1. Meeks, F.R. and D.L. Beveridge, Determination
des forces thermodynamique qui assurent la diffusion isotherm du carbone
dans le fer-gamma. J. Chim. Phys., 1964. 61:
p. 453.
2.
Jones, H.L. and D.L. Beveridge, Lone
Pair Interaction in the Chichibabin Reaction. Tet. Lett., 1964. 24:
p. 1577.
3.
Jaffe, H.H., D.L. Beveridge, and H.L. Jones, Excited
State PK's I. Azobenzene and
Azoxybenzene. J. Am. Chem. Soc., 1964. 86:
p. 2932.
4.
Beveridge, D.L. and H.H. Jaffe, The
Electronic Structure and Spectra of cis- and trans-Stilbene. J. Am.
Chem. Soc., 1965. 87: p. 5340.
5.
Beveridge, D.L. and H.H. Jaffe, The
Electronic Structure and Spectra of cis- and trans-Azobenzene. J. Am.
Chem. Soc., 1966. 88: p. 1948.
6.
Jaffe, H.H., D.L. Beveridge, and M. Orchin, Understanding
Ultraviolet Spectra of Organic Molecules. J. Chem. Ed., 1967. 44: p. 383.
7.
Pople, J.A., D.L. Beveridge, and P.A. Dobosh, Approximate
Self Consistent Field Molecular Orbital Theory V.
Intermediate Neglect of Differential Overlap. J. Chem. Phys.,
1967. 47: p. 2026.
8.
Pople, J.A., D.L. Beveridge, and N.S. Ostlund, Recent
Progress in Approximate Self-Consistent Field Theory. Int. J. Quantum
Chem., 1967. 15: p. 293.
9.
Pople, J.A. and D.L. Beveridge, Molecular
Orbital Theory of Geometry and Hyperfine Coupling Constants of Fluorinated
Methyl Radicals. J. Chem. Phys., 1968. 48:
p. 4801.
10.
Pople, J.A., D.L. Beveridge, and P.A. Dobosh, Molecular
Orbital Theory of the Electronic Structure of Organic Compounds II.
Spin Densities in Paramagnetic Species. J. Am. Chem. Soc.,
1968. 90: p. 4201.
11.
Beveridge, D.L. and P.A. Dobosh, Spin
Contamination in Spin-Unrestricted INDO Molecular Orbital Wavefunctions.
J. Chem. Phys., 1968. 48: p. 5322.
12.
Beveridge, D.L. and K. Miller, An
INDO Molecular Orbital Study of Vibronic Effects in Isotopically
Substituted Methyl Radicals. Mol. Phys., 1968. 14:
p. 401.
13.
Pople, J.A. and D.L. Beveridge, Delocalization
of Unpaired Electron Density of Free Radicals into Substituent Phenyl
Groups. J. Chem. Phys., 1968. 49:
p. 4725.
14.
Beveridge, D.L. and J.W. McIver Jr., INDO
Molecular Orbital Calculation of Anisotropic Hyperfine Coupling Constants.
Chem. Phys. Lett., 1969. 4: p.
126.
15.
Pople, J.A. and D.L. Beveridge, Approximate
Molecular Orbital Theory. 1970, New York:
McGraw-Hill.
16.
Beveridge, D.L. and J.W. McIver Jr., INDO
Molecular Orbital Study of Hyperfine Tensors: Theory, Methodology and
Application to CH, CH3, and Radicaloid Derivatives of Malonic
Acid. J. Chem. Phys., 1971. 54:
p. 4681.
17.
Beveridge, D.L. and R.J. Radna, Structural
Chemistry of Cholinergic Neural Transmission Systems I.
A Quantum Theoretical Study of the Molecular Electronic Structure
of Acetylcholine. J. Am. Chem. Soc., 1971. 93:
p. 3759.
18.
Beveridge, D.L. and B.J. Bulkin, Descriptive
Crystal Orbital Theory of Electrical Conduction in Diamond and Graphite.
J. Chem. Ed., 1971. 48: p. 587.
19.
Beveridge, D.L. and E. Guth, Quantum
Theoretical Considerations of the ortho:para Ratio of Proton Hyperfine
Coupling Constants in Benzyle Radical. J. Chem. Phys., 1971. 55:
p. 458.
20.
Beveridge, D.L. and J. Hinze, Parametrization
of Semiempirical Pi-Electron Molecular Orbital Calculations.
Systems Containing C, N, O and F. J. Am. Chem. Soc., 1971. 93: p. 3107.
21.
Kang, S. and D.L. Beveridge, Molecular
Orbital Aspects of Substituent Effects. Theoret. Chem. Acta, 1971. 23:
p. 312.
22.
Bulkin, G.J., F.T. Prochanska, and D.L. Beveridge, Raman
Spectrum and Quantum Mechanical Study of the Equilibrium Geometry of
para-Azoxydianisole. J. Chem. Phys., 1971. 55:
p. 5828.
23.
Beveridge, D.L., I. Jano, and J. Ladik, INDO
and MINDO/2 Crystal Study of Polyacetylene, Polyethylene and Polyglycine.
J. Chem., 1972. 567: p. 4744.
24.
Beveridge, D.L., R.J. Radna, and E. Guth, An
INDO Molecular Orbital Study of the Conformational Stability of the
Cholinergic O-C-C-N+ Group, in Conformation
of Biological Molecules and Polymers, Proc. 5th Jerusalem Symposium,
B. Pullman and E. Bergmann, Editors. 1973, Academic Press: New York.
25.
Radna, R.J., D.L. Beveridge, and A. Bender, Structural
Chemistry of Cholinergic Neural Transmission Systems II.
A Quantum Theoretical Study of the Molecular Electronic Structure
of Muscarine, Nicotine, Acety-a-Methylcholine,
Acetyl-b-Methylcholine, Acetyl-a,
b-Dimethylcholine and Further Studies on Acetylcholine. J. Am.
Chem. Soc., 1973. 95: p. 3831.
26.
Beveridge, D.L. and W. Wun, A
Comparison of the Photoelectron Spectrum and Crystal Orbital Calculations
of Polyethylene. Chem. Phys. Lett., 1973. 5:
p. 507.
27.
Beveridge, D.L. and E. Guth, Teleprocessing
for Chemists: A Versatile
Remote Batch and Graphics Facility Based on Laboratory Computers, in Computers, Networks, Mini-computers and Chemistry, P.G. Lykos,
Editor. 1973, Elsevier Press: New York.
28.
Beveridge, D.L., M.M. Kelly, and R.J. Radna, A
Theoretical Study of Solvent Effects on the Conformational Stability of
Acetylcholine. J. Am. Chem. Soc., 1974. 96:
p. 3769.
29.
Beveridge, D.L., R.J. Radna, and S. Vishveswara, Structural
Chemicals of Neural Transmission Systems, in Chemical
and Biochemical Reactivity, Proc. 6th Jerusalem Symposium, B. Pullman
and E. Bergmann, Editors. 1974, Academic Press: New York.
30.
Beveridge, D.L. and G.W. Schnuelle, Statistical
Thermodynamic Considerations of Solvent Effects on Conformational
Stability: The Supermolecule
Continuum Model. J. Phys. Chem., 1974. 78:
p. 2004.
31.
Beveridge, D.L., et al., Theoretical
Studies of Solvent Effects on the Conformational Stability of Cholinergic
Molecules, in Molecular and
Quantum Pharmacology, Proc. 7th Jerusalem Symposium, B. Pullman and E.
Bergmann, Editors. 1975, North Holland Publishing Co.
32.
Beveridge, D.L. and E. Guth, Remote
Terminal Computer Graphics, in Computer
Networking and Chemistry, P.G. Lykos, Editor. 1975, American Chemical
Society.
33.
Beveridge, D.L. and G.W. Schnuelle, Free
Energy of a Charge Distribution in Concentric Dielectric Continua. J.
Phys. Chem., 1975. 79: p. 2562.
34.
Schnuelle, G.W. and D.L. Beveridge, A
Statistical Thermodynamic Supermolecule-Continuum Study of Ion Hydration
I. Site Method. J. Phys.
Chem., 1975. 79: p. 2566.
35.
Beveridge, D.L., Approximate
Molecular Orbital Theory of Nuclear and Electron Magnetic Resonance
Parameters, in Modern Theoretical Chemistry, G. Segal, Editor. 1975, Plenum Press.
36.
Harrison, S.W., H.J. Nolte, and D.L. Beveridge, Free
Energy of a Charge Distribution in a Spheroidal Cavity in a Polarizable
Dielectric Contiuum. J. Phys. Chem., 1976. 80:
p. 2580.
37.
Swaminathan, S. and D.L. Beveridge, A
Theoretical Study of the Structure of Liquid Water Based on Quaiscomponent
Distribution Functions. Journal of the American Chemical Society,
1977. 99: p. 8392-8398.
38.
Swaminathan, S., et al., A
Heuristic Intermolecular Potential Function for Formaldehyde-Water Based
on ab initio Molecular Orbital
Calculations. J. Am. Chem. Soc., 1977. 99:
p. 7817.
39.
Schnuelle, B.W., S. Swaminathan, and D.L. Beveridge, A
Statistical Thermodynamic Supermolecule-Continuum Study of Ion Hydration
II. Cell and Shell Methods.
Theoret. Chem. Acta., 1978. 48:
p. 17.
40.
Harrison, S.W., et al., A
Heuristic Intermolecular Potential Function for Methane-Water. Int. J.
Quantum Chem., 1978. 14: p.
319.
41.
Swaminathan, S., S.W. Harrison, and D.L. Beveridge, Monte
Carlo Calculations of the Structure of Dilute Aqueous Solution of Methane.
J. Am. Chem. Soc., 1978. 100:
p. 5705.
42.
Beveridge, D.L., et al., Monte
Carlo Calculations of the Structure of Liquid Water and Dilute Aqueous
Solutions, in Computer Modeling of Matter. 1978.
43.
Mezei, M., S. Swaminathan, and D.L. Beveridge, Ab
Initio Calculation of the Free Energy of Liquid Water. J.
Am. Chem. Soc., 1978. 100:
p. 3255-3256.
44.
Swaminathan, S. and D.L. Beveridge, Monte
Carlo Computer Simulation of Hydrophobic Bonding. J. Am. Chem. Soc.,
1979. 101: p. 5832.
45.
Mezei, M., S. Swaminathan, and D.L. Beveridge, Convergence
Characteristics of Monte Carlo Computer Simulations on Liquid Water.
J. Chem. Phys., 1979. 71: p.
3366.
46.
Klein, M.L., et al., Radical Correlations in Associated Liquids. J. Chem. Phys., 1979. 71:
p. 3889.
47.
Mehrotra, P.K. and D.L. Beveridge, Structural
Analysis of Molecular Solutions Based on Quasi-Component Distribution
Functions. Application to [H2CO]aq
at 25 °C. J. Am. Chem.
Soc., 1980. 102(13): p.
4287-4294.
48.
Beveridge, D.L., et al., Journal of Biomolecular Structure and
Dynamics, 1980. 2:
p. 85.
49.
Mezei, M. and D.L. Beveridge, Monte
Carlo Studies of the Structure of Dilute Aqueous Solutions of Li+,
Na+, K+,
F-, and Cl-.
J. Chem. Phys., 1981. 74: p.
6902-6910.
50.
Mezei, M. and D.L. Beveridge, Theoretical
Studies of Hydrogen Bonding in Liquid Water and Dilute Aqueous Solutions.
J. Chem. Phys., 1981. 74: p.
622.
51.
Mehrotra, P.K., F.T. Marchese, and D.L. Beveridge, Statistical
State Solvation Sites. J. Am. Chem. Soc., 1981. 103: p. 672.
52.
Marchese, F.T., P.K. Mehrotra, and D.L. Beveridge, A
Revised Potential Function for the Water Dimer in the EPEN/2 Form. J.
Phys. Chem., 1981. 85: p. 1.
53.
Beveridge, D.L., et al., Liquid
State Computer Simulation Studies of Biomolecualr Solvaton Problems.
Ann. N.Y. Acad. Sci., 1981. 367:
p. 108.
54.
Mezei, M. and D.L. Beveridge, Further
Quasicomponent Distribution Function Analysis of Liquid Water.
Temperature Dependence of the Results. J. Chem. Phys., 1982. 76: p. 593.
55.
Marchese, F.T., P.K. Mehrotra, and D.L. Beveridge, Transferable
Potential Functions. Quantum
Mechanical Calculations of Intermolecular Interaction Energies. J.
Phys. Chem., 1982. 86: p. 2592.
56.
Ravishanker, G., M. Mezei, and D.L. Beveridge, Monte
Carlo Computer Simulation Studies of the Hydrophobic Effect:
Potential of Mean Force for [(CH4)2] at 25o and 50o
C. Symp. Faraday Soc., 1982.
57.
Marchese, F.T., P.K. Mehrotra, and D.L. Beveridge, Statistical
State Sites: (CHO)2
aq., in Biophysics of Water,
F. Francks and S. Mathias, Editors. 1982, John Wiley: New York
58.
Beveridge, D.L., et al., Monte
Carlo Computer Simulation Studies of the Equilibrium Properties and
Structure of Liquid Water, in Molecular-Based
Study of Fluids, J.M. Haile and G.A. Mansoori, Editors. 1983, American
Chemical Society: Washington, D.C. p. 297-351
59.
Mezei, M., et al., Monte Carlo Studies on Water in the dCpG/Proflavin Crystal Hydrate.
J. Biomol. Struct. Dyn., 1983. 1:
p. 287-297.
60.
Mehrotra, P.K., M. Mezei, and D.L. Beveridge, Convergence
Acceleration in Monte Carlo Computer Simulation on Water and Aqueous
Solutions. J. Chem. Phys., 1983. 78:
p. 3156.
61.
Marchese, F.T. and D.L. Beveridge, A
Pattern Recognition Approach to the Analysis of Geometrical Features of
Solvation: Application to the Aqueous Hydration of Li+,
Na+, K+,
F-, and Cl-.
J. Am. Chem. Soc., 1984. 106:
p. 3713-3720.
62.
Beveridge, D.L., et al., Aqueous
hydration of nucleic acid constituents: Monte Carlo computer simulation
studies. J. Biomol. Struct. Dyn., 1984. 2(2):
p. 261-270.
63.
Beveridge, D.L., G. Ravishanker, and M. Mezei, Solvent
Separated Hydrophobic Interactions, in Structure
and Dynamics of Proteins and Nucleic Acids, E. Clementi, Editor. 1984,
Adenine Press: New York.
64.
Marchese, F.T., P.K. Mehrotra, and D.L. Beveridge, Monte
Carlo Simulation Study of a Dilute Aqueous Solution of Formamide at 25o
C. Aqueous Hydration of a
Peptide Bond. J. Phys. Chem., 1984. 88:
p. 5692.
65.
Marchese, F.T. and D.L. Beveridge, Cooperativity
of Hydrophilic and Hydrophobic Effects in the Aqueous Hydration of
Poly-Functional Solutes. Chem. Phys. Lett., 1984. 105:
p. 431.
66.
Mezei, M., P.K. Mehrotra, and D.L. Beveridge, Monte
Carlo Computer Simulation of the Aqueous Hydration of the Glycine
Zwitterion at T=25o
C. J. Biomol. Struct. Dyn., 1984. 2:
p. 1.
67.
Mezei, M. and D.L. Beveridge, Generic
Solvation Sites in a Crystal. J. Comput. Chem., 1984. 5:
p. 523.
68.
Ravishanker, G., et al., Aqueous
Hydration of Benzene. J. Am. Chem. Soc., 1984. 106:
p. 4102.
69.
Mezei, M. and D.L. Beveridge, QCDF
Analysis of Recent Water Models: TIPS, SPC, TIPS2, TIPS4P, QPEN and CH1.
Mol. Phys., 1984.
70.
Mehrotra, P.K., M. Mezei, and D.L. Beveridge, Monte
Carlo Determination of the Internal Energies of Hydration for the Ala
Dipeptide in the C7, C5, aR
and PII Conformations. Int. J. Quantum Chem., 1984. 11:
p. 301.
71.
Mezei, M., P.K. Mehrotra, and D.L. Beveridge, Monte-Carlo
Determination of the Free Energy and Internal Energy of Hydration for the
Ala Dipeptide at 25 °C. J. Am. Chem. Soc., 1985. 107:
p. 2239-2245.
72.
Beveridge, D.L. and M. Mezei, Free
Energy Simulations: The Coupling Parameter Approach and Topographical
Transition Coordinates, in Molecular
Dynamics and Protein Structure, J. Hermans, Editor. 1985, Polycrystal
Book Service: Western Springs, Ill.
73.
Ravishanker, G. and D.L. Beveridge, Potential
of Mean Force for the Stacking of Phenyl Rings in Aqueous Solution. J.
Am. Chem. Soc., 1985. 107: p.
2565.
74.
Beveridge, D.L., et al., Free
Energy Simulations: Applications
to the Study of Liquid Water, Hydrophobic Interactions and Solvent Effects
on Conformational Stability. Proc. Int. Symp. Biomol. Struct.
Interactions, Suppl. J. Biosci., 1985. 8(192):
p. 167.
75.
Computer Simulation of
Chemical and Biomolecular Systems., D.L. Beveridge and W.L. Jorgensen,
Editors. 1986, Anals of the New-York Academy of Science.: New-York. p.
255-266.
76.
Mezei, M., et al., Monte Carlo Studies of the Aqueous Hydration of cis- and trans-N-Methyl
Acetamide: Sensitivity of
Results to Convergence and to Choice of Intermolecular Potential
Functions. Isr. J. Chem., 1986. 27:
p. 163-172.
77.
Mezei, M. and D.L. Beveridge, Structural
Chemistry of Biomolecular Hydration: The Proximity Criterion. Methods
Enzymol., 1986. 127: p. 21-47.
78.
Mezei, M. and D.L. Beveridge, Free
Energy Simulations, in Computer
Simulations and Biomolecular Systems, D.L. Beveridge and W.L.
Jorgensen, Editors. 1986, Ann. New York Academy of Sciences: New York.
79.
Ravishanker, G. and D.L. Beveridge, Theoretical
Studies of the Hydrophobic Effect, in Theoretical
Chemistry of Biological Systems, G. Naray-Szabo, Editor. 1986,
Elsevier Publishers: Amsterdam.
80.
Beveridge, D.L., et al., Solvent
Effects on Conformational Stability of the Ala Dipeptide:
Full Free Energy Simulations, in Proc.
4th Conversation in Biomolecular Stereodynamics, R.H. Sarma, Editor.
1986, Adenine Press: New York.
81.
Ravishanker, G., M. Mezei, and D.L. Beveridge, Conformational
Stability and Flexibility of the Ala Dipeptide in Free Space and In Water:
Monte Carlo Computer Simulation Studies. J. Comput. Chem.,
1986. 7: p. 345.
82.
Jayaram, B., M. Mezei, and D.L. Beveridge, Monte
Carlo Study of the Aqueous Hydration of Dimethylphosphate Conformations.
J. Comput. Chem., 1987. 8: p.
917-921.
83.
Marchese, F.T. and D.L. Beveridge, Thermal
Motion From Monte Carlo Simulations of Aqueous Ionic Solutions. Int.
J. Quantum Chemistry, 1987. 8:
p. 917.
84.
Beveridge, D.L. and W.L. Jorgensen, eds. Computer
Simulation of Chemical and Biomolecular Systems. Vol. 484. 1987, Ann.
N.Y. Acad. Sci.
85.
Jayaram, B., M. Mezei, and D.L. Beveridge, Conformational
Stability of Dimethyl Phosphate Anion in Water: Liquid-State Free Energy
Simulations. J. Am. Chem. Soc., 1988. 110:
p. 1691-1694.
86.
Jayaram, B., G. Ravishanher, and D.L. Beveridge, Conformational
Preferences of Phosphodiester Torsion Angles in Dimethylphosphate Anion in
Free Space and Water: Quasi-Harmonic Monte Carlo and Hydration Shell
Calculations. J. Phys. Chem., 1988. 92:
p. 1032-1034.
87.
Berman, H.M., et al., A
Systematic Study of Patterns of Hydration in Nucleic Acids I.
Guanine and Cytosine. J. Biomol. Struct. Dyn., 1988. 5: p. 1101-1110.
88.
Subramanian, P.S., G. Ravishanker, and D.L. Beveridge, Theoretical
Considerations on the "Spine of Hydration" in the Minor Groove
of d(CGCGAATTCGCG) Duplex: Monte Carlo Computer Simulation. Proc.
Natl. Acad. Sci. (USA), 1988. 85:
p. 1836-1840.
89.
Jayaram, B. and D.L. Beveridge, Electrostatic
Free Energy of A Charge Distribution
in Concentric Dielectric Continua II.
Extended Kirkwood Tanford Theory. Biopolymers, 1988. 27:
p. 617.
90.
Subramanian, P.S. and D.L. Beveridge, A
Theoretical Study of the Aqueous Hydration of Canonical B d(CGCGAATTCGCG):
Monte-Carlo Simulation and Comparison with Crystallographic Ordered Water
Sites. J. Biomol. Struct. Dyn., 1989. 6:
p. 1093-1122.
91.
Harte Jr., W.E., S. Swaminathan, and D.L. Beveridge. A
Dynamical Model for HIV-1 Protease: Preliminary Results. in 2d
International Conference on Drug Research in Immunologic and Infectious
Diseases: AIDS. 1989. Arlington, Va.: New York Academy of Sciences.
92.
Beveridge, D.L. and F.M. DiCapua, Free
Energy via Molecular Simulation: Applications to Chemical and Biomolecular
Systems. Ann. Rev. Biophys. Biophys. Chem., 1989. 18:
p. 431-492.
93.
Beveridge, D.L. and F.M. DiCapua, Free
Energy via Molecular Simulation: A Primer, in Computation
of Free Energy for Molecular Systems, W.F. van Gunsteren and P.
Weiner, Editors. 1989, Escom Science Publishers: Leiden.
94.
Westhof, E. and D.L. Beveridge, Hydration
of Nucleic Acids, in Water
Science Reviews: The
Molecules of Life, F. Franks, Editor. 1989, Cambridge University
Press: Cambridge. p. 24-136.
95.
Ravishanker, G., et al., Conformational
and helicoidal analysis of 30 PS of molecular dynamics on the
d(CGCGAATTCGCG) double helix: "curves", dials and windows.
J. Biomol. Struct. Dyn., 1989. 6(4):
p. 669-699.
96.
Beveridge, D.L., et al., Monte-Carlo
Studies of DNA Solvation: Our Path to the Double Helix, in Theoretical
Biochemistry and Molecular Biophysics., R. Lavery and D.L. Beveridge,
Editors. 1990, Adenine: New-York. p. 17-38.
97.
Jayaram, B. and D.L. Beveridge, Free
Energy of an Arbitrary Charge Distribution Imbedded in Coaxial Cylindrical
Dielectric Continua: Application Preferences of DNA in Aqueous Solutions.
J. Phys. Chem., 1990. 94: p.
466-4671.
98.
Jayaram, B. and D.L. Beveridge, A
Simple Method to Estimate Free Energy from a Molecular Simulation:
Renormalization on the Unit Interval. J. Phys. Chem., 1990. 94:
p. 7288-7293.
99.
Jayaram, B., S. Swaminathan, and D.L. Beveridge, Monte-Carlo
Simulation Studies of the Structure of the Counteranion Atmosphere of
B-DNA. Variations on the Primitive Dielectric Model. Macromolecules,
1990. 23: p. 3156-3165.
100.
Swaminathan, S., D.L. Beveridge, and H.M. Berman, Molecular
Dynamics Simulation of a Deoxydinucleoside-Drug Intercalation Complex:
dCdG/Proflavin. J. Phys. Chem., 1990. 94:
p. 4660-4665.
101.
Jayaram, B., et al., Monte
Carlo Simulation Studies on the Structure of the Counterion Atmosphere of
B-DNA. Variations on the Primitive Dielectric Model. Macromolecules,
1990. 23: p. 3156-3165.
102.
Subramanien, P.S., et al., Monte
Carlo Studies of the Hydration of rCpG. Biopolymers, 1990. 29:
p. 771-.
103.
Subramanian, P.S., et al., A
Monte Carlo simulation study of the aqueous hydration of r(GpC)2:
comparison with crystallographic ordered water sites. Biopolymers,
1990. 29(4-5): p. 771-783.
104.
Harte, W.E., Jr., et al., Domain
Communication in the Dynamical Structure of Human Immunodeficiency Virus 1
Protease. Proc. Natl. Acad. Sci. (USA), 1990. 87(22):
p. 8864-8868.
105.
Swaminathan, S., et al., Conformational
and Helicoidal Analysis of the Molecular Dynamics of Proteins:
"curves," dials and windows for a 50 psec dynamic trajectory of
BPTI. Proteins, 1990. 8(2): p. 179-193.
106.
Srinivasan, J., J.M. Withka, and D.L. Beveridge, Molecular
dynamics of an in vacuo model of duplex d(CGCGAATTCGCG) in the B-form
based on the amber 30 force field. Biophys. J., 1990. 58(2):
p. 533-547.
107.
Subramanian, P.S., S. Swaminathan, and D.L. Beveridge, Theoretical
account of the 'spine of hydration' in the minor groove of duplex
d(CGCGAATTCGCG). J. Biomol. Struct. Dyn., 1990. 7(5):
p. 1161-1165.
108.
Beveridge, D.L., et al., Molecular
Simulation Studies on the d(CGCGAATTCGCG) Duplex: Hydration, Ion
Atmosphere, Structure and Dynamics, in Structure
and Methods III. DNA AND RNA, R.H. Sarma and M.H. Sarma, Editors.
1990, Adenine Press: New York. p. 79-112.
109.
DiCapua, F.M., S. Swaminathan, and D.L. Beveridge, Theoretical
Evidence for Destabilization of an a-Helix
By Water Insertion: Molecular Dynamics of a Hydrated Deca-Alanine. J.
Am. Chem. Soc., 1990. 112: p.
6768-6771.
110.
Beveridge, D.L., et al., Methodological
Considerations in Molecular Dynamics Simulations of DNA Oligonucleotides,
in Advances in Biomolecular Simulations, R. Lavery, J.-L. Rivail, and
J. Smith, Editors. 1991, American Institute of Physics: New York.
111.
DiCapua, F.M., S. Swaminathan, and D.L. Beveridge, Theoretical
Evidence for Water Insertion in a-Helix
Bending: Molecular Dynamics of Gly30 and Ala30
in Vacuo and in Solution. J. Am. Chem. Soc., 1991. 113: p. 6145-6155.
112.
Jayaram, B. and D.L. Beveridge, Grand
Canonical Monte-Carlo Simulations on Aqueous Solutions of NaCl and NaDNA:
Excess Chemical Potentials and Sources of Nonideality in Electrolyte and
Polyelectrolyte Solutions. J. Phys. Chem., 1991. 95:
p. 2506-2516.
113.
Langley, D.R., T.W. Doyle, and D.L. Beveridge, The
Dynemicin-DNA Intercalation Complex. A Model Based on DNA Affinity
Cleavage and Molecular Dynamics Simulation. J. Am. Chem. Soc., 1991. 113: p. 4395-4403.
114.
Swaminathan, S., W.E. Harte, and D.L. Beveridge, Investigation
of Domain Structure in Proteins via Molecular Dynamics Simulation:
Application to HIV-1 Protease Dimer. J. Am. Chem. Soc., 1991. 113: p. 2717-2721.
115.
Swaminathan, S., G. Ravishanker, and D.L. Beveridge, Molecular
Dynamics of B-DNA Including Water and Counterions: A 140 ps Trajectory for
d(CGCGAATTCGCG) Based on the GROMOS Force Field. J. Am. Chem. Soc.,
1991. 113: p. 5027-5040.
116.
Withka, J.M., et al., Time Dependence of Nuclear Overhauser Effects of Duplex DNA from
Molecular Dynamics Trajectories. J. Am. Chem. Soc., 1991. 113:
p. 5041-5049.
117.
Jayaram, B., F.M. DiCapua, and D.L. Beveridge, A
Theoretical Study of Polyelecrolyte Effects in Protein-DNA Interactions:
Monte Carlo Free Energy Simulations on the Ion Atmosphere Contribution to
the Thermodynamics of Lambda Repressor-Operator Complex Formation. J.
Am. Chem. Soc., 1991. 113: p.
5211-5215.
118.
Swaminathan, S. and D.L. Beveridge, Molecular
Dynamics of B-DNA Including Water and Counterions:
A 140 psec Trajectory for d(CGCGAATTCGCG) Based on the GROMOS Force
Field. J. Am. Chem. Soc., 1991. 113:
p. 5027-5040.
119.
Lavery, R. and D.L. Beveridge, eds. Theoretical
Biochemistry and Molecular Biophysics Volume II.
Proteins. 1991, Adenine Press: New York.
120.
Lavery, R. and D.L. Beveridge, eds. Theoretical
Biochemistry and Molecular Biophysics Volume I.
DNA. 1991, Adenine Press: New York.
121.
Harte Jr., W.E., S. Swaminathan, and D.L. Beveridge, Molecular
Dynamics of HIV-1 Protease. PROTEINS: Structure, Function and
Energetics, 1992. 13: p.
175-194.
122.
Berman, H.M., et al., The
Nucleic Acid Database: A Comprehensive Relational Database of
Three-dimensional Structures of Nucleic Acids. Biophys. J., 1992. 63:
p. 751-759.
123.
Withka, J.M., et al., Toward a dynamical structure of DNA: comparison of theoretical and
experimental NOE intensities of d(CGCGAATTCGCG). Science, 1992. 255(5044):
p. 597-599.
124.
Harte Jr., W.E. and D.L. Beveridge, Mechanism
for the Destabilization of the Dimer Interface in a Mutant HIV-1 Protease:
A Molecular Dynamics Study. Journal of the American Chemical Society,
1993. 115: p. 1231-1234.
125.
Vijayakumar, S., et al., Differential
stability of b-sheets and a-helices
in b-lactamase: a high temperature
molecular dynamics study of unfolding intermediates. Biophys. J.,
1993. 65(6): p. 2304-2312.
126.
Prevost, C., et al., Persistence
analysis of the static and dynamical helix deformations of DNA
oligonucleotides: application to the crystal structure and molecular
dynamics simulation of d(CGCGAATTCGCG)2. Biopolymers, 1993. 33(3):
p. 335-350.
127.
Beveridge, D.L., et al., Molecular
Dynamics Simulations on the Hydration, Structure and Motions of DNA
Oligomers, in Water and Biological Molecules, E. Westhof, Editor. 1993, The
Macmillan Press, Ltd.: London. p. 165-225.
128.
Harte Jr., W.E. and D.L. Beveridge, Prediction
of the Protonation State within the Active Site of an HIV-1 Protease
Inhibitor Complex. J. Am. Chem. Soc., 1993. 115:
p. 3883-3886.
129.
Fritsch, V., et al., Molecular dynamics simulations of poly(dA).poly(dT): comparisons between
implicit and explicit solvent representations. Biopolymers, 1993. 33(10):
p. 1537-1552.
130.
Subramanian, P.S. and D.L. Beveridge, A
Monte Carlo Simulation Study of the Aqueous Hydration of d(CGCGCG) in Z
Form. Theoretica Chimica Acta, 1993. 85:
p. 3-15.
131.
Young, M.A., et al., Analysis of Helix Bending in Crystal Structures and Molecular Dynamics
Simulations of DNA Oligonucleotides, in Structural
Biology: The State of the Art. Proceedings of the 8th Conversation.,
R.H. Sarma and R.H. Sarma, Editors. 1994, Adenine Press: Albany, New York.
p. 197-214.
132.
McConnell, K.M., et al., A
Nanosecond Molecular Dynamics Trajectory for a B DNA Double Helix:
Evidence for Substates. J. Am. Chem. Soc., 1994. 116:
p. 4461-4462.
133.
Beveridge, D.L. and G. Ravishanker, Molecular
Dynamics Studies of DNA. Curr. Opin. Struct. Bio., 1994. 4:
p. 246-255.
134.
Beveridge, D.L., et al., Molecular
Dynamics Simulations of DNA and Protein-DNA Complexes Including Solvent:
Recent Progress. ACS symposium series, 1994. 568:
p. 381-394.
135.
Balasubramanian, S., et al., Comparison
of the 13C relaxation times and proton scalar couplings of BPTI with
values predicted by molecular dynamics. J. Magn. Reson. B, 1994. 104(3):
p. 240-249.
136.
Harte, W.E., Jr. and D.L. Beveridge, Probing
structure-function relationships in human immunodeficiency virus type 1
protease via molecular dynamics simulation. Methods Enzymol., 1994. 241:
p. 178-195.
137.
Ptaszek, L.M., et al., Molecular
dynamics studies of the human CD4 protein. Biopolymers, 1994. 34(9):
p. 1145-1153.
138.
Langley, D.R., T.W. Doyle, and D.L. Beveridge, Probing
the Underlying Basis for the Binding Specificity of Calicheamicin gI.
A Molecular Dynamics Study. Tetrahedron, 1994. 50:
p. 1379-1396.
139.
Langley, D.R., et al., The
DNA-Esperamicin A1 Complex: A
Model Based on Solvated Molecular Dynamics Simulation. J. Am. Chem.
Soc., 1994. 116: p. 15-29.
140.
Ravishanker, G., S. Vijayakumar, and D.L. Beveridge, STRIPS:
An Algorithm for Generating Two-Dimensional Hydrogen-Bond Topology
Diagram for Proteins, in Modeling the Hydrogen Bond, D.A. Smith, Editor. 1994. p. 209-219.
141.
Vijayakumar, S., et al., Analysis
of Hydrogen Bonding and Stability of Protein Secondary Structures in
Molecular Dynamics Simulations, in Modeling
the Hydrogen Bond, D.A. Smith, Editor. 1994. p. 175-193.
142.
Auffinger, P. and D.L. Beveridge, A
simple test for evaluating the truncation effects in simulations of
systems involving charged groups. Chem. Phys. Lett., 1995. 234(4/6):
p. 413-415.
143.
Vijayakumar, S., et al., Molecular
Dynamics Simulation of a Class A -Lactamase: Structural and Mechanistic
Implications. J. Am. Chem. Soc., 1995. 117(6):
p. 1722-1730.
144.
Young, M.A., et al., Analysis of Local Helix Bending in Crystal Structures of DNA
Oligonucleotides and DNA-Protein Complexes. Biophysical Journal, 1995.
68(6): p. 2454-2468.
145.
Young, M.A., et al., Structure determination and analysis of local bending in an A-tract DNA
duplex: comparison of results from crystallography, nuclear magnetic
resonance, and molecular dynamics simulation on d(CGCAAAAATGCG).
Methods Enzymol., 1995. 261: p.
121-144.
146.
Beveridge, D.L., et al., Molecular
Dynamics Simulations on DNA and a Protein-DNA Complex Including Solvent,
in Modeling of Biomolecular Structures and Mechanisms, A. Pullman and
B. Pullman, Editors. 1995, Kluew Academic Publishers. p. 409-423.
147.
Beveridge, D.L., et al., Molecular
dynamics simulations of DNA and a protein-DNA complex including solvent.
Mol. Eng., 1995. 5(1-3): p.
255-69.
148.
Jayaram, B. and D.L. Beveridge, Modeling
DNA in Aqueous Solution: Theoretical And Computer Simulation Studies on
the Ion Atmosphere of DNA. Ann. Rev. Biophys. Biomol. Struct., 1996. 25:
p. 367-394.
149.
Jayaram, B. and D.L. Beveridge, Modeling
DNA in aqueous solutions: theoretical and computer simulation studies on
the ion atmosphere of DNA. Annu Rev Biophys Biomol Struct, 1996. 25:
p. 367-94.
150.
Berman, H.M., et al., The
Nucleic Acid Database Project, in Biological
Structures and Dynamics, R.H. Sarma and M.H. Sarma, Editors. 1996,
Adenine Press: Albany. p. 1-13.
151.
Young, M.A., B. Jayaram, and D.L. Beveridge, Intrusion
of Counterions into the Spine of Hydration in the Minor Groove of B-DNA:
Fractional Occupancy of Electronegative Pockets. J. Am. Chem. Soc.,
1997. 119(1): p. 59-69.
152.
Ravishanker, G., et al., Treatment
of Counterions in Computer Simulations of DNA. Rev. of Comp. Chem.,
1997. 11: p. 317-372.
153.
Young, M.A., G. Ravishanker, and D.L. Beveridge, A
5-Nanosecond Molecular Dynamics Trajectory for B-DNA: Analysis of
Structure, Motions and Solvation. Biophys. J., 1997. 73(5):
p. 2313-2336. [PDF]
154.
Flatters, D., et al., Conformational
Properties of the TATA Box Binding Sequence of DNA. J. Biomol. Struct.
Dyn., 1997. 14(6): p. 1-9.
155.
Beveridge, D.L., Monte Carlo
and Molecular Dynamics Simulations in Polymer Science (Book Review).
J. Am. Chem. Soc., 1997. 119:
p. 9938.
156.
Beveridge, D.L., Molecular
Dynamics of Deoxyribonucleic Acids, in Encyclopedia
Of Computational Chemistry, P.v.R. Schleyer, et al., Editors. 1998,
John Wiley & Sons: Chichester.
157.
Young, M.A. and D.L. Beveridge, Molecular
Dynamics Simulations of an Oligonucleotide Duplex with Adenine Tracts
Phased by a Full Helix Turn. Journal of Molecular Biology, 1998. 281(4):
p. 675-687.
158.
Beveridge, D.L., M.A. Young, and D. Sprous, Modeling
of DNA via Molecular Dynamics Simulation: Structure, Bending, and
Conformational Transitions, in Molecular
Modeling of Nucleic Acids, N.B. Leontis and J. Santa Lucia, J.,
Editors. 1998, American Chemical Society: Washington, D.C. p. 260-284.
159.
Kombo, D.C., M.A. Young, and D.L. Beveridge, Molecular
Dynamics Simulation of the OL1 DNA Operator:
The Unusual Geometrical Features at the Center of the DNA Operator
Site in the Absence of Bound Protein. submitted, 1998.
160.
Sprous, D., M.A. Young, and D.L. Beveridge, Molecular
Dynamics Studies of the Conformational Preferences of a DNA Double Helix
in Water and in an Ethanol/Water Mixture:
Theoretical Considerations of the A/B Transition. J. Phys.
Chem., 1998. 102: p. 4658-4667.
161.
Jayaram, B., Y. Liu, and D.L. Beveridge, A
Modification of the Generalized Born Theory for Improved Estimates of
Solvation Energies and pKa Shifts. J. Chem. Phys., 1998. 109:
p. 1465-1471.
162.
Sprous, D., et al., Molecular Dynamics Information Extraction, in Rational Drug Design, W.J.H. D.G. Truhlar, A.J. Hopfinger, J. Blaney,
R.A. Dammkoehler, Editor. 1998, Springer-Verlag: New York. p. 127-148.
163.
Young, M.A., B. Jayaram, and D.L. Beveridge, Local
Dielectric Environment of B-DNA in Solution: Results from a 14 Nanosecond
Molecular Dynamics Trajectory. The Journal of Physical Chemistry B,
1998. 102(39): p. 7666-7669.
164.
Jayaram, B., et al., Free
Energy Analysis of the Conformational Preferences of A and B forms of DNA
in Solution. Journal of the American Chemical Society, 1998. 120(41):
p. 10629-10633.
165.
Jayaram, B., D. Sprous, and D.L. Beveridge, Solvation
Free Energy of Biomacromolecules: Parameters for a Modified Generalized
Born Model Consistent with the AMBER Force Field. J. Phys. Chem.,
1998. 102(47): p. 9571-9576.
166.
Beveridge, D.L., Molecular
Modeling: Principles and Applications (Book Review). J. Am. Chem.
Soc., 1998. 120: p. 10629-10633.
167.
Sprous, D., M.A. Young, and D.L. Beveridge, Molecular
Dynamics Studies of Axis Bending in d(G5-(GA4T4C)2-C5)
and d(G5-(GT4A4C)2-C5):
Effects of Sequence Polarity on DNA Curvature. J. Mol. Biol., 1999. 285:
p. 1623-1632.
168.
Jayaram, B., et al., Free
Energy Analysis of Protein-DNA Binding: The EcoRI Endonuclease - DNA
Complex. J. Comput. Phys., 1999. 151(1):
p. 333-357.
169.
Jayaram, B. and D.L. Beveridge, Excess
Thermodynamic Properties of Dipole Liquids from Kirkwood Dielectric
Theory. J. Chem. Phys., 1999. MS
in Preparation.
170.
Kombo, D.C., et al., Computational
analysis of variants of the operator binding domain of the bacteriophage
lambda repressor. International Journal of Quantum Chemistry, 1999. 75(3): p. 313-325.
171.
Kombo, D.C., M.A. Young, and D.L. Beveridge, One
Nanosecond Molecular Dynamics Simulation of the N-Terminal Domain of the l-Repressor Protein.
Biopolymers, 2000. 53:
p. 596-605.
172.
McConnell, K.J. and D.L. Beveridge, DNA
Structure: What's in 'Charge'? J.Mol. Biol., 2000. in
press.
173.
Beveridge, D.L. and K.J. McConnell, Nucleic
acids: theory and computer simulation, Y2K. Curr Opin Struct Biol,
2000. 10(2): p. 182-196.
174.
Kombo, D.C., M.A. Young, and D.L. Beveridge, Molecular
dynamics simulation accurately predicts the experimentally-observed
distributions of the (C, N, O) protein atoms around water molecules and
sodium ions. Proteins, 2000. 39 (3): p. 212-215.
175.
Liu, Y. and D.L. Beveridge, A
Refined Prediction Method for Gel Retardation of DNA Oligonucleotides from
Dinucleotide Step Parameters:Reconciliation of DNA Bending Models with
Crystal Structure Data. J. Biomol. Strut. & Dyn., 2001. In Press
176.
Jayaram, B., et al., Analysis
of the Binding Free Energy of Protein-DNA Complexes Based on 40 X-ray
Crystal Structures. Submitted J. Comp. Chem., 2001.
177.
McConnell, K.J. and D.L. Beveridge, Molecular
Dynamics Simulations of B'-DNA: Sequence Effects on A-tract Bending and
Bendability. Submitted J. Mol. Biol., 2001.
178.
Kombo, D., et al., Calculation
of the Affinity of the lamda Repressor-Operator Complex Based on free
Energy Component Analysis. Molecular Simulation, 2001: In Press.
179.
McConnell, K.J., M.A. Young, and D.L. Beveridge, Molecular
Dynamics Simulations on Crystallographic Unit Cells of d(CGCGAATTCGCG)2
and d(CGCAAAATGCG)2 Comparison with Predicted Solution
Structures and Studies of Packing Effects. MS in preparation..
180.
McConnell, K.J., et al., Solution
Structure of DNA: Comparing Molecular Dynamics and NMR Results on the
Duplexes d(CGCGAATTCGCG) and d(CGCAAAAATGCG). MS in Preparation.
181.
Beveridge, D.L., The Compleat
Journal Club: How a
Collaborative Learning Structure Supports Students in the Transition From
Classroom Science to Independent Research. MS In Preparation..
182.
Sprous, D. and D.L. Beveridge, d[G5-{GA4T4C}2-C5]
simulated in 37.5% MPD shows reduced curvature. manuscript in
preparation..