Computational Chemistry Publications

Computational Chemistry Journal Articles and Book Chapters:

Angel, L., Majors, L., Dharmaratne, A., & Dass, A. (2010). Ion Mobility Mass Spectrometry of Au25(SCH2CH2Ph)18 Nanoclusters. ACS Nano, 4(8), 4691-4700.

Cho, J., Hollis, T. K., Valente, E. J., & Trate, J. M. (2011). CCC-N-heterocyclic carbene pincer complexes: Synthesis, characterization and hydroamination activity of a hafnium complex. Journal of Organometallic Chemistry, 696(1), 373-377.

Daga, P. R., Duan, J., & Doerksen, R. J. (2010). Computational model of hepatitis B virus DNA polymerase: Molecular dynamics and docking to understand resistant mutations. Protein Science, 19, 796-807.

Daga, P. R., Patel, R. Y., & Doerksen, R. J. (2010). Template-based protein modeling: Recent methodological advances. Current Topics in Medicinal Chemistry, 10, 84-94.

Dayan, F. E., Daga, P. R., Duke, S. O., Lee, R. M., Tranel, P. J., & Doerksen, R. J. (2010). Biochemical and structural consequences of a glycine deletion in the ?-8 helix of protoporphyrinogen oxidase. Biochimica et Biophysica Acta 1804(7), 1548-1556.

Ghosh, B. D., & Ritchie, J. E. (2010). Effect of Polymer Structure on Ion Transport in an Anhydrous Proton Conducting Electrolyte Chemistry of Materials, 22, 1483-1491.

Graham, J. D., & Hammer, N. I. (2011). Photocatalytic Water Splitting and Carbon Dioxide Reduction Handbook of Climate Change Mitigation.

Kellum, M. G., Harris, C. A., McCormick, C. L., & Morgan, S. E. (2011). Stimuli-Responsive Micelles of Amphiphilic AMPS-b-AAL Copolymers in Layer-by-Layer Films. Journal of Polymer Science Part A: Polymer Chemistry, 49(5), 1104-1111.

Kellum, M. G., Smith, A. E., York, S. K., & McCormick, C. L. (2010). Reversible Interpolyelectrolyte Shell Cross-Linked Micelles from pH/Salt-Responsive Diblock Copolymers Synthesized via RAFT in Aqueous Solution. Macromolecules, 43(17), 7033-7040.

Knoppe, S., Dharmarne, A., Schreiner, E., Dass, A. D., & Burgi, T. (2010). Ligand Exchange Reactions on Au38 and Au40 Clusters: A Combined Circular Dichroism and Mass Spectrometry Study. Journal of the American Chemical Society, 132(47), 16783-11678.

Kudrimoti, S., Ahmed, S. A., Daga, P. R., Wahba, A. E., Khalifa, S. I., Doerksen, R. J., et al. (2009). Semisynthetic latrunculin B analogs: Studies of actin docking support a proposed mechanism for latrunculin bioactivity. Bioorganic & Medicinal Chemistry, 17(21), 7517-7522.

McDowell, M., Wright, A. E., & Hammer, N. I. (2010). Semiconductor Nanocrystals Hybridized with Functional Ligands: New Composite Materials with Tunable Properties. Materials, 3(1), 614-637.

Peng, J., Kudrimoti, S., Prasanna, S., Odde, S., Doerksen, R. J., Pennaka, H. K., et al. (2010). Structure--Activity Relationship and Mechanism of Action Studies of Manzamine Analogues for the Control of Neuroinflammation and Cerebral Infections. Journal of Medicinal Chemistry, 53(1), 61-76.

Petrova, T., Tarabara, I., Palchikov, V., Kasyan, L., Kosenkov, D., Okovytyy, S., et al. (2010). Discovery of diverse pathways depending on substituent's character. Organic and Biomolecular Chemistry, 8, 2142-2157.

Puzyn, T., Gajewicz, A., Leszczynska, D., & Leszczynski, J. (2009). Nanomaterials- the next Great Challenge for QSAR Modelers. In T. Puzyn & J. Leszczynski (Eds.), Recent Advances in QSAR Studies: Methods and Applications (pp. 383-410): Springer.

Puzyn, T., Leszczynska, D., & Leszczynski, J. (2009). Towards development of 'Nano-QSARs': Advances and Challenges. Small, 5(22), 2494-2509.

Puzyn, T., Rasulev, B., Gajewicz, A., Hu, X., Dasari, T. P., Michalkova, A., et al. (2011). Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles. [10.1038/nnano.2011.10]. Nat Nano, advance online publication.

Reilly, S. M., Krick, T., & Dass, A. (2009). Surfactant-free Synthesis of Ultrasmall Gold Nanoclusters. [doi: 10.1021/jp9067944]. The Journal of Physical Chemistry C, 114(2), 741-745.

Toropov, A. A., Toropova, A. P., Benfenati, E., Leszczynska, D., & Leszczynski, J. (2010a). QSAR analysis of 1,4-dihydro-4-oxo-1-(2-thiazolyl)-1,8-naphthyridines exhibiting anticancer activity by optimal SMILES-based descriptors. Journal of Mathematical Chemistry, 47, 647-666.

Toropov, A. A., Toropova, A. P., Benfenati, E., Leszczynska, D., & Leszczynski, J. (2010b). SMILES-Based Optimal Descriptors: QSAR Analysis of Fullerene-Based HIV-1 PR Inhibitors by Means of Balance of Correlations. J Computational Chemistry 31, 381-392.

Toropov, A. A., Toropova, A. P., Benfenati, E., Leszczynska, D., & Leszczynski, J. (2010c). Use of the international chemical identifier for constructing QSPR-model of normal boiling points of acyclic carbonyl substances. Journal of Mathematical Chemistry, 47, 355-369.

Toropova, A. P., Toropov, A. A., Benfenati, E., Gini, G., Leszczynska, D., & Leszczynski, J. (2010). InChI-based optimal descriptors: QSAR analysis of fullerene[C60]-based HIV-1 PR inhibitors by correlation balance. European Journal of Medicinal Chemistry, 45, 1387-1394.

Turabekova, M. A., Rasulev, B. F., Dzhakhangirov, F. N., Leszczynska, D., & Leszczynski, J. (2010). Aconitum and Delphinium Alkaloids of Curare-Like Activity. QSAR Analysis and Molecular Docking of Alkaloids into AChBP. European Journal of Medicinal Chemistry, 45(9), 3885-3894.

Munroe, K., Magers, D., & Hammer, N. (2011). Raman Spectroscopic Signatures of Noncovalent Interactions Between Trimethylamine N-oxide (TMAO) and Water. Journal of Physical Chemistry B.

Petrova, T., Rasulev, F. B., Toropov, A. A., Leszczynska, D., & Leszczynski, J. (2011). Improved model for fullerene C60 solubility in organic solvents based on quantum-chemical and topological descriptors. J Nanopart Res(10.1007), 11051.

Pustovit, V. N., & Shahbazyan, T. V. (2011). Resonance energy transfer near metal nanostructures mediated by surface plasmons. PHYSICAL REVIEW B, 83, 085427.

Puzyn, T., Rasulev, B., Gajewicz, A., Hu, X., P. Dasari, T., Michalkova, A., Hwang, H-M., Toropov, A., Leszczynska, D., & Leszczynski, J. (2011). Using nano-QSAR to predict the cytotoxicity of metal oxide nanoparticles. NATURE NANOTECHNOLOGY, 6, 175-178.

Reinemann, D. N., Wright, A. M., Wolfe, J. D., Tschumper, G. S., & Hammer, N. I. (2011). Vibrational Spectroscopy of N-Methyliminodiacetic Acid (MIDA)-Protected Boronate Ester: Examination of the B-N Dative Bond. The Journal of Physical Chemistry A.

Scardino, D. J., Howard, A. A., McDowell, M. D., & Hammer, N. I. (2011). Raman Spectroscopy as the Method of Detection for Constructing a Binary Liquid Vapor Phase Diagram. Journal of Chemical Education.

Scardino, D. J., McDowell, M., Graham, J. D., & Hammer, N. I. (2011). The Multiphoton Ionization Spectrum of Methyl Iodide Revisted: 1.67 - 2.2 eV Excitation. Journal of Atomic and Molecular Sciences, 2, 93-98.

Smith, D., Holley, A. C., & McCormick, C. L. (2011). RAFT-Synthesized Copolymers and Conjugates Designed for Therapeutic Delivery of SiRNA. Polymer Chemistry.

Stoddard, S. V., Yu, X., Potter, P.M., and Wadkins, R.M. (2010). in silico Design of Carboxylesterase Inhibitors. Journal of Pesticide Science, 35, 240-249.

Sun, C., & Ritchie, J. E. (2010). Effects of Bulky Copolymers on Ion Transport in an Anhydrous Proton-Conducting Electrolyte. Journal of the Electrochemical Society, 157, B1549-B1155.

Wright, A. M., Joe, L. V., Howard, A. A., Tschumper, G. S., & Hammer, N. I. (2011). Spectroscopic and Computational Insight into Weak Noncovalent Interactions in Crystalline Pyrimidine. Chemical Physics Letters, 501, 319-323.

Xie, A., Clark, S. R., & Doerksen, R. J. (2009). 3D quantitative structure-farnesyltransferase inhibition analysis for some diaminobenzophenones. Journal of Enzyme Inhibition & Medicinal Chemistry, 24, 1220-1228.

Xu, X., Flores, J., & McCormick, C. L. (2011). Reversible Imine Shell Cross-Linked Micelles From Aqueous RAFT-Synthesized Thermo-Responsive Triblock Copolymers as Potential Nanocarriers for "pH-Triggered" Drug Release. Macromolecules, 44(6), 1327-1334.

Yancey, B., & Ritchie, J. E. (2011). Conductivity and Viscosity Dependence of the Structures of PEG Based Anhydrous Proton Conducting Sol-Gel Electrolytes. Journal of Electroanalytical Chemistry, submitted.

Zhao, Q., Wang, J., Freeman, J. L., Murphy-Jolly, M., Wright, A. M., Scardino, D. J., Hammer, N., et al. (2011). Syntheses, and Optical, Fluorescence and Nonlinear Optical Characterization of Phosphine-Substituted Terthiophenes. Inorganic Chemistry, 50, 2015-2027.

 

Computational Chemistry Conference Papers and Presentations:

Abel, B. A., Smith, D., & McCormick, C. L. (2011a). Preparation of Advanced Macromolecular Architectures for siRNA Delivery using Controlled Polymer Synthetic Techniques. Paper presented at the 4th Annual Meeting of the Mississippi Biophysical Consortium, The University of Mississippi, Oxford, MS.

Abel, B. A., Smith, D., & McCormick, C. L. (2011b). RAFT-ROMP Molecular Brushes for siRNA Delivery. Paper presented at the 242nd ACS National Meeting & Exposition, Denver, CO.

Bates, D., & Tschumper, G. (2010). Development of a 3-body:Many-body fragmentation method for weakly bound clusters and application to water clusters (H2O)n n=3-10. Paper presented at the 62nd Southeastern Regional Meeting of the American Chemical Society, New Orleans, LA.

Cao, B., & Tschumper, G. (2010). Structures and Energetics of Two Small Phosphorus-Containing van der Waals Dimers, (P2)2 and (PCCP)2. Paper presented at the 62nd Southeastern Regional Meeting of the American Chemical Society, New Orleans, LA.

Carrell, E., & Tschumper, G. (2010). Identification of compact basis sets for the reliable characterization of higher-order effects in pi-type interactions. Paper presented at the Conference on Current Trends in Computational Chemistry (CCTCC), Jackson, Mississippi.

Carrell, E., & Tschumper, G. (2011). Identification of compact basis sets for the reliable characterization of higher-order effects in pi-type interactions. Paper presented at the 40th Meeting of the Southeast Theoretical Chemistry Association (SETCA), Mississippi State University, Starkville, MS.

Craine, L., D. N., Doerksen, R. J., & Fu, G. (2010). Evaluation and comparison of 3D-QSAR CoMSIA/CoMFA models for CDK1, CDK5, and GSK-3? inhibition by paullones. Paper presented at the 2010 Annual Biomedical Research Conference for Minority Students (ABRCMS).

Copeland, K., & Tschumper, G. (2010). Investigating interactions between hydrocarbons and water. Paper presented at the 62nd Southeastern Regional Meeting of the American Chemical Society, New Orleans, LA.

Dornshuld, E., & Tschumper, G. (2010). Exploring the Mechanism for Aqueous Glycine Condensation. Paper presented at the Conference on Current Trends in Computational Chemistry (CCTCC), Jackson, Mississippi.

Dornshuld, E., & Tschumper, G. (2011). The Molecular Structures of the P2 and PCCP Dimers. Paper presented at the 40th Meeting of the Southeast Theoretical Chemistry Association (SETCA), Mississippi State University, Starkville, MS.

Flores, J. D., Treat, N., & McCormick, C. L. (2010). Structopendent Transformation of RAFT Block Copolymers via Sequential Urethane and Thiol-Ene Click Reactions: A Facile Route to Well-Defined Functional Systems. Paper presented at the International Symposium on Stimuli-Responsive Materials, USM.

Fu, G., Sivaprakasam, P., Dale, O., Manly, S., Cutler, S., & Doerksen, R. (2011). Pharmacophore Modeling, Ensemble Docking and Virtual Screening Studies on Glycogen Synthase Kinase-3?. Paper presented at the 242nd American Chemical Society (ACS) National Meeting & Exposition, Denver, CO, USA.

Hailey, A. K., Shi, G., Chen, W.-Y., & Hammer, N. I. (2010). New Catalysts for the Photocatalytic Conversion of Carbon Dioxide to Hydrocarbons. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

Holley, A. C., Smith, D., & McCormick, C. L. (2011). Optimizing the Binding/Release of siRNA/Hydrophilic-block-Cationic Copolymer Complexes. Paper presented at the 4th Annual Meeting of the Mississippi Biophysical Consortium, The University of Mississippi, Oxford, MS.

Holley, A. C., York, A. W., Smith, D., & McCormick, C. L. (2010). Tailoring the Binding/Release of siRNA via Hydrophilic-b-Cationic Copolymers Synthesized via RAFT Polymerization. Paper presented at the International Symposium on Stimuli-Responsive Materials.

Kevin, D. A., Patel, R. Y., & Doerksen, R. J. (2011). Virtual screening evaluation of the MarinLit natural products database for cannabinoid receptor 2 (CB2) agonist-like features. Paper presented at the 241st ACS National Meeting & Exposition.

Kou, X., Smith, A., Xu, X., & McCormick, C. (2010). RAFT-Synthesized, Thermally-Responsive Triblock Copolymer for in Situ Formation of Gold Nanoparticle-Decorated, Shell Cross-linked Micelles. Paper presented at the International Symposium on Stimuli-Responsive Materials.

McClellan, A. K., Joe, L. V., Howard, J. C., Tschumper, G. S., & Hammer, N. I. (2010). Surface enhanced Raman spectra (SERS) of pyrimidine/water mixtures. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

McCormick, C. L. (2010). Construction of Targeted siRNA-Polymer Polyplexes and Their Delivery to Cancer Cells with Subsequent Specific Gene Down-Regulation. Paper presented at the International Symposium on Stimuli-Responsive Materials, USM.

McCormick, C. L. (2011). Aqueous RAFT Polymerization: Milestones, Successes and Challenges. Paper presented at the Cytec Engineered Materials and Cytec Specialty Chemicals, USM.

McCormick, C. L., York, A. W., Smith, D., Holley, A. C., Flores, J., Abel, B. A., et al. (2011). Biorelevant Macromolecules with Designed Architectures from Facile Transformation of Functional RAFT and aRAFT Copolymers. Paper presented at the 242nd ACS National Meeting & Exposition, Denver, CO.

Morgan, S. E., McCormick, C. L., Kellum, M. G., & Harris, C. A. (2010). Layer-by-Layer Films Containing Stimuli-Responsive Micelles. Paper presented at the ACS Joint 66th SWRM and 62nd SERMACS, New Orleans, LA.

Munroe, K. L., Magers, D. H., & Hammer, N. I. (2010a). Raman Spectroscopic Signatures of Noncovalent Interactions Involving Trimethylamine N-oxide (TMAO). Paper presented at the XXII International Conference on Raman Spectroscopy, Boston, MA.

Munroe, K. L., Magers, D. H., & Hammer, N. I. (2010b). Raman Spectroscopic Signatures of Noncovalent Interactions Involving Trimethylamine N-oxide (TMAO)_. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

Reinemann, D. N., Wright, A. M., Wolfe, J. D., Tschumper, G. S., & Hammer, N. I. (2010a). Infrared, Raman, and SERS Spectroscopy of N-Methyliminodiacetic Acid (MIDA)-Protected Boronate Esters. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

Reinemann, D. N., Wright, A. M., Wolfe, J. D., Tschumper, G. S., & Hammer, N. I. (2010b). Raman and SERS Spectroscopy of N-Methyliminodiacetic Acid (MIDA)-Protected Boronate Esters. Paper presented at the XXII International Conference on Raman Spectroscopy, Boston, MA.

Scardino, D. J., Kota, R., Mattern, D. L., & Hammer, N. I. (2010). Single Molecule Spectroscopic and Computational Studies of Two Organic Rectifiers. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

Smith, D., Holley, A. C., & McCormick, C. L. (2010). siRNA BLock Copolymer Conjugates as Therapeutic and Diagnostic Agents in Nanomedicine. Paper presented at the ACS Joint 66th SWRM and 62nd SERMACS, New Orleans, LA.

Tschumper, G. (2010a). Integrated fragmentation methods for weakly interacting, non-covalent clusters. Paper presented at the 62nd Southeastern Regional Meeting of the American Chemical Society, New Orleans, LA.

Tschumper, G. (2010b). Structures, energetics and vibrational spectra of hydrated pyrimidine. Paper presented at the 2010 International Chemical Congress of Pacific Basin Societies (PACIFICHEM), Honolulu, Hawaii.

Tschumper, G. (2011a). Effects of Dihydrogen Bonding on the Structure, Energetics and Vibrations of BH3NH3. Paper presented at the 40th Meeting of the Southeast Theoretical Chemistry Association (SETCA), Mississippi State University, Starkville, MS.

Tschumper, G. (2011b). Effects of Dihydrogen Bonding on the Structure, Energetics, and Vibrations of BH3NH3. Paper presented at the WATOC 2011: 9th Triennial Congress of the World Association of Theoretical and Computational Chemists, Santiago de Compostela, Spain.

Tschumper, G. (2011c). Integrated fragmentation method for weakly interacting, non-covalent clusters: 2-body:many-body and 3-body:many-body implementations and applications. Paper presented at the 241st National Meeting of the American Chemical Society, Anaheim, CA.

Treat, N. J., Smith, D., Flores, J., York, A. W., & McCormick, C. L. (2011). Direct RAFT Polymerization of a Guanidine-Containing Methacrylamide with Potential Cell Penetrating Peptide Mimicry. Paper presented at the 242nd ACS National Meeting & Exposition, Denver, CO.

Treat, N. J., Flores, J. D., & McCormick, C. L. (2011). Direct Aqueous RAFT Polymerization of a Guanidine-Containing Methacrylamide with Potential Cell Penetrating Peptide Mimicry. Paper presented at the The Waterborne Symposium, New Orleans, LA.

Wright, A., & Tschumper, G. (2011). Computational and Spectroscopic Study of Ammonia Borane. Paper presented at the 40th Meeting of the Southeast Theoretical Chemistry Association (SETCA), Mississippi State University, Starkville, MS.

Wright, A. M., Howard, A. A., Tschumper, G. S., & Hammer, N. I. (2010a). Raman Spectroscopic Investigations of Noncovalent Interactions between Pyrimidine and Hydrogen Bonded Networks. Paper presented at the XXII International Conference on Raman Spectroscopy, Boston, MA.

Wright, A. M., Howard, A. A., Tschumper, G. S., & Hammer, N. I. (2010b). Spectroscopic and computational investigations of noncovalent interactions between pyrimidine and hydrogen bonded networks. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

Wright, A. M., Joe, L. V., Howard, A. A., Tschumper, G. S., & Hammer, N. I. (2010). Spectroscopic and computational studies of weak noncovalent interactions in crystalline pyrimidine. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

Wright, A. M., Tschumper, G. S., & Hammer, N. I. (2010). High level ab initio calculations on ammonia borane. Paper presented at the 62nd Annual Meeting of the Southeastern Region of the American Chemical Society (SERMACS), New Orleans, LA.

Zhang, Y., York, A. W., McCormick, C. L., Guo, Y., & Huang, F. (2010). Analysis of Folate-Conjugated Copolymers/siRNA Complexes Trafficking in Cancer Cells through Fluorescence Imaging Techniques. Paper presented at the ACS Joint 66th SWRM and 62nd SERMACS, New Orleans, LA.