Director: Michael B. Hall Manager: Lisa M. Pérez

Phone: (979) 845-9384Fax (979) 845-2971Rm. 2109 Chemistry
e-mail: mouse@mail.chem.tamu.edu

Education

Ph.D., Physical Chemistry, Texas A&M University, College Station, TX, December 2002
Adviser: Professor Michael B. Hall

B.S., Chemistry: Minors, Mathematics and Computer Information Systems
Humboldt State University, Arcata, CA, 1994
Adviser: Professor T. Clark

Highlights

Fourteen years of research experience in the theoretical investigation of reaction mechanisms for transition metal containing enzyme systems.

Experience installing and using the following software packages: ADF, AMBER, AMPAC, Cerius², CHARMm, Dalton, Gaussian, GaussView, Gamess-UK, Gamess-US, InsightII, Jaguar, LAMMPS, Macromodel, MOLPRO, NWCHEM, PBS, PGI Compilers, Q-Chem, NAMD, VMD, Materials Studio, Discovery Studio, and Quanta.

System administration skills on SGI (IRIX & SUSE), IBM (AIX), CRAY (UNICOS), SUN (Solaris), Linux (Most Flavors), Windows, and Macintosh platforms.

Skill in the scripting and programming languages: FORTRAN, C++, HTML, CSS, JAVA, PHP, PASCAL, PERL, BASIC, T-Shell, and BASH.

Strong communication and presentation skills

Professional Appointments

Research Interest

The examination of electronic structure and bonding capabilities in bioinorganic systems using modern theoretical methods.

Drug design.

The effect of mutations on protein function.

Intercalation of inorganic molecules into DNA.

Conformational studies of dendrimers.

Teaching Experience

Graduate Courses

Lecturer

Special Topics in Molecular Modeling (CHEM689), TAMU Chemistry
Laboratory Supervisor

Structural Inorganic Chemistry (CHEM 641), TAMU Chemistry

Computational Chemistry and Molecular Modeling for Engineers (CHEN 689), TAMU Chemical Engineering

Special Topics in Nanomechanics (MEMA 689), TAMU Aerospace Engineering

Special Topics in Organic Chemistry (CHEM 689), TAMU Chemistry

Special Topics in Biophysical Chemistry (CHEM 689), TAMU Chemistry

Coordination and Bioinorganic Chemistry (CHEM 628), TAMU Chemistry

Bioinformatics (BIO 651), TAMU Biology

Advanced Organic Chemistry I (CHEM 646), TAMU Chemistry

Modern Topics in Physical Chemistry (CHEM 689), TAMU Chemistry

Molecular Spectra and Structure (CHEM 650), TAMU Chemistry

Special Topics in Computational Organic and Bioorganic Chemistry (CHEM 689), TAMU Chemistry

Molecular Quantum Mechanics (CHEM 649), TAMU Chemistry

Applications of Thermodynamics to Chemical Engineering (CHEN 643), TAMU Chemistry

Undergraduate Courses

Lecturer

General Chemistry (CHEM 101), TAMU Chemistry
Laboratory Supervisor

Organic Synthesis and Analysis Laboratory (CHEM 234), TAMU Chemistry

Physical Chemistry Laboratory (CHEM 325), TAMU Chemistry

Experimental Physical Chemistry II (CHEM 334), TAMU Chemistry

Advanced Inorganic Chemistry Laboratory (CHEM 433), TAMU Chemistry

Honors And Awards

1st place, 2nd Annual Student Research Week Competition, Texas A&M University, 1999

GAANN grant, Texas A&M University, 1997

Graduate Studies Travel Award, Texas A&M University, 1997

PLU Travel Grant, Texas A&M University, 1997

A.E. Martell Travel Award, Texas A&M University, 1996 and 1997

ACTC '96 (American Conference on Theoretical Chemistry) scholarship, 1996

Professional Activities

Vice-president, Phi Lambda Upsilon (PLU), 1996-97

Professional Societies

2003-Present

Sigma Xi

2000-Present

American Chemical Society

1996-Present

Phi Lambda Upsilon

Publications

1. Kim, Y.I.; Manalo, M.N.; Pérez L.M.; LiWang, A. Computational and empirical trans-hydrogen bond deuterium isotope shifts suggest that N1-N3 A : U hydrogen bonds of RNA are shorter than those of A : T hydrogen bonds of DNA. J. Biomol. NMR, 2006, 34, 229.
2. Schottel, B.L.; Chifotides, H.T.; Shatruk, M.; Chouai, A.; Pérez L.M.; Bacsa, J.; Dunbar, K.R. Anion-pi interactions as controlling elements in self-assembly reactions of Ag(I) complexes with pi-acidic aromatic rings. J. Am. Chem. Soc., 2006, 128, 5895.
3. Mohamed, A.A.; Pérez L.M.; Fackler, J.P. Unsupported intermolecular argentophilic interaction in the dimer of trinuclear silver(I) 3,5-diphenylpyrazolates. Inorg. Chim. Acta, 2005, 358, 1657.
4. Szalay, P.S.; Galan-Mascaros, J.R.; Schottel, B.L.; Bacsa, J.; Pérez L.M.; Ichimura, A.S.; Chouai, A.; Dunbar, K.R. Experimental and computational studies of charge-transfer and reduction products of 1,4,5,8,9,11-hexaazatriphenylene-hexacarbonitrile: HAT-(CN)(6) J. Cluster Sci., 2004, 15, 503.
5. Darensbourg, D.J.; Billodeaux, D.R.; Pérez;, L.M. 113Cd NMR Determination of the Binding Parameters of Alicyclic Epoxides to [Hydrotris(3-phenylpyrazol-1-yl)borate]Cd(II) Acetate. Organometallics, 2004, 23, 5286.
6. Wang, H.D.; Webster, C.E.; Pérez L.M.; Hall M.B.; Gabbai, F.P. Reaction of the 1,8-bis(diphenylmethylium)naphthalenediyl dication with fluoride: Formation of a cation containing a C-F -> C bridge. J. Am. Chem. Soc., 2004, 126, 8189.
7. Zhang, W.; Tichy, S.E.; Pérez L.M.; Maria, G.C.; Lindahl, P.A.; Simanek, E.E. Evaluation of Multivalent Dendrimers Based on Melamine: Kinetics of Thiol-Disulfide Exchange Depends on the Structure of the Dendrimer. J. Am. Chem. Soc., 2003, 125, 5086.
8. Cotton, F.A.; Donahue, J.P.; Murillo, C.A.; Pérez L.M. Polyunsaturated Dicarboxylate Tethers Connecting Dimolybdenum Redox and Chromophoric Centers: Absorption Spectra and Electronic Structures. J. Am. Chem. Soc., 2003, 125, 5486.
9. Chifotides, H.T.; Koshlap, K.M. Pérez L.M.; Dunbar, K.R. Novel Binding Interactions of the DNA Fragment d(pGpG) Cross-Linked by the Antitumor Active Compound Tetrakis(mu-carboxylato)dirhodium(II,II). J. Am. Chem. Soc., 2003, 125, 10715.
10. Chifotides, H.T.; Koshlap, K.M.; Pérez L.M.; Dunbar, K.R. Unprecedented Head-to-Head Conformers of d(GpG) Bound to the Antitumor Active Compound Tetrakis (mu-carboxylato)dirhodium(II,II). J. Am. Chem. Soc., 2003, 125, 10703.
11. Cotton, F.A.; Donahue, J.P.; Murillo, C.A.; Pérez L.M.; Yu, R. Cyclic Polyamidato Dianions as Bridges between Mo24+ Units: Synthesis, Crystal Structures, Electrochemistry, Absorption Spectra, and Electronic Structures. J. Am. Chem. Soc., 2003, 125, 8900.
12. Peterson, P.A.; Li, Y.M.; Francisco, J.S.; Zou, P.; Webster, C.E.; Pérez L.M.; Hall, M.B. North, S.W. The role of triplet states in the long wavelength absorption region of bromine nitrate. J. Chem. Phys., 2003, 119, 7864.
13. Zhang, W.; Jiang, J.; Qin, C.H.; Pérez L.M.; Parrish, A.R.; Safe, S.H.; Simanek, E.E. Triazine dendrimers for drug delivery: Evaluation of solubilization properties, activity in cell culture, and in vivo toxicity of a candidate vehicle. Supramolecular chemistry, 2003, 15, 607.
14. Georgakaki, I.P.; (Pérez) Thomson, L.M.; Lyon, E.J.; Hall, M.B.; Darensbourg, M.Y. Fundamental properties of small molecule models of Fe-only hydrogenase: computations relative to the definition of an entatic state in the active site.Coordin. Chem. Rev., 2003, 238, 255.
15. Saraf, S.R.; Rogers, W.J.; Mannan, M.S.; Hall, M.B.; (Pérez) Thomson, L.M. Theoretical Thermochemistry: Ab Initio Heat of Formation for Hydroxylamine. J. Phys. Chem. A, 2003, 107, 1077.
16. Ruotolo, B.T.; Verbeck, G.F.; (Pérez) Thomson, L.M.; Gillig, K.J.; Russell, D.H. Observation of Conserved Solution-Phase Secondary Structure in Gas-Phase Tryptic Peptides J. Am. Chem. Soc., 2002, 124, 4214.
17. Campos-Fernandez, C.S.; (Pérez) Thomson, L.M.; Galan-Mascaros, J.R.; Ouyang, X.; Dunbar, K.R. Homologous Series of Redox-Active, Dinuclear Cations [M₂(O₂CCH₃)₂(pynp)₂]²⁺ (M = Mo, Ru, Rh) with the Bridging Ligand 2-(2-Pyridyl)-1,8-naphthyridine (pynp) Inorg. Chem. 2002, 41, 1523.
18. Kaasjager, V.E.; Bouwman, E.; Gorter, S.; Reedijk, J.; Grapperhaus, C.A.; Reibenspies, J.H.; Smee, J.J.; Darensbourg, M.Y.; Derecskei-Kovacs, A.; (Pérez) Thomson, L.M. Unique Reactivity of a Tetradentate N2S2 Complex of Nickel: Intermediates in the Production of Sulfur Oxygenates. Inorg. Chem. 2002, 41, 1837.
19. Zhang, W.; Nowlan III, D.T.; (Pérez) Thomson, L.M.; Lackowski, W.M.; Simanek, E.E. Orthogonal, Convergent Syntheses of Dendrimers Based on Melamine with One or Two Unique Surface Sites for Manipulation J. Am. Chem. Soc. 2001, 123, 8914.
20. Meloni, G.; (Pérez) Thomson, L.M.; Gingerich, K.A. Structure Thermodynamic Stability of the OsC and OsC₂ Molecules by Theoretical Calculations and by Knudsen Cell Mass Spectrometry J. Chem. Phys. 2001, 115, 4496.
21. (Pérez) Thomson, L.M.; Hall, M.B. A Theoretical Study of the Primary Oxo Transfer Reaction of a Dioxo Molybdenum(VI) Compound with Imine Thiolate Chelator Ligands: A Molybdenum Oxotransferase Analogue J. Am. Chem. Soc. 2001, 123, 3995.
22. (Pérez) Thomson, L.M.; Hall, M.B. A Theoretical Study of the Thermal Decomposition of N,N'-Diacyl-N,N'-Dialkoxyhydrazines: A Comparison of HF, MP2 and DFT J. Phys. Chem. 2000, 104, 6247.
23. Niu, S.; (Pérez) Thomson, L.M.; Hall, M.B. Theoretical Characterization of the Reaction Intermediates in a Model of the Nickel-Iron Hydrogenase of Desulfovibrio J. Am. Chem. Soc. 1999, 121, 4000.
24. Barton, D.H.R.; Hall, M.B.; De Almeida, M.V. Bytheway, I.; Ferreira, J.A.; Liu, W.; Taylor, D.K.; (Pérez) Thomson, L.M. Preparation and Thermal Decomposition of N,N'-Diacyl-N,N'-Dialkoxyhydrazines: Synthetic Applications and Mechanistic Insights J. Am. Chem. Soc. 1995, 117, 4870.

Oral Presentations

1. Molecular Modelling of Biological Systems: Basic Visualization, and Calculations using Molecular Mechanics, Dynamics, and Density Functional Theory. Invited Speaker for the Computation Biology seminar series, Texas A&M University, 2002.
2. The Fe/Fe Site in Methane Monooxygenase. Invited Speaker for the Chemical Biology seminar series, Texas A&M University, 2001.
3. A Theoretical Study of Metalloenzymes Invited Speaker for the Pharmaceutical Symposium at Texas A&M University, 2000.
4. Theoretical Study of Biologically Important Diiron Diamond Core Compounds Industry-University Cooperative Chemistry Program (IUCCP), Texas A&M University, 1999.
5. A Computational Study of Methanotrophic Bacteria and Its Potential Use in Environmental Applications 2nd Annual Student Research Week at Texas A&M University, 1999.
6. Modeling the Active Site in Methane Monooxygenase Invited Speaker for Metals in Biological Systems Seminar series at Texas A&M University, 1998.

Poster Presentations

1. DFT Investigation of Vinyl Acetate Formation on Pd/Au(100) and Pd/Au(111) Bimetallic Surfaces Lisa M. Pérez 2006 Ab initio Modeling in Solid State Chemistry, Torino, Italy.
2. Theoretical study of platinum-metal mono and dicarbides Lisa M. (Pérez) Thomson, G. Meloni, and Karl A. Gingerich. 2002 National ACS Meeting, Orlando, Fl.
3. A Theoretical Study of a Molybdenum Oxotransferase That Experiences Significant Ligand Rearrangement Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 2000 Conference on Contemporary Inorganic Chemistry. College Station, TX.
4. Modeling the Active Site in Methane Monooxygenase Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1999 International Conference on Biological Inorganic Chemistry. Minneapolis, MN
5. Modeling the Active Site in Methane Monooxygenase Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1998 Southwest Theoretical Chemistry Conference. Arlington, TX.
6. Modeling the Active Site in Methane Monooxygenase Lisa M. (Pérez) Thomson and Michael B. Hall. 1998 34th Symposium for Theoretical Chemistry: Large Molecules Gwatt-Zentrum am Thunersee, Switzerland.
7. Modeling the Active Site in Methane Monooxygenase Lisa M. (Pérez) Thomson and Michael B. Hall. 1998 National ACS Meeting. Dallas, TX.
8. Modeling the Active Site in Methane Monooxygenase Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1997 Southwest Theoretical Chemistry Conference. New Orleans, LA.
9. Modeling the Active Site in Methane Monooxygenase Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1997 Conference on Current Trends in Computational Chemistry. Vicksburg, MI
10. Modeling the Active Site in Methane Monooxygenase Lisa M. (Pérez) Thomson and Michael B. Hall. 1997 International Conference on Quantum Chemistry. Atlanta, GA
11. Theoretical Study of a Molybdenum Oxotransferase That Experiences Significant Ligand Rearrangement Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1996 National ACS Meeting. Orlando, FL.
12. A Theoretical Study of the Reaction Mechanism for the Decomposition of N,N'-Diacyl-N,N'-Dialkoxyhydrazines Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1996 American Conference on Theoretical Chemistry. Park City, Utah.
13. A Theoretical Study of the Reaction Mechanism for the Decomposition of N,N-Diacyl-N,N-Dialkoxyhydrazines Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1996 Southwest Regional ACS Meeting. Houston, TX.
14. A Theoretical Study of the Reaction Mechanism for the Decomposition of N,N'-Diacyl-N,N'-Dialkoxyhydrazines Lisa M. (Pérez) Thomson and Dr. Michael B. Hall. 1995 Southwest Theoretical Chemistry Conference. Galveston, TX.

REFERENCES

Dr. Michael B. Hall
Dept. of Chemistry, Texas A&M University
P.O. Box 30012
College Station, TX 77842-3012
(979) 845-1843
hall@mail.chem.tamu.edu

Dr. Jaan Laane
Dept. of Chemistry, Texas A&M University
P.O. Box 30012
College Station, TX 77842-3012
(979) 845-3352
laane@mail.chem.tamu.edu

Dr. Robert R. Lucchese
Dept. of Chemistry, Texas A&M University
P.O. Box 30012
College Station, TX 77842-3012
(979) 845-0187
lucchese@mail.chem.tamu.edu

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