Publications

 [ 1984 - 1989 ]    [ 1990 - 1994 ]    [ 1995 - 1999 ]    [ 2000 - 2004 ]    [ 2005 - 2009 ]    [ 2010 - 2014 ] 
[ 2015 - 2020 ]   [ 2021 - 2025 ]

1995 - 1999

• Stanton, R. V., Hartsough, D. S., and Merz, K. M. (1995) AN EXAMINATION OF A DENSITY-FUNCTIONAL MOLECULAR MECHANICAL COUPLED POTENTIAL, Journal of Computational Chemistry 16, 113-128. 
• Hartsough, D. S., and Merz, K. M. (1995) POTENTIAL OF MEAN FORCE CALCULATIONS ON THE S(N)1 FRAGMENTATION OF TERT-BUTYL CHLORIDE, Journal of Physical Chemistry 99, 384-390. 
• Stanton, R. V., Little, L. R., and Merz, K. M. (1995) QUANTUM FREE-ENERGY PERTURBATION STUDY WITHIN A PM3-MM COUPLED POTENTIAL, Journal of Physical Chemistry 99, 483-486. 
• Marrone, T. J., and Merz, K. M. (1995) MOLECULAR RECOGNITION OF K+ AND NA+ BY VALINOMYCIN IN METHANOL, Journal of the American Chemical Society 117, 779-791. 
• Steel, E. A., Merz, K. M., Selinger, A., and Castleman, A. W. (1995) MASS-SPECTRAL AND COMPUTATIONAL FREE-ENERGY STUDIES OF ALKALI-METAL ION-CONTAINING WATER CLUSTERS, Journal of Physical Chemistry 99, 7829-7836. 
• Rossi, K. A., Merz, K. M., Smith, G. M., and Baldwin, J. J. (1995) APPLICATION OF THE FREE-ENERGY PERTURBATION METHOD TO HUMAN CARBONIC-ANHYDRASE-II INHIBITORS, Journal of Medicinal Chemistry 38, 2061-2069.
• Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A 2ND GENERATION FORCE-FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC-ACIDS, AND ORGANIC-MOLECULES, Journal of the American Chemical Society 117, 5179-5197. 
• Damodaran, K. V., and Merz, K. M. (1995) INTERACTION OF THE FUSION INHIBITING PEPTIDE CARBOBENZOXY-D-PHE-L-PHE-GLY WITH N-METHYLDIOLEOYLPHOSPHATIDYLETHANOLAMINE LIPID BILAYERS, Journal of the American Chemical Society 117, 6561-6571.
• Stanton, R. V., Dixon, S. L., and Merz, K. M. (1995) General formulation for a quantum free energy perturbation study, Journal of Physical Chemistry 99, 10701-10704. 
• Hartsough, D. S., and Merz, K. M. (1995) Dynamic force field models: Molecular dynamics simulations of human carbonic anhydrase II using a quantum mechanical/molecular mechanical coupled potential, Journal of Physical Chemistry 99, 11266-11275. 
• Vincent, J. J., and Merz, K. M. (1995) A highly portable parallel implementation of AMBER4 using the message-passing interface standard, Journal of Computational Chemistry 16, 1420-1427. 
• Best, S. A., Bianconi, P. A., and Merz, K. M. (1995) Structural analysis of carbyne network polymers, Journal of the American Chemical Society 117, 9251-9258.
• Stanton, R. V., Little, L. R., and Merz, K. M. (1995) AN EXAMINATION OF A HARTREE-FOCK MOLECULAR MECHANICAL COUPLED POTENTIAL, Journal of Physical Chemistry 99, 17344-17348. 
• Damodaran, K. V., Merz, K. M., and Gaber, B. P. (1995) INTERACTION OF SMALL PEPTIDES WITH LIPID BILAYERS, Biophysical Journal 69, 1299-1308. 
• Best, S. A., Bianconi, P. A., and Merz, K. M. (1995) STRUCTURAL-ANALYSIS OF CARBYNE NETWORK POLYMERS, In Computer-Aided Molecular Design: Applications in Agrochemicals, Materials, and Pharmaceuticals ACS Symposium Series, 589, 304-315. 
• Cheng, A., and Merz, K. M. (1996) The pressure and pressure tensor for macromolecular systems, Journal of Physical Chemistry 100, 905-908. 
• Cheng, A. L., and Merz, K. M. (1996) Application of the Nose-Hoover chain algorithm to the study of protein dynamics, Journal of Physical Chemistry 100, 1927-1937. 
• Dixon, S. L., and Merz, K. M. (1996) Semiempirical molecular orbital calculations with linear system size scaling, Journal of Chemical Physics 104, 6643-6649.
• Toba, S., Hartsough, D. S., and Merz, K. M. (1996) Solvation and dynamics of chymotrypsin in hexane, Journal of the American Chemical Society 118, 6490-6498. 
• Merz, K. M., and Banci, L. (1996) Binding of azide to human carbonic anhydrase .2. The role electrostatic complementarity plays in selecting the preferred resonance structure of azide, Journal of Physical Chemistry 100, 17414-17420. 
• Jackman, J. E., Merz, K. M., and Fierke, C. A. (1996) Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer, Biochemistry 35, 16421-16428. 
• Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1996) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol 117, pg 5179, 1995), Journal of the American Chemical Society 118, 2309-2309. 
• Stanton, R. V., Dixon, S. L., and Merz, K. M. (1996) Free energy perturbation calculations within quantum mechanical methodologies, In Chemical Applications of Density-Functional Theory, ACS Symposium Series, 629, 142-153. 
• Merz, K. M., and Banci, L. (1997) Binding of bicarbonate to human carbonic anhydrase II: A continuum of binding states, Journal of the American Chemical Society 119, 863-871. 
• Dixon, S. L., and Merz, K. M. (1997) Fast, accurate semiempirical molecular orbital calculations for macromolecules, Journal of Chemical Physics 107, 879-893. 
• Toba, S., and Merz, K. M. (1997) The concept of solvent compatibility and its impact on protein stability and activity enhancement in nonaqueous solvents, Journal of the American Chemical Society 119, 9939-9948. 
• Cheng, A. L., and Merz, K. M. (1997) Ice-binding mechanism of winter flounder antifreeze proteins, Biophysical Journal 73, 2851-2873. 
• Best, S. A., Merz, K. M., and Reynolds, C. H. (1997) GB/SA-based continuum solvation model for octanol, Journal of Physical Chemistry B 101, 10479-10487. 
• Glennon, T. M., and Merz, K. M. (1997) A carbohydrate force field for AMBER and its application to the study of saccharide to surface adsorption, Journal of Molecular Structure-Theochem 395, 157-171.
• Merz, K. M. (1997) Molecular dynamics simulations of lipid bilayers, Current Opinion in Structural Biology 7, 511-517.
• Vincent, J. J., Dixon, S. L., and Merz, K. M. (1998) Parallel implementation of a divide and conquer semiempirical algorithm, Theoretical Chemistry Accounts 99, 220-223. 
• Nadig, G., Van Zant, L. C., Dixon, S. L., and Merz, K. M. (1998) Charge-transfer interactions in macromolecular systems: A new view of the protein/water interface, Journal of the American Chemical Society 120, 5593-5594.
• Hartmann, M., Merz, K. M., van Eldik, R., and Clark, T. (1998) The important role of active site water in the catalytic mechanism of human carbonic anhydrase II - A semiempirical MO approach to the hydration of CO2, Journal of Molecular Modeling 4, 355-365.
• Best, S. A., Merz, K. M., and Reynolds, C. H. (1999) Free energy perturbation study of octanol/water partition coefficients: Comparison with continuum GB/SA calculations, Journal of Physical Chemistry B 103, 714-726. 
• Allcock, H. R., Napierala, M. E., Olmeijer, D. L., Best, S. A., and Merz, K. M. (1999) Ionic conduction in polyphosphazene solids and gels: C-13, P-31, and N-15 NMR spectroscopy and molecular dynamics simulations, Macromolecules 32, 732-741. 
• Ermolaeva, M. D., van der Vaart, A., and Merz, K. M. (1999) Implementation and testing of a frozen density matrix - Divide and conquer algorithm, Journal of Physical Chemistry A 103, 1868-1875. 
• Toba, S., Colombo, G., and Merz, K. M. (1999) Solvent dynamics and mechanism of proton transfer in human carbonic anhydrase II, Journal of the American Chemical Society 121, 2290-2302. 
• Toba, S., Damodaran, K. V., and Merz, K. M. (1999) Binding preferences of hydroxamate inhibitors of the matrix metalloproteinase human fibroblast collagenase, Journal of Medicinal Chemistry 42, 1225-1234. 
• Colombo, G., Toba, S., and Merz, K. M. (1999) Rationalization of the enantioselectivity of subtilisin in DMF, Journal of the American Chemical Society 121, 3486-3493.
• van der Vaart, A., and Merz, K. M. (1999) Divide and conquer interaction energy decomposition, Journal of Physical Chemistry A 103, 3321-3329.
• Gogonea, V., and Merz, K. M. (1999) Fully quantum mechanical description of proteins in solution. Combining linear scaling quantum mechanical methodologies with the Poisson-Boltzmann equation, Journal of Physical Chemistry A 103, 5171-5188. 
• Cheng, A. L., and Merz, K. M. (1999) Application of a multiple time step algorithm to biomolecular systems, Journal of Physical Chemistry B 103, 5396-5405. 
• Colombo, G., and Merz, K. M. (1999) Stability and activity of mesophilic subtilisin E and its thermophilic homolog: Insights from molecular dynamics simulations, Journal of the American Chemical Society 121, 6895-6903. 
• van der Vaart, A., and Merz, K. M. (1999) The role of polarization and charge transfer in the solvation of biomolecules, Journal of the American Chemical Society 121, 9182-9190.
• Monard, G., and Merz, K. M. (1999) Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems, Accounts of Chemical Research 32, 904-911.