initio Molecular Orbital Study of 1-Fluorosilatrane G. I. Csonka and P. Hencsei 385 Modulation of Intramolecular Proton Transfer by Electronic Excitation and Environment: 2-Pyridone as a Case Study Vincenzo Barone and Carlo Adamo 395 Transferable Semiempirical Quadratic Force Fields: The Case of Polythiophene and Shorter Oligomers F. J. Ramirez, V. Hernandez, and J. T. Lopez Navarrete 405 MRD-CI Studies of Vertical Excitation Energies of Unsaturated Hydrocarbon Molecules S. Grimme 424 Monte Carlo Simulations on Short Single-Stranded Oligonucleotides. I. Application to RNA Trimers Mahmoud Ghomi, Jean-Marc Victor, and Charles Henriet 433 Optimization of Solute Cavities and van der Waals Parameters in Ab Initio MST-SCRF Calculations of Neutral Molecules M. Bachs, F. J. Luque, and Modesto Orozco 446 Parametrization of a Force Field for Studying Some Beta-Lactams Berta Fernandez and Miguel A. Rios 455 Relativistic Dirac-Fock Calculations for Closed-Shell Molecules L. Pisani and E. Clementi 466 Announcements 475 Diskette Submission Instructions 477 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Volume 15 / Number 5 / May 1994 CONTENTS Theoretical Analysis of the Role of the Solvent on the Reaction Mechanisms: One-Step versus Two-Step Ketene-Imine Cycloaddition X. Assfeld, M. F. Ruiz-Lopez, J. Gonzalez, R. Lopez, J. A. Sordo, and T. L. Sordo 479 ICM-A New Method for Protein Modeling and Design: Applications to Docking and Structure Prediction from the Distorted Native Conformation Ruben Abagyan, Maxim Totrov, and Dmitry Kuznetsov 488 On the Analytical Calculation of van der Waals Surfaces and Volumes: Some Numerical Aspects Michel Petitjean 507 New Approach to the Semiempirical Calculation of Atomic Charges for Polypeptides and Large Molecular Systems Ulrich Sternberg, Frank-Thomas Koch, and Margit Moellhoff 524 A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications Philippe Derreumaux, Guihua Zhang, Tamar Schlick, and Bernard Brooks 532 Variation of Atomic Charges during Proton Transfer in Hydrogen Bonds Jan Florian and Steve Scheiner 553 Analysis of the Ring-Form Tautomers of Psicose with MM3(92) Alfred D. French and Michael K. Dowd 561 Announcement 571 Diskette Submission Instructions 572 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Volume 15 / Number 6 / June 1994 CONTENTS Direct One-Index Transformations in Multiconfiguration Response Calculations Olav Vahtras, Hans Agren, and Hans Jrgen Aa. Jensen 573 Interaction between Carbon Dioxide and Naphthalene: A Molecular Modeling Approach P. Battersby, J. R. Dean, S. M. Hitchen, W. R. Tomlinson, and P. M. Myers 580 Application of Genetic Algorithms in Molecular Modeling Tilman Brodmeier and Ernoe Pretsch 588 Structures and Stabilization Energies of Methyl Anions with Main Group Substituents from the First Five Periods Ahmed M. El-Nahas and Paul von Rague Schleyer 596 Direct Search Methods for the Molecular Conformation Problem J. C. Meza and M. L. Martinez 627 Shape Analysis of Hydrogen-Bonded Networks in Solvation Clusters Gustavo A. Arteca 633 Effect of Charge on Bond Strength in Hydrogenated Amorphous Silicon B. W. Clare, G. Talukder, P. J. Jennings, J. C. L. Cornish, and G. T. Hefter 644 Atomic Orbital Basis Sets for Molecular Interactions Herbert F. M. da Costa and David A. Micha 653 X-PLORing Extraribosomal Peptide Folding during Synthesis Carl W. David 662 Diskette Submission Instructions 666 [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Volume 15 / Number 7 / July 1994 CONTENTS New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation Peter J. Steinbach and Bernard R. Brooks 667 Internal Dynamics of a Globular Protein under External Force Field Shuzo Yoshioki 684 Thermodynamic Integration Calculations on the Relative Free Energies of Complex Ions in Aqueous Solution: Application to Ligands of Dihydrofolate Reductase Peter L. Cummins and Jill E. Gready 704 Failure of Net Atomic Charge Models to Represent the van der Waals Envelope Electric Potential of n-Alkanes Donald E. Williams 719 Fast Geometry Optimization Using a Modifed Extended Hueckel Method: Results for Molecules Containing H, C, N, O, and F Steven L. Dixon and Peter C. Jurs 733 Iterative Methods for the Calculation of a Few of the Lowest Eigenvalues and Corresponding Eigenvectors of the AX = ;wL=+=+BX Equation with Real Symmetric Matrices of Large Dimension Alexander V. Mitin 747 Force Field for Computation of Conformational Energies, Structures, and Vibrational Frequencies of Aromatic Polyesters H. Sun 752 Expanding Molecular Dynamics Simulations to the NMR Time Scale. I. Studies of Conformational Interconversions of 1,1-Difluoro-4,4-Dimethylcycloheptane Using MM3-MD Fanbing Li, Weili Cui, and Norman L. Allinger 769 High-Precision Atomic Computations from Finite Element Techniques: Second- Order Correlation Energies for Be, Ca, Sr, Cd, Ba, Yb, and Hg Jesus R. Flores and P. Redondo 782 Diskette Submission Instructions 791 ============================================================= JCC 15(9) On the Functional Representation of Bond Energy Functions 919 U. Dinur and A. T. Hagler Structure of Disiloxane: A Semiempirical and Post-Hartree-Fock Study Gabor I. 925 Csonka, Miklos Erdosy,and Jozsef Reffy D-CICADA: A Software for Conformational PES Elucidation on Network of Workstations 937 Ludek Matyska and Jaroslav Koca Conformational Study of Dipeptides: A Sensitivity Analysis Approach 947 Roberta Susnow, Clarence Schutt, Herschel Rabitz, and Shankar Subramaniam Principal Component Analysis of Dipeptides 963 Roberta Susnow, Clarence Schutt, and Herschel Rabitz Structural and Electronic Property Changes of the Nucleic Acid Bases upon Base Pair Formation 981 R. Santamaria and A. Vazquez Long-Time Overdamped Langevin Dynamics of Molecular Chains 997 Niels Gronbech-Jensen and Sebastian Doniach Decomposition Analyses of the Intermolecular Interaction Energies in Two *gp_*gp Stacking Complexes: Quinhydrone and N,N,N', N'-Tetramethyl-p-Diaminobenzene-Chloranil Complex 1013 Yasuyuki Kurita, Chiyozo Takayama, and Shizuya Tanaka A Force Field for Monosaccharides and (1-4) Linked Polysaccharides 1019 Timothy M. Glennon, Ya-Jun Zheng, Scott M. Le Grand, Brad A. Shutzberg, and Kenneth M. Merz, Jr. Application of the Multiple Computer Automated Structure Evaluation Methodology to a Quantitative Structure-Activity Relationship Study of Acidity 1041 Gilles Klopman and Dan Fercu Diskette Submission Instructions ================================================= JCC 15(12) CONTENTS Molecular Mechanics Calculations (MM2 and MM3) on Enamines 1321 and Aniline Derivatives N. L. Allinger, Liqun Yan, and Kuchsiang Chen Algorithms for Clustering Molecular Dynamics Configurations 1331 Andrew E. Torda and Wilfred F. van Gunsteren Ab Initio Study of Some CH3OCXYCH2 Radicals: The Influence of Anomeric 1341 Effects on Their Structure and Their Stability R. Arnaud A Variational Biorthogonal Valance Bond Method 1357 Nathaniel O. J. Malcolm and Jospeh J. W. McDouall A Variational Biorthogonal Valance Bond Descriptions of 1,3-Dipoles 1365 Nathaniel O. J. Malcolm and Jospeh J. W. McDouall Application of a High-Performance, Special-Purpose Computer, 1372 GRAPE-2A, to Molecular Dynamics Junichi Higo, Shigeru Endo, Kuniaki Nagayama, Tomoyoshi Ito, Toshiyuki Fukushige, Toshikazu Ebisuzaki, Dalichiro Sugimoto, Hiroo Miyagawa, Kunihiro Kitamura, and Junichiro Makino Anisotropy of Atom-Atom Repulsions 1377 A. J. Stone and C.-S. Tong Implementation of Artificial Intelligence for Automatic Drug Design. 1393 I. Stepwise Computation of the Interactive Drug-Design Sequence Alexander A. Cohen and Shimon E. Shatzmiller A Rapid and Efficient Algorithm for Packing Polypeptide Chains by 1414 Energy Minimization Kenneth D. Gibson and Harold A. Scheraga ToBaD: A Method for the Estimation of Torsion Barriers from Crystal 1429 Structure Data; Conformational Analysis of N,N-Dimethylaniline and Derivatives M. L. Verdonk, R. W. Tjerkstra, I. S. Ridder, J. A. Kanters, J. Kroon, and W. J. M. van der Kemp Heats of Formation of Organic Molecules Calculated from Ab Initio 1437 Theory and a Group Equivalent Scheme: Alkenes Lawrence R. Schmitz and Yi Ren Chen Molecular Mechanics (MM3) Calculations on Azoxy Compounds 1446 Yi Fan and Norman L. Allinger Author Index 1463 Subject Index 1469 Volume Contents I Diskette Submission Instructions II