Publications

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

2000 - 2004

• Gogonea, C. B., Gogonea, V., Ali, Y. M., Merz, K. M., and Siddiqui, S. S. (1999) Computational prediction of the three-dimensional structures for the Caenorhabditis elegans tubulin family, Journal of Molecular Graphics & Modelling 17, 90-100. 
• Van der Vaart, A., and Merz, K. M. (2000) Charge transfer in biologically important molecules: Comparison of high-level ab initio and semiempirical methods, International Journal of Quantum Chemistry 77, 27-43. 
• Gogonea, V., and Merz, K. M. (2000) A quantum mechanical-Poisson-Boltzmann equation approach for studying charge flow between ions and a dielectric continuum, Journal of Chemical Physics 112, 3227-3235. 
• Gogonea, V., and Merz, K. M. (2000) Charge flow between ions and a dielectric continuum. 2. Variational method for distributing charge into the dielectric, Journal of Physical Chemistry B 104, 2117-2122.
• van der Vaart, A., Bursulaya, B. D., Brooks, C. L., and Merz, K. M. (2000) Are many-body effects important in protein folding?, Journal of Physical Chemistry B 104, 9554-9563.
• N. Diaz; D. Suarez; K. M. Merz, Jr. (2000)  Zinc Metallo-beta-Lactamase from Bacteroides fragilis: A Quantum Chemical Study on Model Systems of the Active Site,  J. Am. Chem. Soc. 2000, 122, 4197-4208. 
• Cheng, A., Best, S. A., Merz, K. M., and Reynolds, C. H. (2000) GB/SA water model for the Merck molecular force field (MMFF), Journal of Molecular Graphics & Modelling 18, 273-282. 
• Diaz, N., Suarez, D., and Merz, K. M. (2000) Hydration of zinc ions: theoretical study of Zn(H2O)(4) (H2O)(8)(2+) and Zn(H2O)(6) (H2O)(6)(2+), Chemical Physics Letters 326, 288-292.
• Egan, W. J., Merz, K. M., and Baldwin, J. J. (2000) Prediction of drug absorption using multivariate statistics, Journal of Medicinal Chemistry 43, 3867-3877. 
• Gogonea, V., Westerhoff, L. M., and Merz, K. M. (2000) Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrodinger equation for large molecular systems using a composite density functional-semiempirical Hamiltonian, Journal of Chemical Physics 113, 5604-5613. 
• van der Vaart, A., Suarez, D., and Merz, K. M. (2000) Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems, Journal of Chemical Physics 113, 10512-10523. 
• Colombo, G., Ottolina, G., Carrea, G., and Merz, K. M. (2000) Modelling the enantioselectivity of subtilisin in water and organic solvents: insights from molecular dynamics and quantum mechanical/molecular mechanical studies, Chemical Communications, 559-560.
• Diller, D. J., and Merz, K. M. (2001) High throughput docking for library design and library prioritization, Proteins-Structure Function and Genetics 43, 113-124. 
• Diaz, N., Suarez, D., Sordo, T. L., and Merz, K. M. (2001) Molecular dynamics study of the IIA binding site in human serum albumin: Influence of the protonation state of Lys195 and Lys199, Journal of Medicinal Chemistry 44, 250-260. 
• Van der Vaart, A., Gogonea, V., Dixon, S. L., and Merz, K. M. (2000) Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method, Journal of Computational Chemistry 21, 1494-1504. 
• Shim, J. H., Wall, M., Benkovic, S. J., Diaz, N., Suarez, D., and Merz, K. M. (2001) Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations, Journal of the American Chemical Society 123, 4687-4696. 
• Suarez, D., and Merz, K. M. (2001) Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus, Journal of the American Chemical Society 123, 3759-3770. 
• Diaz, N., Suarez, D., Sordo, T. L., and Merz, K. M. (2001) A theoretical study of the aminolysis reaction of lysine 199 of human serum albumin with benzylpenicillin: Consequences for immunochemistry of penicillins, Journal of the American Chemical Society 123, 7574-7583. 
• Suarez, D., and Merz, K. M. (2001) Quantum chemical study of ester aminolysis catalyzed by a single adenine: A reference reaction for the ribosomal peptide synthesis, Journal of the American Chemical Society 123, 7687-7690. 
• Diaz, N., Suarez, D., and Merz, K. M. (2001) Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism, Journal of the American Chemical Society 123, 9867-9879. 
• Diaz, N., Suarez, D., Sordo, T. L., and Merz, K. M. (2001) Acylation of class a beta-lactamases by penicillins: A theoretical examination of the role of serine 130 and the beta-lactam carboxylate group, Journal of Physical Chemistry B 105, 11302-11313. 
• Dixon, S. L., and Merz, K. M. (2001) One-dimensional molecular representations and similarity calculations: Methodology and validation, Journal of Medicinal Chemistry 44, 3795-3809. 
• Brothers, E. N., and Merz, K. M. (2002) Sodium parameters for AM1 and PM3 optimized using a modified genetic algorithm, Journal of Physical Chemistry B 106, 2779-2785.  
• van der Vaart, A., and Merz, K. M. (2002) Charge transfer in small hydrogen bonded clusters, Journal of Chemical Physics 116, 7380-7388. 
• Diller, D. J., and Merz, K. M. (2002) Can we separate active from inactive conformations?, Journal of Computer-Aided Molecular Design 16, 105-112. 
• Suarez, D., Brothers, E. N., and Merz, K. M. (2002) Insights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis, Biochemistry 41, 6615-6630. 
• Suarez, D., Diaz, N., and Merz, K. M. (2002) Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from bacteroides fragilis complexed with imipenem, Journal of Computational Chemistry 23, 1587-1600. 
• Cheng, A., Diller, D. J., Dixon, S. L., Egan, W. J., Lauri, G., and Merz, K. M. (2002) Computation of the physio-chemical properties and data mining of large molecular collections, Journal of Computational Chemistry 23, 172-183. 
• Diaz, N., Sordo, T. L., Merz, K. M., and Suarez, D. (2003) Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin, Journal of the American Chemical Society 125, 672-684. 
• Park, H., and Merz, K. M. (2003) Molecular dynamics and quantum chemical studies on the catalytic mechanism of Delta(5)-3-ketosteroid isomerase: The catalytic diad versus the cooperative hydrogen bond mechanism, Journal of the American Chemical Society 125, 901-911. 
• Cheng, A. L., and Merz, K. M. (2003) Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships, Journal of Medicinal Chemistry 46, 3572-3580. 
• Suarez, D., Diaz, N., and Merz, K. M. (2003) Ureases: Quantum chemical calculations on cluster models, Journal of the American Chemical Society 125, 15324-15337. 
• Raha, K., and Merz, K. M. (2004) A quantum mechanics-based scoring function: Study of zinc ion-mediated ligand binding, Journal of the American Chemical Society 126, 1020-1021.
• Wang, B., Brothers, E. N., van der Vaart, A., and Merz, K. M. (2004) Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: A divide-and-conquer approach, Journal of Chemical Physics 120, 11392-11400. 
• Wang, B., Raha, K., and Merz, K. M. (2004) Pose scoring by NMR, Journal of the American Chemical Society 126, 11430-11431. 
• Brothers, E. N., Suarez, D., Deerfield, D. W., and Merz, K. M. (2004) PM3-compatible zinc parameters optimized for metalloenzyme active sites, Journal of Computational Chemistry 25, 1677-1692. 
• Estiu, G., Merz, K. M. The Hydrolysis of Urea and the Proficiency of Urease. Journal of the American Chemical Society 2004, 126, 6932-6944. 
• Estiu, G., and Merz, K. M. (2004) Enzymatic catalysis of urea decomposition: Elimination or hydrolysis?, Journal of the American Chemical Society 126, 11832-11842.
• Brothers, E. N., and Merz, K. M. (2004) Performance of density functionals with small split valence basis sets, Journal of Physical Chemistry A 108, 2904-2911. 
• Yu, N., and Merz, K. M. (2004) Theoretical study of the electron density distributions of glycyl-L-threonine dihydrate, Molecular Physics 102, 2545-2557.