Recent UCSD Chemistry & Biochemistry Publications

Recent publications from the Department of Chemistry and Biochemistry faculty, retrieved from Web of Science.

Cirera, J.; Paesani, F., Theoretical Prediction of Spin-Crossover Temperatures in Ligand-Driven Light-Induced Spin Change Systems. Inorganic Chemistry 2012, 51 (15), 8194-8201.

Garner, A. L.; Struss, A. K.; Fullagar, J. L.; Agrawal, A.; Moreno, A. Y.; Cohen, S. M.; Janda, K. D., 3-Hydroxy-1-alkyl-2-methylpyridine-4(1H)-thiones: Inhibition of the Pseudomonas aeruginosa Virulence Factor LasB. ACS Medicinal Chemistry Letters 2012, 3 (8), 668-672.

Moree, W. J.; Phelan, V. V.; Wu, C. H.; Bandeira, N.; Cornett, D. S.; Duggan, B. M.; Dorrestein, P. C., Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America 2012, 109 (34), 13811-13816.

Ortiz-Sanchez, J. M.; Bucher, D.; Pierce, L. C. T.; Markwick, P. R. L.; McCammon, J. A., Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics. Journal of Chemical Theory and Computation 2012, 8 (8), 2752-2761.

Rios, A. C.; Tor, Y., Refining the Genetic Alphabet: A Late-Period Selection Pressure? Astrobiology 2012, 12 (9), 884-891.

Schlamadinger, D. E.; Wang, Y.; McCammon, J. A.; Kim, J. E., Spectroscopic and Computational Study of Melittin, Cecropin A, and the Hybrid Peptide CM15. Journal of Physical Chemistry B 2012, 116 (35), 10600-10608.

Stout, E. P.; Yu, L. C.; Molinski, T. F., Antifungal Diterpene Alkaloids from the Caribbean Sponge Agelas citrina: Unified Configurational Assignments of Agelasidines and Agelasines. European Journal of Organic Chemistry 2012, (27), 5131-5135.

Taylor, S. S.; Keshwani, M. M.; Steichen, J. M.; Kornev, A. P., Evolution of the eukaryotic protein kinases as dynamic molecular switches. Philosophical Transactions of the Royal Society B-Biological Sciences 2012, 367 (1602), 2517-2528. [OPEN ACCESS]

VanWart, A. T.; Eargle, J.; Luthey-Schulten, Z.; Amaro, R. E., Exploring Residue Component Contributions to Dynamical Network Models of Allostery. Journal of Chemical Theory and Computation 2012, 8 (8), 2949-2961.

Wang, C.; Berg, C. J.; Hsu, C. C.; Merrill, B. A.; Tauber, M. J., Characterization of Carotenoid Aggregates by Steady-State Optical Spectroscopy. Journal of Physical Chemistry B 2012, 116 (35), 10617-10630.

Chapp, T. W.; Schoenfeld, A. J.; Sanderson, M. D.; Chang, C. L.; Glueck, D. S.; Golen, J. A.; Moore, C. E.; Rheingold, A. L., Synthesis, Structure, Dynamics, and Selective Methylation of Platinum and Palladium Diphosphametallacyclobutane Complexes. Organometallics 2012, 31 (15), 5573-5585.

Dowen, R. H.; Pelizzola, M.; Schmitz, R. J.; Lister, R.; Dowen, J. M.; Nery, J. R.; Dixon, J. E.; Ecker, J. R., Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences of the United States of America 2012, 109 (32), E2183-E2191. [OPEN ACCESS]

Gu, L.; Ruff, L. E.; Qin, Z. T.; Corr, M.; Hedrick, S. M.; Sailor, M. J., Multivalent Porous Silicon Nanoparticles Enhance the Immune Activation Potency of Agonistic CD40 Antibody. Advanced Materials 2012, 24 (29), 3981-3987.

Guo, L.; Ghassemian, M.; Komives, E. A.; Russell, P., Cadmium-Induced Proteome Remodeling Regulated by Spc1/Sty1 and Zip1 in Fission Yeast. Toxicological Sciences 2012, 129 (1), 200-212.

Haste, N. M.; Talabani, H.; Doo, A.; Merckx, A.; Langsley, G.; Taylor, S. S., Exploring the Plasmodium falciparum cyclic-adenosine monophosphate (cAMP)-dependent protein kinase (PfPKA) as a therapeutic target. Microbes and Infection 2012, 14 (10), 838-850.

Liang, F. X.; Kelly, T. L.; Luo, L. B.; Li, H.; Sailor, M. J.; Li, Y. Y., Self-Cleaning Organic Vapor Sensor Based on a Nanoporous TiO2 Interferometer. ACS Applied Materials & Interfaces 2012, 4 (8), 4177-4183.

Lindert, S.; Durrant, J. D.; McCammon, J. A., LigMerge: A Fast Algorithm to Generate Models of Novel Potential Ligands from Sets of Known Binders. Chemical Biology & Drug Design 2012, 80 (3), 358-365.

Parent, K. N.; Deedas, C. T.; Egelman, E. H.; Casjens, S. R.; Baker, T. S.; Teschke, C. M., Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials 2012, 33 (22), 5628-5637.

Park, K.; Gotz, A. W.; Walker, R. C.; Paesani, F., Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems. Journal of Chemical Theory and Computation 2012, 8 (8), 2868-2877.

Reynolds, S. C.; Hughes, R. P.; Glueck, D. S.; Rheingold, A. L., Synthesis, Reactivity, and Resolution of a C-2-Symmetric, P-Stereogenic Benzodiphosphetane, a Building Block for Chiral Bis(phosphines). Organic Letters 2012, 14 (16), 4238-4241.

Rogers, K. E.; Keranen, H.; Durrant, J. D.; Ratnam, J.; Doak, A.; Arkin, M. R.; McCammon, J. A., Novel Cruzain Inhibitors for the Treatment of Chagas’ Disease. Chemical Biology & Drug Design 2012, 80 (3), 398-405.

Schauer, A. J.; Kunasek, S. A.; Sofen, E. D.; Erbland, J.; Savarino, J.; Johnson, B. W.; Amos, H. M.; Shaheen, R.; Abaunza, M.; Jackson, T. L.; Thiemens, M. H.; Alexander, B., Oxygen isotope exchange with quartz during pyrolysis of silver sulfate and silver nitrate. Rapid Communications in Mass Spectrometry 2012, 26 (18), 2151-2157.

Shongwe, M. S.; Al-Zaabi, U. A.; Al-Mjeni, F.; Eribal, C. S.; Sinn, E.; Al-Omari, I. A.; Hamdeh, H. H.; Matoga, D.; Adams, H.; Morris, M. J.; Rheingold, A. L.; Bill, E.; Sellmyer, D. J., Accessibility and Selective Stabilization of the Principal Spin States of Iron by Pyridyl versus Phenolic Ketimines: Modulation of the (6)A(1) <-> T-2(2) Ground-State Transformation of the FeN4O2 (+) Chromophore. Inorganic Chemistry 2012, 51 (15), 8241-8253.

Zhou, Z. H.; Qiu, J. S.; Liu, W.; Zhou, Y.; Plocinik, R. M.; Li, H.; Hu, Q. D.; Ghosh, G.; Adams, J. A.; Rosenfeld, M. G.; Fu, X. D., The Akt-SRPK-SR Axis Constitutes a Major Pathway in Transducing EGF Signaling to Regulate Alternative Splicing in the Nucleus. Molecular Cell 2012, 47 (3), 422-433.

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