Publications
1) "Tunnelling Dynamics of
Cyclobutadiene" M. J. S. Dewar, K. M. Merz Jr., and J. J. P.
Stewart J. Am. Chem. Soc. 1984, 106, 4040-4041.
2) "Vibrationally Assisted Tunnelling
(VAT) in a 1,5 Hydrogen Shift" M. J. S. Dewar, K.
M.
Merz, Jr. and J. J. P. Stewart
J. Chem. Soc., Chem. Commun. 1984, 166-168.
3) "Ground States of Molecules. 69.
Aspects of Organotin Chemistry" M. J. S. Dewar, G. L.
Grady, D. R. Kuhn, and K. M. Merz Jr. J. Am. Chem. Soc. 1984, 106, 6773-6777.
4) "The MNDO Potential Energy Surface
and Tunnelling Dynamics of the Cyclobutane
Radical Cation" M. J. S. Dewar and K.
M. Merz Jr. J. Mol. Struct.,
Theochem. 1985,122, 59-65.
5) "Does Chair Cyclooctatetraene
Exist?" M. J. S. Dewar and K. M. Merz Jr. J. Chem. Soc.,
Chem. Commun. 1985, 343-344.
6) "On the Double Proton Shift in
Azophenine" M. J. S. Dewar and K. M. Merz Jr. J. Mol.
Struct., Theochem. 1985,
124, 183-185.
7) "Mechanism of the Azulene to
Naphthalene Rearrangement" M. J. S. Dewar and K. M.
Merz Jr. J. Am. Chem. Soc. 1985, 107, 6111-6112.
8) "Potential Energy Surfaces and
Tunnelling Dynamics of Some Jahn-Teller Active
Molecules" M. J. S. Dewar and K. M.
Merz Jr. J. Phys. Chem. 1985, 89, 4739-4744.
9) "MNDO Calculations for Compounds Containing
Mercury" M. J. S. Dewar, G. L. Grady,
K. M. Merz Jr., and J. J. P. Stewart Organometallics 1985, 4, 1964-1966.
10)
"Aspects of Organomercury Chemistry" M. J. S. Dewar and K. M. Merz Jr.
Organometallics
1985, 4, 1967-1972.
11) "MNDO
Calculations for the Dehydrocyclooctatetraenes" M. J. S. Dewar and K. M.
Merz
Jr. J.
Am. Chem. Soc. 1985, 107, 6175-6179.
12) "MNDO
Calculations for Compounds Containing Zinc" M. J. S. Dewar and K. M. Merz
Jr.
Organometallics 1986, 5, 1494-1496.
13) "The
C10H8 Potential Energy Surface: The Azulene to
Naphthalene Rearrangement" M. J.
S. Dewar and K. M. Merz Jr. J.
Am. Chem. Soc. 1986, 108, 5142-5145.
14)
"Thermal Rearrangement of C10H8 Species: Benzvalene
Analogues and the
Automerization of
Naphthalene" M. J. S. Dewar and K. M. Merz Jr. J. Am. Chem. Soc.
1986,
108, 5146-5153.
15) "
Heavy Atom Tunnelling in the 2-Norbornyl Cation" M. J. S. Dewar and K. M.
Merz Jr.
J.
Am. Chem. Soc. 1986, 108, 5634-5635.
16) "The
Mechanism of The Reformatsky Reaction" M. J. S. Dewar and K. M. Merz Jr. J. Am.
Chem. Soc. 1987,109, 6553-6554.
17) "3,4
Connected Carbon Nets: Through-Space and Through-Bond Interactions in the Solid
State" K. M. Merz Jr., R. Hoffmann,
and A. T. Balaban J. Am.Chem. Soc. 1987, 109, 6742- 6751.
18) "AM1
Calculations for Compounds Containing Zinc" M. J. S. Dewar and K. M. Merz
Jr.
Organometallics
1988, 7, 522-524.
19)
"Hydrogen Migrations in Porphines" C. H. Reynolds and K. M. Merz Jr. J.
Chem. Soc.,
Chem. Commun. 1988, 90-92.
20) "d10-d10
Interactions: Multinuclear Copper(I) Complexes" K. M. Merz Jr., R.
Hoffmann,
and J. Strahle Inorg. Chem. 1988, 27, 2120-2127.
21) "An ab initio Investigation of the Double
Proton Shift in Azophenine" M. K.
Holloway, C. H. Reynolds, and K.
M. Merz, Jr. J. Am. Chem. Soc. 1989, 111, 3466-3468.
22) "The
Catalytic Mechanism of Carbonic Anhydrase" K. M. Merz Jr., R.
Hoffmann, and M.
J. S. Dewar J. Am. Chem. Soc. 1989,
111, 5636-5649.
23) "The
Inhibition of Thermolysin" K. M. Merz Jr. and P. A. Kollman J. Am. Chem. Soc.
1989,
111, 5649-5658.
24) "Free
Energy Calculations on Protein Stability: The Thr 157 -> Val 157 Mutation of
T4
Lysozyme" L. X. Dang, K. M. Merz,
Jr., and P. A. Kollman J. Am. Chem. Soc. 1989, 111,
8505-8508.
25)
"Atomic Charges Derived from Semiempirical Methods" B. H. Besler, K.
M. Merz, Jr., and P. A. Kollman J.
Comput. Chem.1990, 11, 431-439.
26)
"Computer Modeling of the Interactions of Complex Molecules" P. A.
Kollman and K. M.
Merz, Jr. Acc. Chem. Res. 1990, 23, 246-252.
27)
"Insights into the Function of the Zinc-hydroxide-Thr199-Glu106 Hydrogen
Bonding
Network in Carbonic Anhydrases" K. M.
Merz, Jr., J. Mol. Biol. , 1990, 214, 799-802.
28) "The
Gas-Phase and Solution Phase Potential Energy Surfaces for CO2 + nH2O
(n=1,2)"
K. M. Merz, Jr., J. Am. Chem. Soc. 1990, 117, 7973-7980.
29) "The
Binding of CO2 to Human Carbonic Anhydrase II" K. M. Merz, Jr.,
J. Am. Chem. Soc. 1991, 113, 406-411.
30) "The
Inhibition of Carbonic Anhydrase" K. M. Merz, Jr. M. A. Murcko, and P. A. Kollman
J. Am. Chem. Soc. 1991, 113, 4484-4490.
31)
"Determination of pKas of Ionizable Groups in Proteins: The pKa
of Glu 7 and 35 in Hen
Egg-White Lysozyme and Glu 106 in Human
Carbonic Anhydrase II" K. M. Merz, Jr., J.
Am. Chem. Soc. 1991, 113, 3572-3575.
32) "Free
Energy Calculations on the Relative Solvation Free Energies of Benzene, Anisole
and 1,2,3-Trimethoxybenzene: Theoretical
and Experimental Analysis of Aromatic
Methoxy Solvation" L. F. Kyper, R. N.
Hunter, D. Ashton, K. M. Merz, Jr., and
P. A.
Kollman J. Phys. Chem. 1991, 95, 6661-6666.
33)
"Force Field Design for Metalloproteins" S. C. Hoops, K. A. Anderson,
and K. M. Merz, Jr. J. Am. Chem. Soc. 1991, 113, 8262-8270.
34)
"Gas-Phase and Solution-Phase Free Energy Surfaces for CO2 +OH-
-> HCO3-" Z. Peng,
K. M. Merz, Jr. J. Am.Chem. Soc. 1992, 114, 2733-2734.
35)
"Analysis of a Large Database of Electrostatic Potential Derived Atomic
Point Charges "
K. M. Merz, Jr. J. Comput. Chem. 1992, 13, 749-771.
36)
"Conformational Preferences for Hydroxyl Groups in Substituted
Tetrahydropyrans" Y.-J.
Zheng, S. M. Le Grand, and K. M. Merz, Jr.
J. Comput. Chem. 1992, 13, 722-791.
37)
"Structure and Dynamics of the Dilauroylphosphatidylethanolamine (DLPE)
Lipid Bilayer" K. V. Damodaran, K. M. Merz, Jr., and B. P. Gaber Biochemistry 1992,
31, 7656-7664.
38)
"Molecular Recognition of the Potassium Ion by the Naturally Occurring
Ionophore
Nonactin" T. J. Marrone and K. M.
Merz, Jr. J. Am. Chem. Soc. 1992, 114, 7542-7549.
39)
"Study of Hydrogen Bonding Interactions Relevant to Biomolecular Structure
and
Function" Y.-J. Zheng and K. M. Merz,
Jr. J. Comput. Chem. 1992, 13, 1151-1169.
40)
"Mechanism of the Human Carbonic Anhydrase II Catalyzed Hydration of
Carbon Dioxide" Y.-J. Zheng
and K. M. Merz, Jr. J. Am. Chem. Soc.
1992, 114, 10498-10507.
41)
"Protein Flexibility in Aqueous and Non-Aqueous Solutions" D. S.
Hartsough and K. M. Merz, Jr. J. Am. Chem. Soc. 1992, 114, 10113-10116.
42)
"Application of the Genetic Algorithm to the Minimization of Potential
Energy Functions" S. M. Le
Grand and K. M. Merz, Jr Optimization J.
1993, 3, 49-66.
43) "A
Rapid Analytic Approximation to Molecular Surface Area via the Use of Boolean Logic and Look-up Tables" S. M.
LeGrand and K. M. Merz, Jr. J. Comput.
Chem. 1993, 14, 349-352.
44) "The
C6H6 Potential Energy Surface: Automerization of
Benzene" K. M. Merz, Jr, and L. T.
Scott J. Chem. Soc Chem. Commun. 1993, 412-414.
45) "Head
Group - Water Interactions in Lipid Bilayers: A Comparison Between DMPC and DLPE Based Lipid Bilayers" K.
V. Damodaran and K. M. Merz, Jr. Langmuir 1993,
9, 1179-1183.
46)
"Transferability of Metal Ion Parameters" T. J. Marrone and K. M.
Merz Jr J. Phys. Chem. 1993, 97, 6524-6529.
47)
"Theoretical Examination of the Mechanism of Aldose-Ketose
Isomerization" Y.-J. Zheng,
K. M. Merz, Jr, and G. K. Farber Protein Engineering 1993, 6, 479-484.
48)
"Protein Dynamics and Solvation in Aqueous and Nonaqueous
Environments" D. S. Hartsough
and K. M. Merz, Jr. J. Am. Chem. Soc.
1993, 114, 6529-6537.
49)
"Cyanide Binding of Human Carbonic Anhydrase II" Z. Peng; K. M. Merz,
Jr.; L. Banci Proteins
1993, 17,
203-216.
50)
"Theoretical Investigation of the CO2 + OH- -> HCO3- Reaction in
the Gas and Aqueous Phases" Z. Peng;
K. M. Merz, Jr. J. Am. Chem. Soc. 1993, 115, 9640-9647.
51)
"Calculation of Solvation Free Energies Using a Density
Functional/Molecular Dynamics Coupled
Potential" R. V. Stanton; D. S. Hartsough; K. M. Merz, Jr. J.
Phys.Chem.. 1993, 97, 11868-11870.
52)
"Rapid Electrostatic Potential Evaluation" R. V. Stanton; K. M. Merz,
Jr. QCPE Bull. 1993,
13, 50-53.
53)
"Density Functional Transition States of Organic and Organometalllic
Reactions" R. V. Stanton; K. M.
Merz, Jr. J. Chem. Phys. 1994, 100, 434-443.
54)
"Determination of Atomic Charges Including Solvation and Conformational
Effects" T. J. Marrone; D. S.
Hartsough; K. M. Merz, Jr. J. Phys. Chem.
1994, 98, 1341-1343.
55) "A
Comparison of DMPC- and DLPE-Based Lipid Bilayers" K. V. Damodaran and K.
M. Merz, Jr. Biophys. J. 1994, 66, 1076-1087.
56) "A
Force Field for Monosaccharides and (1->4) Linked Polysaccharides" T.
M. Glennon; Y.-J. Zheng; S. M.
LeGrand; B. A. Shutzberg; K. M. Merz, Jr. J.
Comput. Chem. 1994, 15, 1019-1040.
57) "A
Density Functional Study of Symmetric Proton Transfers" R. V. Stanton; K.
M. Merz, Jr. J. Chem. Phys. 1994, 101, 6658-6665.
58) "An
Examination of a Density Functional/Molecular Mechanical Coupled
Potential" R. V. Stanton;
Hartsough, D. S.; K. M. Merz, Jr. J.
Comput. Chem. 1995, 16, 113-128.
59)
"Potential of Mean Force Calculations on the SN1 Fragmentation
of tert-Butyl Chloride" D. S. Hartsough; K. M. Merz, Jr. J. Phys. Chem. 1995, 99, 384-390.
60) "Quantum Free Energy Perturbation Study Within a
PM3/MM Coupled Potential" R. V. Stanton,
L. R. Little; K. M. Merz, Jr.J. Phys.
Chem.. 1995, 99, 483-486.
61) "Molecular Recognition of K+ and Na+ by
Valinomycin in Methanol" T. J. Marrone; K. M. Merz, Jr. J. Am. Chem.
Soc. 1995, 117, 779-791.
62) "Mass Spectral and Computational Free Energy
Studies of Alkali Metal Ion-Containing Water
Clusters" E. A. Steel; K. M. Merz, Jr.; A. Selinger; A. W. Castleman, Jr. J. Phys. Chem.
1995, 99, 7829-7836.
63) "Application of the Free Energy Perturbation Method
on Human Carbonic Anhydrase II Inhibitors"
K. A. Rossi; K. M. Merz, Jr.; G. M. Smith; J. J. Baldwin J. Med. Chem.. 1995, 38, 2061-2069.
64) "A Second Generation Force Field for the
Simulation of Proteins, Nucleic Acids and Organic
Molecules" W. D. Cornell; P. Cieplak; C. I. Bayly; I. R. Gould; K. M.
Merz, Jr. D. M.
Ferguson; D. C. Spellmeyer; T. Fox; J. W. Cladwell; P. A. Kollman J. Am. Chem. Soc. 1995, 117, 5179-5197.
65) "Interaction of the Fusion Inhibiting Peptide
Carbobenzoxy-D-phenyalanyl-L- phenylalanylglycine
with N-Methyl DOPE Lipid Bilayers" K. V. Damodaran; K. M. Merz, Jr. J. Am. Chem. Soc. 1995, 117, 6561-6571.
66) "A General Formulation for a Quantum Mechanical
Free Energy Perturbation Study" R. V.
Stanton; S. L. Dixon; K. M. Merz, Jr. J.
Phys. Chem. 1995, 99, 10701-10704.
67) "Dynamic Force Field Models: Molecular Dynamics
Simulations of Human Carbonic Anhydrase
II Using a Quantum Mechanical/Molecular Mechanical Coupled Potential" D. S. Hartsough; K. M. Merz, Jr.J. Phys. Chem. 1995, 99, 11266-11275.
68) "A Highly Portable Parallel Implementation of AMBER
4 Using the Message Passing Interface
Standard" J. J. Vincent; K. M. Merz, Jr. J. Comput. Chem.. 1995, 16,
1420-1427
69) "A
Structural Analysis of Carbyne Network Polymers" S. A. Best; P. A.
Bianconi; K. M. Merz, Jr. J. Am. Chem. Soc. 1995, 117, 9251-9258.
70) "An Examination of a Hartree-Fock/Molecular
Mechanical Coupled Potential" R. V. Stanton;
L. R. Little; K. M. Merz, Jr. J. Phys.
Chem. 1995, 99, 17344-17348.
71)
"Interaction of Small Peptides with Lipid Bilayers" K. V. Damodaran;
K. M. Merz, Jr.; B. P. GaberBiophys. J. 1995, 69, 1299-1308.
72) "The
Pressure and Pressure Tensor for Macromolecular Systems" A. Cheng; K. M. Merz, Jr. J. Phys. Chem. 1996, 100, 905-908.
73) "Application of the Nose-Hoover Chain Method to the
Study of Protein Dynamics" A. Chang,
K. M. Merz, Jr. J. Phys. Chem. 1996, 100, 1927-1937.
74) "Semiempirical Molecular Orbital Calculations with
Linear System Size Scaling" S. L. Dixon;
K. M. Merz, Jr.J. Chem. Phys. 1996, 104, 6643-6649.
75) "Solvation and Dynamics of Chymotrypsin in
Hexane" S. Toba; D. S. Hartsough; K. M. Merz,
Jr. J. Am. Chem. Soc. 1996, 118, 6490-6498.
76) "Azide Binding to Human Carbonic Anhydrase II"
K. M. Merz, Jr.; L. Banci J. Phys.Chem. 1996, 100, 17414-17420.
77) "Disruption of the Active Site Solvent Network in
Carbonic Anhydrase II Decreases the Efficiency
of Proton Transfer" J. E. Jackman; K. M. Merz, Jr.; C. A. Fierke Biochemistry. 1996, 35, 16421-16428
78) "Bicarbonate Binding to Human Carbonic Anhydrase
II" K. M. Merz, Jr.; L. Banci J. Am.
Chem. Soc. 1997, 119, 863-871.
79) "Fast, Accurate Semiempirical Molecular Orbital
Calculations for Macromolecules" S. L. Dixon;
K. M. Merz, Jr. J. Chem. Phys. 1997, 107, 879-893.
80) "The Concept of Solvent Compatibility and Its
Imapct on protein Stability and Activity in Nonaqueous
Solvents" S. Toba; K. M. Merz, Jr. J.
Am. Chem. Soc. 1997, 119, 9939-9948.
81)
"Ice-Binding Mechanism of Winter Flounder Antifreeze Proteins" A.
Cheng; K. M. Merz, Jr. Biophys J.1997,73, 2851-2873.
82) "A GB/SA Based Continuum Solvation Model For
Octanol" S. A. Best; K. M. Merz, Jr.; C.
H. Reynolds J. Phys. Chem. 1997, 101, 10479-10487.
83) "Parallel Implementation of a Divide and Conquer
Semiempirical Algorithm" J. J. Vincent; K. M. Merz, Jr. Theor. Chem. Acc. 1998, 99, 220-223.
84) "Charge-Transfer Interactions in Macromolecular
Systems: A New View of the Protein/Water
Interface" G. Nadig, L. C. Van Zant; S. L. Dixon; K. M. Merz, Jr J. Am Chem.
Soc 1998, 120, 5593-5594.
85) “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” M. Hartmann; K. M.
Merz, Jr.; R. van Eldik; T. Clark J. Mol.
Model, 1998, 4, 355-365.
86) "Free
Energy Perturbation Study of Octanol/Water Partition Coefficients: Comparison
with Continuum and GB/A Calculations" S. A. Best; K. M. Merz, Jr.; C, H,
Reynolds J. Phys. Chem. 1999, 103, 714-726.
87) "Ionic Conduction in Polyphosphazene Solids abd Gels: 13C, 31P, and 15N NMR Spectroscopy and Molecular Dynamics Simulations" H. R. Allcock: M. E.
Napierala: D.
L. Olmeijer: S. A. Best; K. M. Merz, Jr Macromolecules. 1999, 32, 732-741.
88) "Implementation and Testing of a Frozen Density
Matrix-Divide and Conquer Algorithm" M.
Ermolaeva; A. van der Vaart; K. M. Merz, Jr. J. Phys. Chem. 1999, 103, 1868-1875.
89) "Solvent Dynamics and Mechanism of Proton Transfer
in Human Carbonic Anhydrase II" S.
Toba; G. Colombo; K. M. Merz, Jr. J. Am.
Chem. Soc 1999, 121, 2290-2302.
90) "Binding Preferences of Hydroxamate Inhibitors of the Matrix Metalloproteinase Human
Fibroblast Collagenase (HFC)" S. Toba; K. V. Damodaran; K. M. Merz, Jr. J. Med. Chem. 1999, 42, 1225-1234.
91) "Rationalization of the Enantioselectivity of
Subtilisin in DMF" G. Colombo; S. Toba; K. M. Merz, Jr. J. Am. Chem. Soc
1999, 121, 3486-3493.
92)
"Divide and Conquer Interaction Energy Decomposition" A. van der
Vaart; K. M. Merz, Jr.J. Phys. Chem.A
1999, 103, 3321-3329.
93)
"Fully Quantum Mechanical Description of Proteins in Solution. Combining
Linear Scaling Quantum Mechanical Methodologies with the Poisson-Boltzmann
Equation" V. Gogonea; K. M. Merz, Jr. J.
Phys. Chem. A. 1999, 103,
5171-5188.
94) "Application of a Multiple Time Step Algorithm to
Biomolecular Systems" A. Cheng; K. M.
Merz, Jr. J. Phys. Chem.B 1999, 103, 5396-5405.
95) “
Stability and Activity of Mesophilic Subtilisin E and its Thermophilic
Homolog:Insights from Molecular Dynamics Simulations” G. Colombo; K. M. Merz,
Jr. J. Am. Chem. Soc. 1999, 121, 6895-6903.
96) “The Role
of Polarization and Charge Transfer in the Solvation of Biomolecules” A. van
der Vaart; K. M. Merz, Jr. J. Am. Chem.
Soc. 1999, 121, 9182-9190.
97)
“Computational Prediction of the Three-Dimensional Strucures for the
Caenorhabditis Elegans Tubulin Family” C. A. Gogonea; V. Gogonea; Y. M. Ali; K.
M. Merz, Jr.; S. S. Siddiqui J. Mol.
Graphics. Mod. 2000, 17, 90-100.
98) “Charge
Transfer in Biologically Important Biomolecules: A Comparison of High Level ab initio and Semiempirical Models” A.
van der Vaart; K. M. Merz, Jr. Int. J.
Quantum Chem. 2000,77, 27-43.
99) “A Quantum
Mechanical-Poisson-Boltzmann Equation Approach for Studying Charge Flow Between
Ions and a Continuum Dielectric” V. Gogonea; K. M. Merz, Jr. J. Chem. Phys. 2000, 112, 3227-3235.
100) “Charge
Flow Between Ions and a Dielectric Continuum: 2. Variational Method for
Distributing Charge into the Dielectric”
V. Gogonea; K. M. Merz, Jr. J.
Phys. Chem 2000, 104, 2117-2122.
101) “Are
Many-Body Effects Important in Protein Folding” A. van der Vaart; B. D.
Bursulaya; C. L. Brooks, III, K. M. Merz, Jr. J. Phys. Chem. 2000 104, 9554-9563.
102) “ Zinc
Metallo-b-Lactamase from Bacteroides fragilis: A Quantum Chemical
Study on Model Systems of the Active Site” N. Diaz; D. Suarez; K. M. Merz, Jr. J. Am. Chem. Soc. 2000, 122, 4197-4208.
103) “GB/SA
Water Model for the Merck Molecular Force Field (MMFF)” A. Cheng; S. A. Best;
K. M. Merz, Jr.; C. H. Reynolds J. Mol.
Graphics Mod. 2000, 18, 273-282.
104)
“Hydration of Zinc Ions: Theoretical Study of [Zn(H2O)4](H2O)82+ and [Zn(H2O)6](H2O)62+” N. Diaz; D. Suarez; K. M. Merz, Jr. 2000, 326, 288-292.
105)
“Prediction of Drug Absoption Using Multivariate Statistics” W. J. Egan; K. M.
Merz, Jr.; J. J. Baldwin J. Med. Chem.2000, 43, 3867-3877.
106) “QM/QM
Methods: 1. A Divide and Conquer Strategy for Solving the Schrödinger Equation
for Large Molecular Systems using a Composite Density Functional -
Semiempirical Hamiltonian” V. Gogonea;
L. M. Westerhoff; K. M. Merz, Jr. J. Chem. Phys. 2000 113, 5604-5613.
107) “Critical
Assessment of the Performance of the Semiempirical Divide and Conquer Method
for Single Point Calculations and Geometry Optimizations of Large Chemical
Systems” A. van der Vaart; D. Suarez; K.
M. Merz, Jr. J. Chem. Phys. 2000, 113, 10512-10523
108) Modelling
the Enantioselectivity of Subtilisin in Water and Organic Solvents: Insights
from Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Studies” G.
Colombo; G. Ottolina; G. Carrea; K. M. Merz, Jr. Chem. Commun. 2000,
559-560.
109) “ High
Throughput Docking for Library Design and Library Prioritization” D. J.Diller;
K. M. Merz, Jr. PROTEINS: Struct. Func. Genetics 2001, 43, 113-124.
110) “A Molecular Dynamics Study of the IIA
Binding Site in Human Serum Albumin: Influence of the Protonation State of
Lys195 and Lys199” N.Díaz; D. Suárez; T. L. Sordo; K. M. Merz, Jr. J. Med. Chem. 2001 44, 250-260
111) “Evaluation of the Catalytic Mechanism of AICAR Transformylase by pH-dependent Kinetics, Mutagenesis, and Quantum Chemical Calculations” J. H. Shim; M. Wall; S. J. Benkovic; N. Díaz; D. Suárez; K. M. Merz, Jr. J. Am. Chem. Soc.2001, 123, 4687-4696.
112)
“Molecular Dynamics Simulations of the Mononuclear Zinc b-lactamase from Bacillus
cereus” D. Suárez; K. M. Merz, Jr. J.
Am. Chem. Soc. 2001, 123, 3759-3770.
113) “The
Effect of a Penetration Enhancer on Lipid Membrane - From Computational
Prospective” H. A., Wahab; J. Anwar; D. Barlow; K. V.Damodaran; K. M.Merz, Jr. Biophys J.2001, 80, 327a
114) “A Theoretical Study of the Aminolysis
Reaction of Lysine 199 of Human Serum Albumin with Benzylpenicillin:
Consequences for Immunochemistry of Penicillins” N. Díaz; D. Suárez; T. L.
Sordo; K. M. Merz, Jr. J. Am. Chem. Soc.2001, 123, 7574-7583.
115) “Quantum Chemical Study of Ester
Aminolysis Catalyzed by a Single Adenine: A Reference Reaction for the
Ribosomal Petide Synthesis” D. Suárez; K. M. Merz, Jr.. J.
Am. Chem. Soc.2001, 123, 7687-7690.
116)
“Molecular Dynamics Simulations of the Mononuclear b-lactamase from Bacillus
cereus Complexed with Benzylpenicillin and Quantum Chemical Study of the
Reaction Mechanism” N. Díaz; D. Suárez; K. M. Merz, Jr. J. Am. Chem. Soc.2001, 123, 9867-9879.
117) “Acylation of Class A b-lactamases by Penicillins: A Theoretical Examination of the
Role of Serine 130 and the b-lactam
Carboxylate Group” N. Díaz; D. Suárez;
T.
L. Sordo; K. M. Merz, Jr. J. Phys. Chem.
B 2001, 105, 11302-11313.
118) “One
Dimesional Molecular Representations and Similarity Calculations: Methodology
and Validation” S. Dixon; K.M. Merz Jr., J.
Med. Chem. 2001, 44, 3795-3809.
119) “Sodium
Parameters for AM1 and PM3 Optimized Using a Modified Genetic Algorithm” E.
Brothers; K. M. Merz, Jr. J. Phys. Chem.
B 2001, 106, 2779-2785.
120) “Charge
Transfer in Small Hydrogen Bonded Clusters” A. van der Vaart; K. M. Merz, Jr. J. Chem. Phys. 2002, 116, 7380-7388.
121) “Can we
Separate Active from Inactive Conformations.”, D.J. Diller; K.M. Merz Jr., J. Comp. Aided Mol. Des. 2002,
16, 105-112.
122) “Insights
into the Structure and Dynamics of the Dinuclear Zinc b-lactamase Site from Bacteroides
fragilis” D. Suárez; E. N. Bothers; K. M. Merz, Jr. Biochemistry 2002, 41, 6615-6630
123)
“Molecular Dynamics Simulations of the Dinuclear Zinc-b-lactamase from Bacteroides
fragilis Complexed with Imipenem” D. Suárez; N. Díaz; K. M. Merz, Jr J.
Comp. Chem. 2002, 23, 1587-1600
124) “
Insights into the Acylation Mechanism of Class A b-lactamases
from Molecular Dynamics Simulations of the TEM-1 enzyme complexed with
Benzylpenicillin” N. Díaz; T. L. Sordo; K. M. Merz, Jr.; D. Suárez J. Am.
Chem. Soc. 2003, 125, 672-684.
125)
“Molecular Dynamics and Quantum Chemical Studies on the Catalytic Mechanism of D5-3-Ketosteroid
Isomerase: The Catalytic Diad versus Cooperative Hydrogen Bond Mechanism” H.
Park; K. M. Merz, Jr. J. Am. Chem. Soc. 2003, 125, 901-911.
126)
“Prediction of Aqueous Solubility of a Diverse Set of Compounds using
Quantitative Structure-Property Relationships”, A. Cheng; K. M. Merz, Jr., J. Med. Chem.2003, 46, 3572-3580.
127)” Ureases:
Quantum Chemical Calculations on Cluster Models D. Suárez, N. Díaz, K. M. Merz,
Jr. J. Am. Chem. Soc. 2003, 125(50); 15324-1533.
128) “A
Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand
Binding” K. Raha; K. M.
Merz, Jr. J. Am. Chem. Soc., 2004, 126, 1020-1021.
129) “Fast
Semiempirical Calculations for NMR Chemical Shifts: A Divide-and-Conquer Approach” B. Wang; E. N. Brothers; A. van der
Vaart; K. M. Merz, Jr. J. Chem. Phys. 2004, 120, 11392-11400
130) “Pose Scoring by NMR” B. Wang; K. Raha; K. M. Merz, Jr. J. Am. Chem. Soc. 2004, 126, 11430-11431.
131) “PM3
Compatible Zinc Parameters Optimized for Metalloenzyme Active Sites” E. N.
Brothers; K. M. Merz, Jr. J. Comp. Chem. 2004, 25, 1677-1692.
132) "The
Hydrolysis of Urea and the Proficiency of Urease” G. Estiu; K. M. Merz, Jr. J. Am. Chem. Soc. 2004, 126, 6932-6944.
133)
“Enzymatic Catalysis of Urea Decomposition- Elimination or Hydrolysis?” G.
Estiu; K. M. Merz, Jr. J. Am. Chem. Soc. 2004, 126, 11832-11842.
134)
“Performance of Density Functionals with Small Split Valence Basis Sets” E. N.
Brothers; K. M. Merz, Jr. J. Phys. Chem.
A, 2004, 108, 2904-2911.
135) “A
Theoretical Study of the Electron Density Distributions of Glycyl-L-threonine
Dihydrate” N. Yu; K. M. Merz, Jr. Mol.
Phys.2004, 23-24, 2545-2557.
136) “Force
Field Design and Molecular Dynamics Simulations of the Dinuclear Zinc Metallo- b -lactamase CcrA from Bacteroides
fragilis and its Complex with a Biphenyl Tetrazole Inhibitor" H. Park;
K. M. Merz, Jr. J. Med. Chem. 2004, 48, 1630-1637.
137) “QMQSAR:
Utilization of a Semi-Empirical Probe Potential in a Field-Based QSAR Method”
S. Dixon; K. M. Merz Jr.; G. Lauri; J. C. Ianni J. Comp. Chem. 2005, 26, 23-34.
138)
“Simulation of Liquid Water Using Semi-empirical Hamiltonians and the Divide
and Conquer approach” G. Monard, M. I. Bernal-Uruchurtu, A. van der Vaart, K.
M. Merz Jr. and M.F. Ruiz-López J. Phys.
Chem. 2005, 109, 3425-3432.
139)
“Refinement of Protein Crystal Structures Using Energy Restraints Derived from
Linear-scaling Quantum Mechanics” N. Yu; K. M. Merz, Jr. N. Yu; Yennawar, H. P.; K. M. Merz, Jr. Acta.
Cryst. D. Biol. Cryst. 2005, 51, 322-332.
140)
“Molecular Dynamics Simulations of the TEM-1 b-lactamase
Complexed with Cephalothin” D. Suárez; N. Díaz; K. M. Merz, Jr.; T. L. Sordo J.
Med. Chem. 2005, 48, 780-791.
141) “Hybrid
QM/MM and DFT Investigations of the Catalytic Mechanism and Inhibition of the
Dinuclear Zinc Metallo-b-lactamase
CcrA from Bacteroides fragilis” H.
Park; K. M. Merz, Jr. J. Am. Chem. Soc. 2005, 127, 4232-4221.
142) “Validation of the Binding Site Structure of the Cellular Retinol-Binding Protein (CRBP) by Ligand NMR Chemical Shift Perturbations” B. Wang; K. M. Merz, Jr. J. Am. Chem. Soc. 2005,