99.              Lu, Daqi, Bryan Marten, Yixiang Cao, Murco Ringnalda, Richard A. Friesner and William  A. Goddard, III, Ab initio predictions of large hyperpolarizability push-pull polymers:  Julolidinyl-n-isoxazolone and julolidinyl-n-N,N’ -diethylthiobarbituric acids, Chem. Phys. Lett., 242, 543-547 (1995).

100.          Zorman, B., M. V. Ramakrishna, and R. Friesner,  Quantum Confinement Effects in CdSe Quantum Dots, J. Phys. Chem., 99, 7649 (1995)  

101.          Monge, Alessandro; Elizabeth J.P. Lathrop, John R. Gunn, Peter S. Shenkin, and Richard A. Friesner,  Computer Modeling of Protein Folding: Conformational and Energetic Analysis of Reduced and Detailed Protein Models, J. Mol. Biol., 247, 995-1012 (1995).

102.          Felts, A., W. T. Pollard, and R. Friesner, Multilevel Redfield Treatment of Bridge-Mediated Electron Transfer: A Mechanism for Anomalous Distance Dependence, J. Phys. Chem. 99, 9, 2929-2940 (1995).

103.          Antikainen, J., R. Friesner, and C. Leforestier, Adiabatic Pseudospectral Calculation of Four Atom Molecules: Application to Hydrogen Peroxide, J. Chem. Phys., 102, 1270 (1995).

104.          Humphreys, D.D., R. Friesner, and B. J. Berne, Simulated Annealing of a Protein in a Continuum Solvent via Multiple Timescales Molecular Dynamics, J. Phys. Chem.  99, 10674 (1995).

105.          Murphy, R.B., M. Beachy, M. Ringnalda, and R. Friesner, Pseudospectral localized MØller-Plesset methods: Theory and calculation of conformational energies, J. Chem. Phys. 103, 1481 (1995).

106.          Zhang, L., and R. Friesner, Ab Initio Self-Consistent Reaction Field Calculation of the Redox Potentials of Bacteriochlorophyll and Bacteriopheophytin in Solution, J. Phys. Chem. 99, 16479 (1995).

107.          Gunn, John R. and Richard A. Friesner, Parallel Implementation of a Protein Structure Refinement Algorithm, J. Comp. Chem., 17, 10, 1217-1228 (1996).

108.          Pollard, A. K. Felts, and R. A. Friesner, The Redfield Equation in Condensed Phase Quantum Dynamics, Adv. Chem. Phys., XCIII, 77, New Methods in Computational Mechanics, eds. I. Prigogine and Stuart A. Rice, ISBN: 0-471-19127-2 (1996).

109.          Friesner, Richard A. and John R. Gunn, Computational Studies of Protein Folding, Ann. Rev. Biophys. Biomol. Struct., 25, 315-342 (1996).  

110.          Lu, Daqi,  Bryan Marten, Murco Ringnalda, Richard A. Friesner, William A. Goddard, III, Saturation of the second dyperpolarizability for polyacetylenes, Chem. Phys. Lett, 257, 224-228 (1996). 

111.          Marten, B., K. Kim, C. Cortis, R. A. Friesner, R. B. Murphy, M. N.  Ringnalda, D. Sitkoff, and B. Honig, New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen Bonding Effects, J. Phys. Chem., 100, 11775 (1996).

112.          Cortis, C., J. M. Langlois, M. Beachy, and R. Friesner, Quantum mechanical geometry optimization in solution using a finite element continuum electrostatics method, J. Chem. Phys., 105, 123, 5472 (1996).

113.          Edinger, Shlomit R.; Christian Cortis; Peter S. Shenkin; and Richard A. Friesner, Solvation Free Energies of Peptides:  Comparision of Approximate Continuum Solvation Models with Accurate Solution of the Poisson-Boltzmann Equation, J. Phys. Chem., 101, 7, 1190-1197 (1997).

114.          Murphy, Robert B., W. Thomas Pollard, and Richard A. Friesner, Pseudospectral localized generalized MØller-Plesset methods with a generalized valence bond reference wave function:  Theory and calculation of conformational energies, J. Chem. Phys., 106, (12) 5073-5084( 1997).

115.          Zhang, L., R. Murphy, and R. Friesner,  Ab Initio  quantum chemical calculation of electronic transfer matrix elements for large molecules, J. Chem. Phys., 107 (2) 450-459 (1997).

116.          Beachy, M., D. Chasman, R. Murphy, T. Halgren, and R. Friesner, Accurate Ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields, J. Am. Chem. Soc., 119, 25, 5908-5920 (1997).

117.          Black, S., R. Friesner, P. Lu, and R. Osgood, Ab Initio Calculation of Molecule-Surface Binding: Methyl Halides on GaAs (110) Surfaces, Surface Science, 382, 154-169 (1997).

118.          Cortis, Christian, and Richard A. Friesner, An Automatic 3D Finite Element Mesh Generation System for the Poisson-Boltzman Equation, J. Comp. Chem., 18, (13), 1570-1590 (1997).

119.          Cortis, Christian, and Richard A. Friesner, Numerical Solution of the Poisson-Boltzmann Equation Using Tetrahedral Finite-Element Meshes, J. Comp. Chem., 18, (13), 1591-1608 (1997).

120.          Cortis, Christian M; Peter J. Rossky; Richard A. Friesner, A three-dimensional reduction of the Ornstein-Zernicke equation for molecular liquids, J. Chem. Phys., 107, (16), 6400-6414 (1997).

121.          Mainz, D., J. Klicic; R.A. Friesner, J. M. Langlois, and Jason K. Perry, Extension of the PS-GVB Electronic Structure Code to Transition Metal Complexes, J. Comp. Chem., 18, 15, 1863-1874 (1997).

122.          Kim, Kyungsun and Richard A. Friesner, Hydrogen bonding between amino acid backbone and side chain analogues:  A high level ab Initio study, J. Am. Chem. Soc., 119, 52, 12952-12961 (1997).

123.          Kawata, M., C.M. Cortis and R.A. Friesner, Efficient recursive implementation of the modified Broyden method and the direct inversion in the iterative subspace method: acceleration of self-consistent calculations, J. Chem. Phys, 108, (11), 4426-4438 (1998).

124.          Liu, Yi-Ping; Kyungsun Kim; B.J. Berne; Richard A. Friesner; and Steven W. Rick, Constructing ab initio force fields for molecular dynamics simulations, J. Chem. Phys., 108, (12), 4739-4755 (1998).

125.          Friesner, Richard A. and Michael Beachy, Quantum mechanical calculations on biological systems, Current Opinion in Structural Biology, 8, 257-262 (1998).

126.          Chasman, David, Michael D. Beachy, L. Wang and Richard A. Friesner, Parallel Pseudospectral Electronic Structure.  I.  Hartree-Fock Calculations, J. Comput. Chem., 19, 9, 1017-1029 (1998).

127.          Beachy, Michael, David Chasman, Richard A. Friesner, Robert B. Murphy, Parallel Pseudospectral Electronic Structure.  II. Localized MØller-Plesset Calculations, J. Comp. Chem., 19, (9), 1030-1038 (1998).

128.          Standley, Daron M.; John R. Gunn; Richard A. Friesner; and Ann E. McDermott, Tertiary Structure Prediction of Mixed alpha/beta Proteins via Energy Minimization,  Proteins: Structure, Function and Genetics, 33, 2, 240-252 (1998).

129.          Murphy, Robert B. and Richard A. Friesner, Accurate Quantum Chemical Calculation of the Relative Energetics of C₂₀ Carbon Clusters via Localized Multireference Perturbation Calculations, Chem. Phys. Letts., 288:  (2-4), 403-407, (1998).

130.          Friesner, Richard A., Robert B. Murphy and Murco N. Ringnalda, Pseudospectral Methods for Ab Initio Quantum Chemistry, Encyclopedia of Comp. Chem., vol. 3, 2290, (1998).

131.          Zhang, Linda, and Richard A. Friesner, Ab initio calculation of electronic coupling in the photosynthetic reaction center, Proc Nat Acad Sci USA, 95, 13603-13605, (1998).

132.          Ghosh, Avijit, Chaya Sendrovic-Rapp; and Richard A. Friesner, Generalized Born Model Based on a Surface Integral Formulation, J. Phys. Chem. B, 102, 52, 10983-10990 (1998).

133.          Dunietz, Barry D., Robert B. Murphy, and Richard A. Friesner, Calculation of atomization energies by a multiconfigurational localized perturbation theory.  Application for closed shell cases, J. Chem. Phys., 110, 4, 1921-1930 (1999).

134.          Golosov, Andrei A., Richard A. Friesner and Philip Pechukas, Efficient memory equation algorithm for reduced dynamics in spin-boson models, J. Chem. Phys, 110, 1, 138-146 (1999).

135.          Banks, Jay L.; George A. Kaminski; Ruhong Zhou; Daniel T. Mainz; Bruce J. Berne; and Richard A. Friesner, Parametrizing a polarizable force field from ab initio data. I: The fluctuating point charge model, J. Chem. Phys., 110, 2, 741-754 (1999).

136.          Standley, Daron M.; Volker A. Eyrich; Anthony K. Felts; Richard A. Friesner, and Ann E. McDermott, A Branch and Bound Algorithm for Protein Structure Refinement from Sparse NMR Data Sets, J. Mol. Biol. 285, 4, 1691-1710 (1999).

137.          Eyrich, Volker A.; Daron M. Standley; Anthony K. Felts; and Richard A. Friesner, Protein Tertiary Structure Prediction Using a Branch and Bound Algorithm, Proteins: Structure, Function and Genetics, 35, 1, 41-57 (1999).

138.          Sendrovic-Rapp, Chaya; and Richard A. Friesner, Prediction of Loop Geometries Using a Generalized Born Model of Solvation Effects, Proteins: Structure, Function and Genetics, 35, 173-183 (1999).

139.          Friesner, Richard A., Robert B. Murphy, Michael D. Beachy, Murco N. Ringnalda, W. Thomas Pollard, Barry D. Dunietz and Yixiang Cao, Correlated Ab Inito Electronic Structure Calculations for Large Molecules, J. Phys. Chem. A, 103, 13, 1913-1928 (1999).

140.          Friedrichs, Mark; Ruhong Zhou; Shlomit R. Edinger; and Richard A. Friesner, Poisson-Boltzmann Analytical Gradients for Molecular Modeling Calculations, J. Phys. Chem. B., 103, 16, 3057-3061 (1999).

141.          Eyrich, Volker A, Daron M. Standley and Richard A. Friesner, Prediction of Protein Tertiary Structure to Low Resolution: Performance for a Large and Structurally Diverse Test Set, J. Mol. Biol., 288, 4, 725-742, (1999).

142.          Klicic, Jasna J. and Richard A. Friesner, 1,3-Dipolar Addition of Phenylazide to the Carbon-Carbon Double Bond - An Ab Initio Study, J. Phys Chem., 103, 9, 1276-1282 (1999).

143.          Stern, Harry A., George A. Kaminski, Jay L. Banks, Ruhong Zhou, B.J. Berne and Richard A. Friesner, Fluctuating Charge, Polarizable Dipole, and Combined Models:  Parameterization from ab Inito Quantum Chemistry, J. Phys. Chem. B., 103, 22, 4730-4737 (1999).

144.          Philipp, Dean M., and Richard A. Friesner, Mixed Ab Initio QM/MM Modeling Using Frozen Orbitals and Tests with Alanine Dipeptide and Tetrapeptide, J. Comput. Chem., 20, 14, 1468-1494, (1999).

145.          Golosov, Andrei A., Stefan I. Tsonchev, Philip Pechukas and Richard A. Friesner, Spin-spin model for two-level system/bath problems:  a numerical study, J. Chem. Phys., 111, 22, 9918-9923, (1999).

146.          Hascall, Tony, Daniel Rabinovich, Vincent J. Murphy, Michael D. Beachy, Richard A. Friesner and Gerard Parkin, Mechanistic and Theoretical Analysis of the Oxidative Addition of H₂ to the Six Coordinate Molybdenum and Tungsten Complexes, M(PMe₃)₄X₂ (M = Mo, W;X = F, Cl, Br, l):  An inverse Equilibrium Isotope Effect and an Unprecedented Halide Dependence, J. Am. Chem. Soc., 121, 49, 11402-11417, (1999).