Faculty Profile

Andrés Cisneros

Title
Professor
Department
Chemistry
College
College of Science

    

    

      


                          

            
Curriculum Vitae

            

              Click Here to View Faculty CV
            

          

        
                          

            
Education

            



  

  


  
PhD, Duke University, 2004. 
Major: Chemistry
BS, Universidad Nacional Autonoma de Mexico, 1999. 
Major: Chemistry





          

        
                

          
Current Scheduled Teaching*


          
No current or future courses scheduled.


          
*
  Texas Education Code 51.974 (HB 2504) requires each institution of
  higher education to make available to the public, a syllabus for
  undergraduate lecture courses offered for credit by the institution.
  

        

      

    

  


    

    

      


        


          


            
Previous Scheduled Teaching*


            
                    

                    CHEM 5660.001, Computational Chemistry and Biochemistry, Fall 2021 Syllabus SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Fall 2021 
                    

                    CHEM 6940.760, Individual Research, Fall 2021 
                    

                    CHEM 4660.001, Introduction to Computational Chemistry, Fall 2021 Syllabus SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Summer 5W1 2021 
                    

                    CHEM 4900.710, Special Problems, Summer 10W 2021 
                    

                    CHEM 6950.760, Doctoral Dissertation, Spring 2021 
                    

                    CHEM 6940.760, Individual Research, Spring 2021 
                    

                    CHEM 3520.001, Physical Chemistry, Spring 2021 Syllabus SPOT
                    

                    CHEM 3520.211, Physical Chemistry, Spring 2021 
                    

                    CHEM 6950.760, Doctoral Dissertation, Fall 2020 
                    

                    CHEM 6940.760, Individual Research, Fall 2020 
                    

                    CHEM 6940.760, Individual Research, Summer 5W2 2020 
                    

                    CHEM 6940.760, Individual Research, Summer 5W1 2020 
                    

                    CHEM 5210.001, Advanced Physical Chemistry, Spring 2020 Syllabus
                    

                    CHEM 6950.760, Doctoral Dissertation, Spring 2020 
                    

                    CHEM 6940.760, Individual Research, Spring 2020 
                    

                    CHEM 2900.710, Introduction to Chemical Research, Spring 2020 
                    

                    CHEM 5660.001, Computational Chemistry and Biochemistry, Fall 2019 Syllabus SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Fall 2019 
                    

                    CHEM 6940.760, Individual Research, Fall 2019 
                    

                    CHEM 2900.710, Introduction to Chemical Research, Fall 2019 
                    

                    CHEM 4660.001, Introduction to Computational Chemistry, Fall 2019 Syllabus SPOT
                    

                    CHEM 5210.001, Advanced Physical Chemistry, Spring 2019  SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Spring 2019 
                    

                    CHEM 6940.760, Individual Research, Spring 2019 
                    

                    CHEM 2900.710, Introduction to Chemical Research, Spring 2019 
                    

                    CHEM 5660.001, Computational Chemistry and Biochemistry, Fall 2018  SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Fall 2018 
                    

                    CHEM 6940.760, Individual Research, Fall 2018 
                    

                    CHEM 4660.001, Introduction to Computational Chemistry, Fall 2018 Syllabus SPOT
                    

                    CHEM 4900.710, Special Problems, Fall 2018 
                    

                    CHEM 5210.001, Advanced Physical Chemistry, Spring 2018  SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Spring 2018 
                    

                    CHEM 6940.760, Individual Research, Spring 2018 
                    

                    CHEM 2900.710, Introduction to Chemical Research, Spring 2018 
                    

                    CHEM 5660.001, Computational Chemistry and Biochemistry, Fall 2017  SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Fall 2017 
                    

                    CHEM 6940.760, Individual Research, Fall 2017 
                    

                    CHEM 4660.001, Introduction to Computational Chemistry, Fall 2017 Syllabus SPOT
                    

                    CHEM 6940.760, Individual Research, Summer 5W1 2017 
                    

                    CHEM 6940.760, Individual Research, Summer 5W2 2017 
                    

                    CHEM 5210.001, Advanced Physical Chemistry, Spring 2017  SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Spring 2017 
                    

                    CHEM 6940.760, Individual Research, Spring 2017 
                    

                    CHEM 5660.001, Computational Chemistry and Biochemistry, Fall 2016  SPOT
                    

                    CHEM 6950.760, Doctoral Dissertation, Fall 2016 
                    

                    CHEM 6940.760, Individual Research, Fall 2016 
                    

                    CHEM 4660.001, Introduction to Computational Chemistry, Fall 2016 Syllabus SPOT

          


          
*
  Texas Education Code 51.974 (HB 2504) requires each institution of
  higher education to make available to the public, a syllabus for
  undergraduate lecture courses offered for credit by the institution.
  

        

      

    

  

  
  	

	

	  

		

		   
Published Publications



  

  
Published Intellectual Contributions


  
Book Chapter
Leddin, E. M., Cisneros, G., Karabencheva-Christova, T., Christov, C. Z. (2019). Chapter Three - Comparison of DNA and RNA substrate effects on TET2 structure. Advances in Protein Chemistry and Structural Biology. 117, 91 - 112. Academic Press. http://www.sciencedirect.com/science/article/pii/S1876162319300501
Cisneros, G., Yang, W.  (2009). Comparison of reaction barriers in energy and free energy for enzyme catalysis. Multi-scale Quantum Models for Biocatalysis. 57–78. Springer Netherlands. 
Cisneros, G., Darden, T., Gresh, N., Pilmé, J., Reinhardt, P., Parisel, O., Piquemal, J.  (2009). Design of next generation force fields from ab initio computations: beyond point charges electrostatics. Multi-scale Quantum Models for Biocatalysis. 137–172. Springer Netherlands. 
Journal Article
Lambros, E., Lipparini, F., Cisneros, G., Paesani, F.  (2020). A Many-Body, Fully Polarizable Approach to QM/MM Simulations.. Journal of Chemical Theory and Computation. 
Hix, M. A., Wong, L., Flath, B., Chelico, L., Cisneros, G.  (2020). Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer.. Other. 2(3), zcaa023. 
Hix, M. A., Cisneros, G.  (2020). Computational Investigation of APOBEC3H Substrate Orientation and Selectivity.. Other. 124(19), 3903-3908. 
Vázquez-Montelongo, E. A., Vázquez-Cervantes, J. E., Cisneros, G.  (2020). Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids.. International Journal of Molecular Sciences. 21(3), . 
Das, R., Vázquez-Montelongo, E. A., Cisneros, G., Wu, J. I. (2019). Ground State Destabilization in Uracil DNA Glycosylase: Let’s Not Forget “Tautomeric Strain” in Substrates. Journal of the American Chemical Society. 141(35), 13739-13743. https://doi.org/10.1021/jacs.9b06447
Vázquez-Montelongo, E. A., Cisneros, G., Flores-Ruiz, H. M. (2019). Multipolar/polarizable molecular dynamics simulations of Liquid–Liquid extraction of benzene from hydrocarbons using ionic liquids. Journal of Molecular Liquids. 111846. http://www.sciencedirect.com/science/article/pii/S0167732219331861
Loco, D., Lagardère, L., Cisneros, G., Scalmani, G., Frisch, M., Lipparini, F., Mennucci, B., Piquemal, J.  (2019). Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings. Other. 10(30), 7200-7211. The Royal Society of Chemistry. http://dx.doi.org/10.1039/C9SC01745C
Walker, A. R., Baddam, N., Cisneros, G.  (2019). Unfolding Pathways of Hen Egg-White Lysozyme in Ethanol. The Journal of Physical Chemistry B. 123(15), 3267-3271. https://doi.org/10.1021/acs.jpcb.9b01694
Duke, R. E., Cisneros, G.  (2019). Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM.. Journal of Molecular Modeling. 25(10), 307. 
Koleva, B. N., Gokcan, H., Rizzo, A. A., Lim, S., Jeanne Dit Fouque, K., Choy, A., Liriano, M. L., Fernandez-Lima, F., Korzhnev, D. M., Cisneros, G., Beuning, P. J. (2019). Dynamics of the E. coli β-Clamp Dimer Interface and Its Influence on DNA Loading.. Biophysical Journal. 117(3), 587-601. 
Gökcan, H., Vázquez-Montelongo, E. A., Cisneros, G.  (2019). LICHEM 1.1: Recent Improvements and New Capabilities.. Journal of Chemical Theory and Computation. 15(5), 3056-3065. 
Antczak, N. M., Walker, A. R., Stern, H. R., Leddin, E. M., Palad, C., Coulther, T. A., Swet, R. J., Cisneros, G., Beuning, P. J. (2018). Characterization of Nine Cancer-Associated Variants in Human DNA Polymerase kappa. Chemical Research in Toxicology. 31(8), 697-711. 
Lohrman, J., Vazquez-Montelongo, E. A., Pramanik, S., Day, V. W., Hix, M. A., Bowman-James, K., Cisneros, G.  (2018). Characterizing Hydrogen-Bond Interactions in Pyrazinetetracarboxamide Complexes: Insights from Experimental and Quantum Topological Analyses. Inorganic Chemistry. 57(16), 9775-9778. 
Blanco-Diaz, E. G., Vazquez-Montelongo, E. A., Cisneros, G., Omar Castrejon-Gonzalez, Edgar,  (2018). Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD. Journal of Chemical Physics. 148(5), 054303. 
Silvestrov, P., Maier, S. J., Fang, M., Cisneros, G.  (2018). DNArCdb: A database of cancer biomarkers in DNA repair genes that includes variants related to multiple cancer phenotypes. DNA Repair. 70, 10-17. 
Cisneros, G., Torabifard, H.  (2018). Insight into wild–type and T1372E TET2–mediated 5hmC oxidation using ab initio QM/MM calculations. Chemical Science. 9(44), 8433-8445. Royal Society of Chemistry. 
Cisneros, G., Silvestrov, P.  (2018). Insights on conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations. Theoretical Chemistry Accounts. 137(6), 1-12. Springer. 
Cisneros, G., Tu, Y., Lin, Z., Allen, M. J. (2018). Molecular Dynamics Investigation of Solvent-Exchange Reactions on Lanthanide Ions in Water/1–Ethyl–3–Methylimidazolium Trifluoromethylsufate ([EMIm][OTf]). Journal of Chemical Physics. 148(2), 024503/1-024503/9. 
Cisneros, G., Vazquez-Montelongo, E. A., Vazquez-Cervantes, J. E. (2018). Polarizable ab initio QM/MM study of the reaction mechanism of N–tert–butyloxycarbonylation of aniline in [EMIm][BF4]. Molecules. 23(11), 2830. 
Gokcan, H., Kratz, E., Darden, T. A., Piquemal, J., Cisneros, G.  (2018). QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential. Journal of Physical Chemistry Letters. 9(11), 3062-3067. 
Cisneros, G., Gahlon, H. L., Walker, A. R., Lamers, M. H., Rueda, D. S. (2018). Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant. Physical Chemistry and Chemical Physics. 20(42), 26892-26902. Royal Society of Chemistry. 
Lagardere, L., Jolly, L., Lipparini, F., Aviat, F., Stamm, B., Jing, Z. F., Harger, M., Torabifard, H., Cisneros, G., Schnieders, M. J., Gresh, N., Maday, Y., Ren, P. Y., Ponder, J. W., Piquemal, J.  (2018). Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical Science. 9(4), 956-972. 
Cisneros, G., DeNizio, J. E., Liu, M. Y., Leddin, E. M., Kohli, R. M. (2018). Selectivity and Promiscuity in TET–mediated oxidation of 5–methylcytosine in DNA and RNA. Biochemistry. Article ASAP, . American Chemical Society. 
Liyanage, P. S., Walker, A. R., Brenlla, A., Cisneros, G., Romano, L. J., Rueda, D.  (2017). Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations. Scientific Reports. 7, 17383. 
Walker, A. R., Bonomi, R., Popov, V., Gelovani, J. G., Cisneros, G.  (2017). Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies. Journal of Molecular Graphics and Modelling. 71, 211–217. Elsevier. 
Liu, M. Y., Torabifard, H., Crawford, D. J., DeNizio, J. E., Cao, X., Garcia, B. A., Cisneros, G., Kohli, R. M. (2017). Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nature Chemical Biology. 13, 181-187. Nature Research. 
Liu, M. Y., Torabifard, H., Crawford, D. J., DeNizio, J. E., Cao, X., Garcia, B. A., Cisneros, G., Kohli, R. M. (2017). Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nature Chemical Biology. 13(2), 181-187. 
Walker, A. R., Cisneros, G.  (2017). Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants. Chemical Research in Toxicology. online(online), online.  Washington DC: ACS. http://pubs.acs.org/doi/full/10.1021/acs.chemrestox.7b00161
Torabifard, H., Cisneros, G.  (2017). Computational investigation of O2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O2 transport. Chemical Science. 8(9), 6230-6238.  london, england: RSC. http://pubs.rsc.org/en/content/articlelanding/2017/sc/c7sc00997f#!divAbstract
O'Brien, J. S., Allen, M. J., Cisneros, G.  (2017). Computational study of pH-responsive di-lanthanide complexes. International Journal of Quantum Chemistry. 117(17), e25406.  ny, ny: wiley. http://onlinelibrary.wiley.com/doi/10.1002/qua.25406/full
Walker, A. R., Silvestrov, P. A., Muller, T., Podolsky, R. H., Dyson, G., Hausinger, R. P., Cisneros, G.  (2017). ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding. PLOS Computational Biology. 13(2), e1005345.  San Francisco, CA: PLOS. http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005345
Zhao, L., Rathnayake, U. M., Dewage, S. W., Wood, W. N., Veltri, A. J., Cisneros, G., Hendrickson, T. L. (2016). Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase. FEBS Letters. 590(18), 3122–3132. 
Gamage, N. H., Stiasny, B., Kratz, E. G., Stierstorfer, J., Martin, P. D., Cisneros, G., Klapötke, T. M., Winter, C. H. (2016). Energetic Materials Trends in 5-and 6-Membered Cyclic Peroxides Containing Hydroperoxy and Hydroxy Substituents. European Journal of Inorganic Chemistry. 2016(31), 5036–5043. 
Kratz, E. G., Walker, A. R., Lagardere, L., Lipparini, F., Piquemal, J., Cisneros, G.  (2016). LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. Journal of Computational Chemistry. 37(11), 1019–1029. 
Kratz, E. G., Duke, R. E., Cisneros, G.  (2016). Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations. Theoretical Chemistry Accounts. 135(7), 1–9. Springer Berlin Heidelberg. 
Cisneros, Gerardo Andrés,, Wikfeldt, K. T., Ojamäe, Lars,, Lu, J., Xu, Y., Torabifard, H., Bartok, A. P., Csanyi, G., Molinero, V., Paesani, F.  (2016). Modeling molecular interactions in water: From pairwise to many-body potential energy functions. Chemical Review. 116(13), 7501–7528. American Chemical Society. 
Tu, Y., Allen, M. J., Cisneros, G.  (2016). Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO 4]) and water. Physical Chemistry Chemical Physics. 18(44), 30877–30877. Royal Society of Chemistry. 
Tu, Y., Allen, M. J., Cisneros, G.  (2016). Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water. Physical Chemistry Chemical Physics. 18(44), 30323–30333. The Royal Society of Chemistry. 
Fang, D., Duke, R. E., Cisneros, G.  (2015). A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations. The Journal of Chemical Physics. 143(4), 044103. AIP Publishing. 
Dewage, S. W., Cisneros, G Andrés,  (2015). Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB). The Journal of Physical Chemistry B. 119(9), 3669–3677. American Chemical Society. 
Torabifard, H., Starovoytov, O. N., Ren, P., Cisneros, G.  (2015). Development of an AMOEBA water model using GEM distributed multipoles. Theoretical Chemistry Accounts. 134(8), 101. Springer Berlin Heidelberg. 
Bonomi, R., Mukhopadhyay, U., Shavrin, A., Yeh, H., Majhi, A., Dewage, S. W., Najjar, A., Lu, X., Cisneros, G., Tong, W. P., others,  (2015). Novel Histone Deacetylase Class IIa Selective Substrate Radiotracers for PET Imaging of Epigenetic Regulation in the Brain. PLOS One. 10(8), e0133512. Public Library of Science. 
Pratt, A. C., Dewage, S. W., Pang, A. H., Biswas, T., Barnard-Britson, S., Cisneros, G., Tsodikov, O. V. (2015). Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. Journal of Structural Biology. 192(1), 76–87. Academic Press. 
Bellow, J. A., Yousif, M., Fang, D., Kratz, E. G., Cisneros, G Andrés,, Groysman, S.  (2015). Synthesis and Reactions of 3d Metal Complexes with the Bulky Alkoxide Ligand [OC t Bu2Ph]. Inorganic Chemistry. 54(12), 5624–5633. American Chemical Society. 
Fang, D., Cisneros, G Andrés,  (2014). Alternative pathway for the reaction catalyzed by DNA dealkylase AlkB from ab initio QM/MM calculations. Journal of Chemical Theory and Computation. 10(11), 5136–5148. American Chemical Society. 
Elias, A. A., Cisneros, G.  (2014). Chapter Two-Computational Study of Putative Residues Involved in DNA Synthesis Fidelity Checking in Thermus aquaticus DNA Polymerase I. Advances in Protein Chemistry and Structural Biology. 96, 39–75. Academic Press. 
Swett, R. J., Elias, A., Miller, J. A., Dyson, G. E., Cisneros, G.  (2014). Corrigendum to “Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S)”[DNA Repair 12 (September (9))(2013) 733–740]. DNA Repair. 15, 60. Elsevier. 
Starovoytov, O. N., Torabifard, H., Cisneros, G Andrés,  (2014). Development of AMOEBA force field for 1, 3-dimethylimidazolium based ionic liquids. The Journal of Physical Chemistry B. 118(25), 7156–7166. American Chemical Society. 
Fang, D., Piquemal, J., Liu, S., Cisneros, G.  (2014). DFT-steric-based energy decomposition analysis of intermolecular interactions. Theoretical Chemistry Accounts. 133(5), 1484. Springer Berlin Heidelberg. 
Duke, R. E., Starovoytov, O. N., Piquemal, J., Cisneros, G Andrés,  (2014). GEM*: A molecular electronic density-based force field for molecular dynamics simulations. Journal of Chemical Theory and Computation. 10(4), 1361–1365. American Chemical Society. 
Silvestrov, P., Müller, T. A., Clark, K. N., Hausinger, R. P., Cisneros, G.  (2014). Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1). Journal of Molecular Graphics and Modelling. 54, 123–130. Elsevier. 
Chaudret, R., Gresh, N., Narth, C., Lagardère, Louis,, Darden, T. A., Cisneros, G Andrés,, Piquemal, J.  (2014). S/G-1: An ab initio force-field blending frozen hermite gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations. The Journal of Physical Chemistry A. 118(35), 7598–7612. American Chemical Society. 
Fang, D., Lord, R. L., Cisneros, G Andrés,  (2013). Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB. The Journal of Physical Chemistry B. 117(21), 6410–6420. American Chemical Society. 
Cisneros, G Andrés,, Karttunen, M., Ren, P., Sagui, C.  (2013). Classical electrostatics for biomolecular simulations. Chemical Reviews. 114(1), 779–814. American Chemical Society. 
Zhao, L., Dewage, S. W., Bell, M. J., Chang, K., Fatma, S., Joshi, N., Silva, G., Cisneros, G., Hendrickson, T. L. (2013). Correction to The Kinase Activity of the Helicobacter pylori Asp-tRNAAsn/Glu-tRNAGln Amidotransferase Is Sensitive to Distal Mutations in Its Putative Ammonia Tunnel. Biochemistry. 52(13), 2381–2381. American Chemical Society. 
Swett, R. J., Cisneros, G., Feig, A. L. (2013). Disruption of intrinsic motions as a mechanism for enzyme inhibition. Biophysical Journal. 105(2), 494–501. Cell Press. 
Burger, S. K., Cisneros, G.  (2013). Efficient optimization of van der waals parameters from bulk properties. Journal of Computational Chemistry. 34(27), 2313–2319. 
Cisneros, G., Babin, V., Sagui, C.  (2013). Electrostatics interactions in classical simulations. Other. 243–270. Humana Press. 
Kraskouskaya, D., Drewry, J. A., Duodu, E., Burger, S., Eaton, J., Cisneros, G., Gunning, P. T. (2013). Exploring the structural determinants of selective phosphopeptide recognition using bivalent metal-coordination complexes. Other. 4(1), 289–292. Royal Society of Chemistry. 
Chaudret, R., Gresh, N., Cisneros, G., Scemama, A., Piquemal, J.  (2013). Further refinements of next-generation force fields—Nonempirical localization of off-centered points in molecules. Canadian Journal of Chemistry. 91(9), 804–810. NRC Research Press. 
Rebecca J. Swett, Angela Elias, Jeffrey A. Miller, Gregory,, E. Dyson, G. Andrés Cisneros,  (2013). Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S). DNA Repair. 12(9), 733–740. Elsevier. 
Bellow, J. A., Fang, D., Kovacevic, N., Martin, P. D., Shearer, J., Cisneros, G., Groysman, S.  (2013). Novel Alkoxide Cluster Topologies Featuring Rare Seesaw Geometry at Transition Metal Centers. Chemistry - A European Journal. 19(37), 12225–12228. WILEY-VCH Verlag. 
Fang, D., Chaudret, R., Piquemal, J., Cisneros, G Andrés,  (2013). Toward a deeper understanding of enzyme reactions using the coupled ELF/NCI analysis: application to dna repair enzymes. Journal of Chemical Theory and Computation. 9(5), 2156–2160. American Chemical Society. 
Cisneros, G Andrés,  (2012). Application of gaussian electrostatic model (GEM) distributed multipoles in the AMOEBA force field. Journal of Chemical Theory and Computation. 8(12), 5072–5080. American Chemical Society. 
Wu, P., Cisneros, G., Hu, H., Chaudret, R., Hu, X., Yang, W.  (2012). Catalytic Mechanism of 4-Oxalocrotonate Tautomerase: Significances of Protein–Protein Interactions on Proton Transfer Pathways. The Journal of Physical Chemistry B. 116(23), 6889–6897. American Chemical Society. 
Graham, S. E., Syeda, F., Cisneros, G Andrés,  (2012). Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I. Biochemistry. 51(12), 2569–2578. American Chemical Society. 
Moore, J. D., Lord, R. L., Cisneros, G., Allen, M. J. (2012). Concentration-independent pH detection with a luminescent dimetallic Eu (III)-based probe. Journal of the American Chemical Society. 134(42), 17372–17375. American Chemical Society. 
Swett, R., Cisneros, G., Feig, A. L. (2012). Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition. PLOS One. 7(7), e41518. Public Library of Science. 
Chaudret, R., Piquemal, J., Cisneros, G.  (2011). Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Physical Chemistry Chemical Physics. 13(23), 11239–11247. Royal Society of Chemistry. 
Zhao, L., Dewage, S. W., Bell, M. J., Chang, K., Fatma, S., Joshi, N., Silva, G., Cisneros, G Andrés,, Hendrickson, T. L. (2011). The kinase activity of the Helicobacter pylori Asp-tRNAAsn/Glu-tRNAGln amidotransferase is sensitive to distal mutations in its putative ammonia tunnel. Biochemistry. 51(1), 273–285. American Chemical Society. 
Chaudret, R., Cisneros, G., Parisel, O., Piquemal, J.  (2011). Unraveling Low-Barrier Hydrogen Bonds in Complex Systems with a Simple Quantum Topological Criterion. Chemistry - A European Journal. 17(10), 2833–2837. WILEY-VCH Verlag. 
Cisneros, G.  (2010). DFT study of a model system for the dealkylation step catalyzed by AlkB. Other. 2(1), 70–77. International Association of Scientists in the Interdisciplinary Areas, co-published with Springer-Verlag GmbH. 
Elking, D. M., Cisneros, G., Piquemal, J., Darden, T. A., Pedersen, L. G. (2009). Gaussian multipole model (GMM). Journal of Chemical Theory and Computation. 6(1), 190–202. ACS Publications. 
Cisneros, G., Perera, L., Schaaper, R. M., Pedersen, L. C., London, R. E., Pedersen, L. G., Darden, T. A. (2009). Reaction mechanism of the $$ subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues!!!. Journal of the American Chemical Society. 131(4), 1550–1556. American Chemical Society. 
Cisneros, G., Perera, L., García-Díaz, M., Bebenek, K., Kunkel, T. A., Pedersen, L. G. (2008). Catalytic mechanism of human DNA polymerase $λ$ with Mg 2+ and Mn 2+ from ab initio quantum mechanical/molecular mechanical studies!!!. DNA Repair. 7(11), 1824–1834. Elsevier. 
Cisneros, G., Tholander, S., Parisel, O., Darden, T., Elking, D., Perera, L., Piquemal, J.  (2008). Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding. International Journal of Quantum Chemistry. 108(11), 1905–1912. Wiley Online Library. 
Gresh, N., Cisneros, G., Darden, T. A., Piquemal, J.  (2007). Anisotropic, polarizable molecular mechanics studies of inter-and intramolecular interactions and ligand- macromolecule complexes. A bottom-up strategy. Journal of Chemical Theory and Computation. 3(6), 1960–1986. American Chemical Society. 
Cisneros, G., Elking, D., Piquemal, J., Darden, T. A. (2007). Numerical fitting of molecular properties to Hermite Gaussians. The Journal of Physical Chemistry A. 111(47), 12049–12056. ACS Publications. 
Cisneros, G., Piquemal, J., Darden, T. A. (2006). Generalization of the Gaussian electrostatic model: Extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. The Journal of Chemical Physics. 125(18), 184101. AIP. 
Cisneros, G., Piquemal, J., Darden, T. A. (2006). Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. The Journal of Physical Chemistry B. 110(28), 13682–13684. American Chemical Society. 
Cisneros, G., Wang, M., Silinski, P., Fitzgerald, M. C., Yang, W.  (2006). Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase. The Journal of Physical Chemistry A. 110(2), 700–708. ACS Publications. 
Piquemal, J., Cisneros, G., Reinhardt, P., Gresh, N., Darden, T. A. (2006). Towards a force field based on density fitting. The Journal of Chemical Physics. 124(10), 104101. AIP. 
Cisneros, G., Piquemal, J., Darden, T. A. (2005). Intermolecular electrostatic energies using density fitting. The Journal of Chemical Physics. 123(4), 044109. AIP. 
Cisneros, G., Liu, H., Lu, Z., Yang, W.  (2005). Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order “chain-of-replicas” methods. The Journal of Chemical Physics. 122(11), 114502. AIP. 
Liu, H., Lu, Z., Cisneros, G., Yang, W.  (2004). Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. The Journal of Chemical Physics. 121(2), 697–706. AIP. 
Cisneros, G., Wang, M., Silinski, P., Fitzgerald, M. C., Yang, W.  (2004). The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: Understanding from theory and experiment. Biochemistry. 43(22), 6885–6892. ACS Publications. 
Cisneros, G., Liu, H., Zhang, Y., Yang, W.  (2003). Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase. Journal of the American Chemical Society. 125(34), 10384–10393. ACS Publications. 
Goj, L. A., Cisneros, G., Yang, W., Widenhoefer, R. A. (2003). Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization. Journal of Organometallic Chemistry. 687(2), 498–507. Elsevier. 
Perez-Marín, L., Castro, M., Otazo-Sánchez, E., Cisneros, G.  (2000). Density functional study of molecular recognition and reactivity of thiourea derivatives used in sensors for heavy metal polluting cations. International Journal of Quantum Chemistry. 80(4-5), 609–622. John Wiley & Sons, Inc.. 
Gutiérrez, J. A., Marín, L. P., Sánchez, E. O., Castro, M., Pulido, D. C., Cisneros, G.  (2000). Molecular and quantum mechanics calculations for the 1-Furoyl-3-Phenylthiourea as a Pb2+ Sensor. Other. 57(487), 180–184. Asociación de Químicos e Ingenieros. 
Cisneros, G., Castro, M., Salahub, D. R. (1999). DFT study of the structural and electronic properties of small Nin (n= 2–4) clusters. International Journal of Quantum Chemistry. 75(4-5), 847–861. John Wiley & Sons, Inc.. 
Other
Cui, Q., Meuwly, M., Ren, P.  (2016). Many-body effects and electrostatics in biomolecules. Pan Stanford. 
Piquemal, J., Cisneros, G.  (2016). Status of the Gaussian Electrostatic Model, a Density-Based Polarizable Force Field. Pan Standford Publishing. 
Ramos, E., Fernández-Flores, R., Santillán-González, A., Cisneros, G.  (2001). Computational Fluid Dynamics. World Scientific. 
UNAM-CRAY Supercomputing Conference (3rd: 1996: Universidad Nacional AutOnoma de,, MExico),, Cisneros, G., Congordan, J., Castro, M., Wang, C.  (1997). Computational Chemistry and Chemical Engineering: Proceedings of the Third UNAM-CRAY Supercomputing Conference. World Scientific. 



	
		
		
	  

	

	

  
    
	

	

	  

		

		   
Awarded Grants



  
  
  	  
          
Contracts, Grants and Sponsored Research  

 	 
	 	 
  
Grant - Research   
Cisneros, G., "Using MD and QM/MM to improve drug candidates for nCoV-19 targets," Sponsored by Microsoft AI for Good, International, $250000 Funded. (May 2020 – Present).
Cisneros, G., "Development of Highly Parallel Software for Classical MD and QM/MM Simulations with Advanced Force Fields and Application to DNA Repair Enzymes," Sponsored by XSEDE-NSF, Federal, $20000 Funded. (April 1, 2020 – Present).
Cisneros, G., "Using MD and QM/MM to improve drug candidates for nCoV-19 targets," Sponsored by COVID-19 HPC Consortium, Federal, $25000 Funded. (April 1, 2020 – Present).
Cisneros, G. A., "R01GM108583-S1 Theory and Simulation of DNA Repair Enzymes; Mechanism, Structure and Function," Sponsored by NIGMS, Federal, $166000 Funded. (August 1, 2019 – Present).
Padilla, P. A. (Principal), Burggren, W. W. (Co-Principal), Hughes, L. E. (Co-Principal), Cisneros, G. (Co-Principal), "G-RISE at UNT," Sponsored by National Institutes of Health - NIGMS, Federal, $2187228 Funded. (May 1, 2021 – April 30, 2026).
Cisneros, G. A. (Principal), "NIH/NIGMS R01GM108583–7: Investigation of DNA Modifying En- zymes by Computational Simulations: Development and Applications--Received score of 15% (council 1/2019)," Sponsored by National Institute of Health, Federal, $1284000 Funded. (August 2019 – July 2023).
Cisneros, G. . (Principal), Ren, P. (Principal), "NSF-CHE 1856162 Collaborative Research: Computational Investigation of Solvent Effects on Enzyme Catalysis," Sponsored by NSF, Federal, $256000 Funded. (August 1, 2019 – July 31, 2022).
Kohli, R. (Principal), Cisneros, G. A. (Co-Principal), "Investigation of multiple oxidation steps by TET family enzymes," Sponsored by NIH, Federal, $1452450 Funded. (January 2017 – December 2021).
Cisneros, G., "NIH/NIGMS R01GM108583–08S1 Investigation of DNA Modifying Enzymes by Computational Simulations: Development and Applications," Sponsored by NIH/NIGMS, Federal, $100000 Funded. (August 2020 – July 2021).
Cisneros, G., "NIH/NIGMS R01GM108583–07S1 Investigation of DNA Modifying Enzymes by Computational Simulations: Development and Applications," Sponsored by NIH/NIGMS, Federal, $78000 Funded. (August 2019 – July 2021).
Andreussi, O. (Principal), Cisneros, G. (Co-Principal), "Multiscale Approaches for Solvation in Room Temperature Ionic Liquids," Sponsored by College of Science, University of North Texas, $9000 Funded. (July 2019 – December 2019).
Cisneros, G., "Computational Determination and Characterization of Cancer Biomarkers," Sponsored by NVIDIA Foundation, Private, $200000 Funded. (January 2017 – December 2019).
Cisneros, G. A., "Theory and Simulation of DNA Repair Enzymes; Mechanism, Structure and Function," Sponsored by NIH, Federal, $1358848 Funded. (March 2014 – March 2019).



	
		
		
	  

	

	

	
	

  
  
  

  	

		

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Summative Rating		
					Challenge and
Engagement Index		
					Response Rate
					
				

			
			
				

					
					
out of 5		
					
out of 7		
					%
 of 
students responded		
					
					
				

			
		


		
    
			
  • Overall Summative Rating (median):
    
			This rating represents the combined responses of students to the four global summative items and is presented to provide an overall index of the class’s quality. Overall summative statements include the following (response options include a Likert scale ranging from 5 = Excellent, 3 = Good, and 1= Very poor):
				
      
					
    • The course as a whole was
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    • The course content was
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    • The instructor’s contribution to the course was
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    • The instructor’s effectiveness in teaching the subject matter was
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  • Challenge and Engagement Index:
    
			This rating combines student responses to several SPOT items relating to how academically challenging students found the course to be and how engaged they were. Challenge and Engagement Index items include the following (response options include a Likert scale ranging from 7 = Much higher, 4 = Average, and 1 = Much lower):
				
      
					
    • Do you expect your grade in this course to be
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    • The intellectual challenge presented was
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    • The amount of effort you put into this course was
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    • The amount of effort to succeed in this course was
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    • Your involvement in course (doing assignments, attending classes, etc.) was
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