55. OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents.
Doherty, B.; Acevedo, O.
2018, (submitted).
54. Virtual Site OPLS Force Field for Imidazolium-Based Ionic Liquids.
Doherty, B.; Zhong, X.; Acevedo, O.
J. Phys. Chem. B, 2018, 122, 2962-2974. doi:10.1021/acs.jpcb.7b11996.
53. Phe 71 in type III Trypanosomal protein arginine methyltransferase 7 (TbPRMT7) restricts the enzyme to monomethylation.
Caceres, T.; Thakur, A.; Price, O.M.; Ippolito, N.; Li, J.; Qu, J.; Acevedo, O.; Hevel, J.M.
Biochemistry, 2018, 57, 1349-1359. doi:10.1021/acs.biochem.7b01265.
52. Novel Curcumin Based Pyrazoline Analogues as Selective inhibitors of hMAO-A.
Nath, C.; Badavath, V.N.; Thakur, A.; Ucar, G.; Acevedo, O.; Siddique, M.U.M.; Jayaprakash, V.
Med. Chem. Commun., 2018, 9, 1164-1171. doi:10.1039/C8MD00196K.
51. Revisiting OPLS Force Field Parameters for Ionic Liquid Simulations.
Doherty, B.; Zhong, X.; Gathiaka, S.; Li, B.; Acevedo, O.
J. Chem. Theory Comput., 2017, 13, 6131-6145. doi:10.1021/acs.jctc.7b00520.
50. Examining Ionic Liquid Effects on Mononuclear Rearrangement of Heterocycles using QM/MM Simulations.
Allen, C.; Ghebreab, R.; Doherty, B.; Li, B.; Acevedo, O.
J. Phys. Chem. B, 2016, 120, 10786-10796. doi:10.1021/acs.jpcb.6b07205.
49. Understanding Protein Arginine Methyltransferase 1 (PRMT1) Product Specificity from Molecular Dynamics.
Gathiaka, S.; Boykin, B.; Caceres, T.; Hevel, J.M.; Acevedo, O.
Bioorg. Med. Chem., 2016, 24, 4949-4960. doi:10.1016/j.bmc.2016.08.009.
• Invited article for special issue honoring William L. Jorgensen for the 2015 Tetrahedron Prize
48. Characterization and Mechanism for the Protection of Photolytic Decomposition of N-halamine Siloxane Coatings by Titanium Dioxide.
Liu, Y.; Li, J.; Li, L.; McFarland, S.; Ren, X.; Acevedo, O.; Huang, T.-S.
ACS Appl. Mater. Interfaces, 2016, 8, 3516-3523. doi:10.1021/acsami.5b12601.
47. Benchmarking Continuum Solvent Models for Keto-Enol Tautomerizations.
McCann, B.W.; McFarland, S.; Acevedo, O.
J. Phys. Chem. A, 2015, 119, 8724-8733. doi:10.1021/acs.jpca.5b04116
46. Ionic Liquid Effects on Nucleophilic Aromatic Substitution Reactions from QM/MM Simulations.
Allen, C.; McCann, B.W.; Acevedo, O.
J. Phys. Chem. B, 2015, 119, 743-752. doi:10.1021/jp504967r
• Invited article for special issue William L. Jorgensen Festschrift
45. Simulating Chemical Reactions in Ionic Liquids Using QM/MM Methodology.
Acevedo, O.
J. Phys. Chem. A, 2014, 118, 11653-11666. doi:10.1021/jp507967z
• Feature Article
• ACS Editors' Choice
• Featured on the cover of J. Phys. Chem. A (Dec. 18 2014)
44. Exploring the Catalytic Mechanism of Alkanesulfonate Monooxygenase using Molecular Dynamics.
Armacost, K.; Muslia, J.; Gathiaka, S.; Ellis, H.R.; Acevedo, O.
Biochemistry, 2014, 53, 3308-3317. doi:10.1021/bi5002085.
43. A Remodeled Protein Arginine Methyltransferase 1 (PRMT1) Generates Symmetric Dimethylarginine.
Gui, S.; Gathiaka, S.; Li, J.; Qu, J.; Acevedo, O.; Hevel, J.M.
J. Biol. Chem., 2014, 289, 9320-9327. doi:10.1074/jbc.M113.535278.
42. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions.
Acevedo, O.; Jorgensen, W.L.
WIREs Comput. Mol. Sci., 2014, 4, 422-435. doi:10.1002/wcms.1180
• Invited article
41. Identification of PLX4032-Resistance Mechanisms and Implications for Novel RAF Inhibitors.
Choi, J.; Landrette, S.; Wang, T.; Evans, P.; Bacchiocchi, A.; Bjornson, R.; Cheng, E.; Stiegler, A.; Gathiaka, S.; Acevedo, O.; Boggon, T.; Krauthammer, M.; Halaban, R.; Xu, T.
Pigment Cell Melanoma Res., 2014, 27, 253-262. doi:10.1111/pcmr.12197.
40. Exploring the Aldol Reaction using Catalytic Antibodies and "On Water" Organocatalysts from QM/MM Calculations.
Armacost, K.; Acevedo, O.
J. Am. Chem. Soc., 2014, 136, 147-156. doi:10.1021/ja405614p.
39. Determination of antiplasmodial activity and binding affinity of curcumin and demethoxycurcumin towards PfTrxR.
Munigunti, R.; Gathiaka, S.; Acevedo, O.; Sahu, R.; Tekwani, B.; Calderon, A.I.
Nat. Prod. Res., 2014, 28, 359-364. doi:10.1080/14786419.2013.866112.
38. Characterization of PfTrxR Inhibitors using Antimalarial Assays and In Silico Techniques.
Munigunti, R.; Gathiaka, S.; Acevedo, O.; Sahu, R.; Tekwani, B.; Calderon, A.I.
Chem. Cent. J., 2013, 7, 175. doi:10.1186/1752-153X-7-175.
37. Pairwise Alternatives to Ewald Summation for Calculating Long-Range Electrostatics in Ionic Liquids.
McCann, B.W.; Acevedo, O.
J. Chem. Theory Comput., 2013, 9, 944-950. doi:10.1021/ct300961e.
36. An Ionic Liquid Dependent Mechanism for Base Catalyzed β-Elimination Reactions from QM/MM Simulations.
Allen, C.; Sambasivarao, S.V.; Acevedo, O.
J. Am. Chem. Soc., 2013, 135, 1065-1072. doi:10.1021/ja3098614.
35. Design, Development and Evaluation of Novel Dual PPARγ/PPARδ Agonists.
Gathiaka, S.; Nanayakkara, G.; Boncher, T.; Acevedo, O.; Wyble, J.; Shane, M.E.; Bonkowski, B.; Wieczorek, J.; Ren, Y.W.; Huggins, K.; Smith, F.; Amin, R.H.
Bioorg. Med. Chem. Lett., 2013, 23, 873-879. doi:10.1016/j.bmcl.2012.11.060.
34. Inter- and Intramolecular Mechanisms for Chlorine Rearrangements in Trimethyl-Substituted N-Chlorohydantoins.
McCann, B.W.; Song, H.; Kocer, H.B.; Cerkez, I.; Acevedo, O.; Worley, S.D.
J. Phys. Chem. A, 2012, 116, 7245-7252. doi:10.1021/jp304610k.
33. Identification of HIV Inhibitors Guided by Free Energy Perturbation Calculations.
Acevedo, O.; Ambrose, Z.; Flaherty, P.T.; Aamer, H.; Jain, P.; Sambasivarao, S.V.
Curr. Pharm. Des., 2012, 18, 1199-1216.
• Invited article
32. Using Electronic Theory To Identify Metabolites Present in 17α-Ethinylestradiol Biotransformation Pathways.
Barr, W.J.; Yi, T.; Aga, D.; Acevedo, O.; Harper Jr., W.F.
Environ. Sci. Technol., 2012, 46, 760-768. doi:10.1021/es201774r.
31. Optimal Scaling Factors for CM1 and CM3 Atomic Charges in Aqueous RM1-Based Simulations.
Vilseck, J.Z.; Sambasivarao, S.V.; Acevedo, O.
J. Comput. Chem., 2011, 32, 2836-2842. doi:10.1002/jcc.21863.
30. Computational Insight into Small Molecule Inhibition of Cyclophilins.
Sambasivarao, S.V.; Acevedo, O.
J. Chem. Inf. Model., 2011, 51, 475-482. doi:10.1021/ci1004114.
• Highlighted by ACS Publications in a HCV Therapies Collection Issue (February 2013)
29. Mechanism of Photolytic Decomposition of N-Halamine Antimicrobial Siloxane Coatings.
Kocer, H.B.; Akdag, A.; Worley, S.D.; Acevedo, O.; Broughton, R.M.; Wu, Y.
ACS Appl. Mater. Interfaces, 2010, 2, 2456-2464. doi:10.1021/am100511x.
28. Effect of Phenyl Derivatization on the Stabilities of Antimicrobial N-Chlorohydantoin Derivatives.
Kocer, H.B.; Worley, S.D.; Broughton, R.M.; Acevedo, O.; Huang, T.S.
Ind. Eng. Chem. Res. 2010, 49, 11188-11194. doi:10.1021/ie101258s.
27. Computing Free-Energy Profiles using Multidimensional Potentials of Mean Force and Polynomial Quadrature Methods, in Annual Reports in Computational Chemistry.
Vilseck, J.Z.; Acevedo, O.
Elsevier, (Wheeler, Ed.) 2010, Vol. 6, 37-49. doi:10.1016/S1574-1400(10)06003-2.
26. Exploring Solvent Effects upon the Menshutkin Reaction using a Polarizable Force Field.
Acevedo, O.; Jorgensen, W.L.
J. Phys. Chem. B, 2010, 114, 8425-8430. doi:10.1021/jp100765v.
25. Claisen Rearrangements: Insight into Solvent Effects and "On Water" Reactivity from QM/MM Simulations.
Acevedo, O.; Armacost, K.
J. Am. Chem. Soc., 2010, 132, 1966-1975. doi:10.1021/ja908680c.
24. Advances in Quantum and Molecular Mechanical (QM/MM) Simulations for Organic and Enzymatic Reactions.
Acevedo, O.; Jorgensen, W.L.
Acc. Chem. Res., 2010, 43, 142-151. doi:10.1021/ar900171c.
23. Role of Water in the Multifaceted Catalytic Antibody 4B2 for Allylic Isomerization and Kemp Elimination Reactions.
Acevedo, O.
J. Phys. Chem. B, 2009, 113, 15372-15381. doi:10.1021/jp9069114.
22. Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids.
Sambasivarao, S.V.; Acevedo, O.
J. Chem. Theory Comput., 2009, 5, 1038-1050. doi:10.1021/ct900009a.
• Featured on the cover of JCTC (June 2009)
21. Determination of Local Effects for Chloroaluminate Ionic Liquids on Diels-Alder Reactions.
Acevedo, O.
J. Mol. Graphics Modell., 2009, 28, 95-101. doi:10.1016/j.jmgm.2009.04.003.
20. Multidimensional Exploration of Valley-Ridge Inflection Points on Potential Energy Surfaces.
Sheppard, A.N.; Acevedo, O.
J. Am. Chem. Soc., 2009, 131, 2530-2540. doi:10.1021/ja803879k.
19. A New Solvent-Dependent Mechanism for a Triazolinedione Ene Reaction.
Acevedo, O.; Squillacote, M.E.
J. Org. Chem., 2008, 73, 912-922. doi:10.1021/jo7022153.
18. Mechanism of 5,5-Dimethylhydantoin Chlorination: Monochlorination through a Dichloro Intermediate.
Akdag, A.; Worley, S.D.; Acevedo, O.; McKee, M.L.
J. Chem. Theory Comput., 2007, 3, 2282-2289. doi:10.1021/ct7001804.
17. Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology.
Acevedo, O.; Jorgensen, W.L.
J. Chem. Theory Comput., 2007, 3, 1412-1419. doi:10.1021/ct700078b.
16. Computation of Accurate Barriers for Methyl Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution.
Gunaydin, H.; Acevedo, O.; Jorgensen, W.L.; Houk, K.N.
J. Chem. Theory Comput., 2007, 3, 1028-1035. doi:10.1021/ct050318n.
15. Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations.
Acevedo, O.; Jorgensen, W.L., Evanseck, J.D.
J. Chem. Theory Comput., 2007, 3, 132-138. doi:10.1021/ct6002753.
14. Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant via QM/MM Simulations
Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W.L.
J. Am. Chem. Soc., 2006, 128, 16904-16913. doi:10.1021/ja065863s.
13. Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations.
Acevedo, O.; Jorgensen, W.L.
J. Am. Chem. Soc., 2006, 128, 6141-6146. doi:10.1021/ja057523x.
12. Medium Effects on the Decarboxylation of a Biotin Model in Pure and Mixed Solvents from QM/MM Simulations.
Acevedo, O.; Jorgensen, W.L.
J. Org. Chem., 2006, 71, 4896-4902. doi:10.1021/jo060533b.
11. Solvent Effects on Organic Reactions from QM/MM Simulations, in Annual Reports in Computational Chemistry.
Acevedo, O.; Jorgensen, W.L.
Elsevier, (Spellmeyer, Ed.) 2006, Vol. 2, 263-278. doi:10.1016/S1574-1400(06)02014-7.
10. Influence of Inter- and Intramolecular Hydrogen Bonding on Kemp Decarboxylations from QM/MM Simulations.
Acevedo, O.; Jorgensen, W.L.
J. Am. Chem. Soc., 2005, 127, 8829-8834. doi:10.1021/ja051793y.
9. Discovery of a Potent, Selective, and Efficacious Class of Reversible α-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase Effective as Analgesics.
Boger, D.L.; Miyauchi, H.; Du, W.; Hardouin, C.; Fecik, R.A.; Cheng, H.; Hwang, I.; Hedrick, M.P.; Leung, D.; Acevedo, O.; Guimaraes, C.R.W.; Jorgensen, W.L.; Cravatt, B.F.
J. Med. Chem., 2005, 48, 1849-1856. doi:10.1021/jm049614v.
8. Transition Structures and Transition States, in Computational Medicinal Chemistry for Drug Discovery.
Acevedo, O.; Evanseck, J.D.
Dekker Inc., New York, 2004, Chapter 12, 323-344.
Computational Medicinal Chemistry for Drug Discovery, Dekker Inc..
7. Solvent Effects and Mechanism for a Nucleophilic Aromatic Substitution from QM/MM Simulations.
Acevedo, O.; Jorgensen, W.L.
Org. Lett., 2004, 6, 2881-2884. doi:10.1021/ol049121k.
6. Density Functional Theory Determination of an Axial Gateway to Explain the Rate and Endo Selectivity Enhancement of Diels-Alder Reactions by Bis(oxazoline)-Cu(II).
DeChancie, J.; Acevedo, O.; Evanseck, J.D.
J. Am. Chem. Soc., 2004, 126, 6043-6047. doi:10.1021/ja037702j.
5. Enhanced Sampling by Multiple Molecular Dynamics Trajectories: Carbonmonoxy Myoglobin 10 μs A0 → A1-3 Transition from Ten 400 Picosecond Simulations.
Loccisano, A.E.; Acevedo, O.; DeChancie, J.; Schulze, B.G.; Evanseck, J.D.
J. Mol. Graphics Modell., 2004, 22, 369-376. doi:10.1016/j.jmgm.2003.12.004.
4. The Effect of Solvent on a Lewis Acid Catalyzed Diels-Alder Reaction Using Computed and Experimental Kinetic Isotope Effects.
Acevedo, O.; Evanseck, J.D.
Org. Lett., 2003, 5, 649-652. doi:10.1021/ol027408g.
3. Transition Structure Models of Organic Reactions in Chloroaluminate Ionic Liquids. Cyclopentadiene and methyl acrylate Diels-Alder reaction in acidic and basic melts of 1-ethyl-3-methylimidazolium chloride with aluminum(III) chloride.
Acevedo, O.; Evanseck, J.D.
ACS Symposium Series, 2003, 856 (Ionic Liquids as Green Solvents: Progress and Prospects), 174-190. doi:10.1021/bk-2003-0856.ch015.
2. Molecular Basis For Carbon Dioxide Sequestration In Coal.
Dick, T.J.; Acevedo, O.; Dalal, P.; Madura, J.D.; Evanseck, J.D.; Mathews, J.P.
Reprints of Symposia-American Chemical Society, Division of Fuel Chemistry, 2002, 47, 14-16.
1. The Gates, Swings and Levers of Biomolecular Mechanics.
Acevedo, O.; Schulze, B.G.; Evanseck, J.D.
Phys. Chem. 2000, Proc. Int. Conf. Fundam. Appl. Aspects Phys. Chem. 5th, 2000, 264-277.
0. Principles of Chemical Reactivity on the Diels-Alder Reaction in Ionic Liquids and Lewis Acid Catalysis Using Large-Scale Computations.
Acevedo, O.
Ph.D. Thesis, Duquesne University, 2003.
Presentations
114. Using Theory and Experiment to Elucidate the Origin of Product Specificity in Protein Arginine Methyltransferases.
Acevedo, O.; Thakur, A.; Caceres, B.; Price, O.M.; Hevel, J.M.;
Florida Section ACS Meeting (FAME), Tampa, FL May 3-5, 2018.
113. F71I mutation in PRMT7 alters product specificity.
Thakur, A.; Caceres, B.; Hevel, J.M.; Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 3-5, 2018.
112. Development of a virtual site OPLS force field for ionic liquid simulations.
Doherty, B.; Zhong, X.; Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 3-5, 2018.
111. Development of OPLS parameters for pyridinium-based ionic liquids.
Zhong, X.; Doherty, B.; Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 3-5, 2018.
110. Chemical Reactions at Aqueous Surfaces, in Ionic Liquids, and within Catalytic Antibodies.
Acevedo, O.
University of South Florida, March 2018 (invited talk).
109. Computational Organic and Medicinal Chemistry.
Acevedo, O.
Barry University, January 2018 (invited talk).
108. Ionic Liquid OPLS-AA force field parameters for imidazolium-based simulations.
Acevedo, O.; Doherty, B.; Zhong, X.
Book of Abstracts, 254th ACS National Meeting, Washington, DC August 20-24, 2017.
107. Elucidating Product Specificity in Protein Arginine Methyltransferase 7 (PRMT7) Using QM/MM/MD.
Thakur, A.; Caceres, B.; Hevel, J.M.; Acevedo, O.
Book of Abstracts, 254th ACS National Meeting, Washington, DC August 20-24, 2017.
106. OPLS-AA force field parameters for ionic liquid molecular dynamics simulations.
Doherty, B.; Zhong, X.; Gathiaka, S.; Li, B.; Acevedo, O.
Book of Abstracts, 254th ACS National Meeting, Washington, DC August 20-24, 2017.
105. OPLS-AA force field parameters for dicationic imidazolium-based ionic liquid simulations.
Zhong, X.; Doherty, B.; Acevedo, O.
Book of Abstracts, 254th ACS National Meeting, Washington, DC August 20-24, 2017.
104. Ionic Liquid OPLS-AA Force Field Parameters for Molecular Dynamics Simulations.
Doherty, B.; Zhong, X.; Gathiaka, S.; Li, B.; Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 4-7, 2017.
103. A Custom OPLS-AA Force Field for Dicationic Imidazolium-based Ionic Liquid Simulations.
Zhong, X.; Doherty, B.; Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 4-7, 2017.
102. Elucidating the Product Specificity and Determining the Active Site Base in Protein Arginine Methyltransferase 7 (PRMT7) Using QM/MM/MD and Molecular Dynamics.
Thakur, A.; Caceres, B.; Hevel, J.M.; Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 4-7, 2017.
101. Properties and Dynamics of Ionic Liquids.
Acevedo, O.
Chemical Science Symposium, Nova Southeastern University, February 26, 2017 (invited talk).
100. Simulating Dicationic Imidazolium-based Ionic Liquids Using Custom OPLS-AA Force Fields.
Zhong, X.; Doherty, B.; Acevedo, O.
Chemical Science Symposium, Nova Southeastern University, February 26, 2017 (invited talk).
• "Honorable Mention Award" from the South Florida ACS Section
99. Development of a Virtual Site OPLS-AA Force Field (OPLS-VSIL) for Ionic Liquid Simulations.
Doherty, B.; Zhong, X.; Gathiaka, S.; Li, B.; Acevedo, O.
Chemical Science Symposium, Nova Southeastern University, February 26, 2017 (invited talk).
98. Elucidating the Product Specificity of Protein Methyltransferase 7 (PRMT7) Using QM/MM and Molecular Dynamics.
Thakur, A.; Caceres, B.; Hevel, J.M.; Acevedo, O.
Chemical Science Symposium, Nova Southeastern University, February 26, 2017.
97. Interpreting Solvent Effects on Chemical Reactivity using QM/MM Simulations.
Acevedo, O.
Book of Abstracts, 252th ACS National Meeting, Philadelphia, PA August 21-25, 2016 (invited talk).
96. Using theory and experiment to elucidate the origin of product specificity in PRMT1.
Acevedo, O.
Book of Abstracts, 252th ACS National Meeting, Philadelphia, PA August 21-25, 2016.
95. Development of inhibitors targeting cyclophilin A guided by free energy perturbation calculations.
Acevedo, O.
Vertex Pharmaceuticals Workshop on Free Energy Methods in Drug Design: Targeting Cancer, Boston, MA May 16-18, 2016 (invited talk).
94. Modeling Solvent Effects on Organic Reactions using QM/MM Calculations.
Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 5-7, 2016 (invited talk).
93. Molecular Dynamic Simulations of Ionic Liquids using a Customized OPLS-AA Force Field.
Doherty, B.; Acevedo, O.
Florida Section ACS Meeting (FAME), Tampa, FL May 5-7, 2016.
92. Modeling Chemical Reactions in Ionic Liquids using QM/MM Calculations.
Acevedo, O.
Book of Abstracts, 251th ACS National Meeting, San Diego, CA March 13-17, 2016.
91. Understanding the Mechanism and Product Specificity of PRMT1 using Theory and Experiment.
Acevedo, O.; Gathiaka, S.; Boykin, B.; Caceres, B.; Hevel, J.M.
Book of Abstracts, 251th ACS National Meeting, San Diego, CA March 13-17, 2016.
90. Development of Ionic Liquid OPLS-AA Force Field Parameters for use in Molecular Dynamics and Monte Carlo Simulations.
Doherty, B.; Acevedo, O.
Book of Abstracts, 251th ACS National Meeting, San Diego, CA March 13-17, 2016.
89. The role of His293 in Protein Arginine Methyltransferases 1 (PRMT1).
Boykin, B.; Gathiaka, S.; Hevel, J.M.; Acevedo, O.
LSAMP Minority Participation Symposium, National Harbor, MD February 22-24, 2016.
88. The role of His293 in Protein Arginine Methyltransferases 1 (PRMT1).
Boykin, B.; Gathiaka, S.; Hevel, J.M.; Acevedo, O.
42nd NOBCChE National Meeting, Orlando, FL September 21-25, 2015.
87. Chemical Reactions at Aqueous Surfaces, in Ionic Liquids, and within Catalytic Antibodies.
Acevedo, O.
Seminar, Florida State University, Tallahassee, Florida, August 2015 (invited talk).
86. Understanding the Mechanism and Product Specificity of PRMT1 using Theory and Experiment.
Acevedo, O., Gathiaka, S.; Boykin, B.; Gui, S.; Li, J.; Qu, J.; Hevel, J.M.
Book of Abstracts, 250th ACS National Meeting, Boston, MA August 16-20, 2015.
85. Identifying Drug Resistance Mechanisms in Melanoma Cells Towards BRAF Inhibitors using Molecular Dynamics.
Ippolito, N.; Choi, J.; Acevedo, O.
Book of Abstracts, 250th ACS National Meeting, Boston, MA August 16-20, 2015.
84. Identifying Protein Conformational Changes of Agonist-Induced PPAR-gamma using Molecular Dynamics.
Boykin, B.; Gathiaka, S.; Amin, R.H.; Boncher, T.; Acevedo, O.
Book of Abstracts, 250th ACS National Meeting, Boston, MA August 16-20, 2015.
83. Development of OPLS-AA Force Field Parameters for Ionic Liquids.
Gathiaka, S.; Li, B.; Acevedo, O.
Book of Abstracts, 249th ACS National Meeting, Denver, CO March 22-26, 2015.
82. Chemical Reactions at Aqueous Surfaces, in Ionic Liquids, and within Catalytic Antibodies from QM/MM Simulations.
Acevedo, O.
Seminar, University of Miami, Coral Gables, Florida, October 2014 (invited talk).
81. Computational Medicinal Chemistry and Biochemistry.
Acevedo, O.
Seminar, Florida International University, Miami, Florida, September 2014 (invited talk).
80. PRMT1: Mechanism and product specificity from QM and MD simulations.
Gathiaka, S.; Gui, S.; Li, J.; Hevel, J.M.; Acevedo, O.
41th NOBCChE National Meeting, New Orleans, LA September 23-26, 2014.
79. Characterization of Agonist-Induced PPAR-gamma Conformational Changes.
Boykin, B.; Gathiaka, S.; Amin, R.H.; Boncher, T.; Acevedo, O.
41th NOBCChE National Meeting, New Orleans, LA September 23-26, 2014.
78. Mechanism and product specificity of PRMT1: Implications from QM and MD Simulations.
Gathiaka, S.; Gui, S.; Li, J. Hevel, J.; Acevedo, O.
Book of Abstracts, 248th ACS National Meeting, San Francisco, CA August 10-14, 2014.
77. Characterization of PfTrxR Inhibitors using in silico Methodology and Antimalarial Assays.
Gathiaka, S.; Munigunti, R.; Becker, K.; Sahu, R.; Tekwani, B.; Calderon, A.I.; Acevedo, O.
Book of Abstracts, 248th ACS National Meeting, San Francisco, CA August 10-14, 2014.
76. Chemical Reactions in Ionic Liquids using QM/MM Calculations.
Acevedo, O.
CECAM Workshop - 'Multiscale modelling of ionic liquids: from quantum methods to coarse-grained models,' Lausanne, Switzerland, June 2014. (invited talk).
75. Chemical Reactions at Aqueous Surfaces, in Ionic Liquids, and within Catalytic Antibodies from QM/MM Simulations.
Acevedo, O.
Seminar, University of Mississippi, Oxford, Mississippi, March 2014 (invited talk).
74. Chemical Reactions at Aqueous Surfaces and in Ionic Liquids from QM/MM Simulations.
Acevedo, O.
Book of Abstracts, ACS Southeastern Regional Meeting (SERMACS), Atlanta, Georgia, November 11-16, 2013. (invited talk).
73. Development of HIV inhibitors targeting cyclophilin A guided by free energy perturbation calculations.
Acevedo, O.
Seminar, Book of Abstracts, ACS Southeastern Regional Meeting (SERMACS), Atlanta, Georgia, November 11-16, 2013. (symposium organizer).
72. PRMT1: Exploring the mechanism and product specificity from molecular dynamics simulations.
Gathiaka, S.; Hevel, J.; Acevedo, O.
Poster, Book of Abstracts, ACS Southeastern Regional Meeting (SERMACS), Atlanta, Georgia, November 11-16, 2013.
71. Understanding room temperature ionic liquid effects upon organic reactions from QM/MM/MC/FEP simulations.
Allen, C.R.; McCann, B.W.; Acevedo, O.
Poster, Book of Abstracts, ACS Southeastern Regional Meeting (SERMACS), Atlanta, Georgia, November 11-16, 2013.
70. Chemical Reactions at Aqueous Surfaces and in Ionic Liquids from QM/MM Simulations.
Acevedo, O.
Seminar, SHPE Conference, Indianapolis, Indiana, November 2013 (invited talk).
69. Design and Biological evaluation of Novel PPAR-gamma/delta Agonists.
Gathiaka, S.; Nanayakkara, G.; Boncher, T.; Acevedo, O.; Wyble, J.; Shane, M.E.; Bonkowski, B.; Wieczorek, J.; Ren, Y.W.; Huggins, K.; Smith, F.; Amin, R.H.; Acevedo, O.
Poster, NOBCChE 2013 National Conference , Indianapolis, Indiana, October 1-4, 2013.
68. Chemical Reactions at Aqueous Surfaces, in Ionic Liquids, and within Catalytic Antibodies from QM/MM Simulations.
Acevedo, O.
Seminar, Bucknell University, Lewisburg, Pennsylvania, July 2013 (invited talk).
67. Elucidating Solvent Effects on Chemical Reactions at Aqueous Surfaces, in Ionic Liquids, and within Catalytic Antibodies from QM/MM Simulations.
Acevedo, O.
Seminar, Texas A&M, College Station, Texas, April 2013 (invited talk).
66. Development of "on water" QM/MM methodology for the Claisen rearrangement of allyl p-R-phenyl ethers and allyl naphthyl ether and Aldol reaction of benzaldehyde and acetone with a chiral organocatalyst.
Armacost, K.A.; Acevedo, O.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
65. Solvent effects of ionic liquids on the aromatic nucleophilic substitution reaction from QM/MM simulations.
Allen, C.; Acevedo, O.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
64. Investigating substrate-induced conformational changes in alkanesulfonate monooxygenase using molecular dynamics simulations.
Armacost, K.A.; Gathiaka, S.; Ellis, H.; Acevedo, O.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
63. QM/MM simulations for the elucidation of ionic liquid effects upon classical organic reactions.
Allen, C.; Acevedo, O.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
62. Exploring ionic liquid induced mechanistic changes for beta-elimination reactions from QM/MM simulations.
Allen, C.; Sambasivarao, S.V.; Acevedo, O.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
61. Development of OPLS-AA force field parameters for ionic liquid simulations and their applications in elimination reactions.
Sambasivarao, S.V.; Allen, C.; Acevedo, O.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
60. Identification of novel PPAR-gamma/delta Agonists.
Gathiaka, S.; Acevedo, O.; et al.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
59. Assessing the applicability of pairwise alternatives to Ewald summation on a wide range of ionic liquids.
McCann, B.; Acevedo, O.
Book of Abstracts, 245th ACS National Meeting, New Orleans, LA April 7-11, 2013.
58. (1) Development of force field parameters and advanced algorithms for ionic liquid simulations and (2) Elucidation of solvent effects from ionic liquids on organic reactions via QM/MM calculations.
Acevedo, O.
Seminar, Universidad de Chile, Santiago, March 2013 (invited talk).
57. Development of HIV inhibitors targeting cyclophilin A guided by free energy perturbation calculations.
Acevedo, O.
Seminar, Auburn University - Harrison School of Pharmacy, Auburn, Alabama, November 2012 (invited talk).
56. Development of HIV inhibitors targeting cyclophilin A guided by free energy perturbation calculations.
Acevedo, O.
Seminar, Utah State University - Department of Chemistry and Biochemistry, Logan, Utah, October 2012 (invited talk).
55. Development of OPLS-AA force field parameters for QM/MM ionic liquid simulations.
Acevedo, O.
Book of Abstracts, 244th ACS National Meeting, Philadelphia, PA August 19-23, 2012.
54. Benchmarking tautomerization reactions using continuum solvation models.
Acevedo, O.
Book of Abstracts, 244th ACS National Meeting, Philadelphia, PA August 19-23, 2012.
53. Development of HIV inhibitors targeting cyclophilin A guided by free energy perturbation calculations.
Acevedo, O.
Book of Abstracts, 244th ACS National Meeting, Philadelphia, PA August 19-23, 2012.
52. Elucidation of Solvent Effects from Water to Ionic Liquids on Organic and Biological Reactions.
Acevedo, O.
Seminar, Quantum Mechanics and Molecular Dynamics of Organic and Biological Reactivity Symposium satellite to The International Congresses of Quantum Chemistry (ICQC), at UCLA, California, June, 21-23 2012 (invited talk).
51. Development of Novel PPAR-delta Agonists prevent PPAR-gamma Related Side Effects.
Gathiaka, S.; Nanayakkara, G.; Amin, R.; Boncher, T.; Acevedo, O.
Poster, Southeast Theoretical Chemistry Association (SETCA), University of Georgia, GA, May 2012.
50. Benchmarking Implicit Solvation Models and Cavities for the Accurate Calculation of Tautomerization Equillibria.
McCann, B.; Acevedo, O.
Poster, Southeast Theoretical Chemistry Association (SETCA), University of Georgia, GA, May 2012.
49. Exploring the Role of Ionic Liquids on Aromatic Nucleophilic Substitution Reactions via QM/MM Simulations.
Allen, C.; McCann, B.; Acevedo, O.
Poster, Southeast Theoretical Chemistry Association (SETCA), University of Georgia, GA, May 2012.
48. Claisen Rearrangements: Insight into Solvent Effects and "on Water" Reactivity from QM/MM Simulations.
Armacost, K.; Acevedo, O.
Poster, Southeast Theoretical Chemistry Association (SETCA), University of Georgia, GA, May 2012.
47. Exploring Aromatic Nucleophilic Substitution in Ionic Liquids from QM/MM Simulations.
Allen, C.; McCann, B.; Acevedo, O.
Poster, Conference on Current Trends in Computational Chemistry, Jackson, MI, Oct. 27-29, 2011.
46. The Development of On Water QM/MM Methodology for Organic Reactions.
Armacost, K.; Acevedo, O.
Poster, Conference on Current Trends in Computational Chemistry, Jackson, MI, Oct. 27-29, 2011.
45. Benchmarking Implicit Solvation Models and Cavities for the Accurate Calculation of Tautomerism.
McCann, B.; Acevedo, O.
Poster, Conference on Current Trends in Computational Chemistry, Jackson, MI, Oct. 27-29, 2011.
44. Understanding On Water Effects for Claisen Rearrangements Using QM/MM Simulations.
Acevedo, O.
Seminar, Southeast Theoretical Chemistry Association (SETCA), University of Mississippi, MS, May 2011 (invited talk).
43. Elucidating the role of solvent in chemical reactions using simulations.
Acevedo, O.
Seminar, Auburn University - Department of Polymer and Fiber Engineering, Auburn, Alabama, April 2011 (invited talk).
42. How the Enzyme KSI Performs Steroid Transformations.
Gorman, T.;* Acevedo, O.
Seminar, 6th Annual AU CMB Undergraduate Research Symposium, April 13-14, 2011.
41. Computational insight into the specific inhibition of cyclophilins A and B
Acevedo, O.;* Sambasivarao, S.V.;
Book of Abstracts, 240th ACS National Meeting, Boston, MA August 22-26, 2010.
40. "On water" reactivity and solvent effects for Claisen rearrangements from QM/MM simulation
Acevedo, O.;* Armacost, K.
Book of Abstracts, 240th ACS National Meeting, Boston, MA August 22-26, 2010.
39. Predicting specific inhibition of cyclophilins A and B using docking, growing, and free energy perturbation calculations
Sambasivarao, S.V.;* Acevedo, O.
Book of Abstracts, 240th ACS National Meeting, Boston, MA August 22-26, 2010.
38. Connecting Resources, Connecting Others: Supercomputing in the Global Age
Acevedo, O.; Miller, P.;
Book of Abstracts, ACS Southeastern Regional Meeting (SERMACS), San Juan, Puerto Rico, October 21-24, 2009.
37. Solvent-dependent mechanisms for triazolinedione and singlet oxygen ene reactions from QM/MM simulations
Acevedo, O.
Book of Abstracts, 238th ACS National Meeting, Washington, D.C. August 16-20, 2009.
36. Computer Simulations of Steroid Transformation in Ketosteroid Isomerase.
Thigpen, C.;* Acevedo, O.
Seminar, 6th Annual AU CMB Undergraduate Research Symposium, April 6-7, 2009.
35. Advances in computational biochemistry: Role of water in catalytic antibodies.
Acevedo, O.
Seminar, University of South Alabama, Sept. 2008 (invited talk).
34. Advances in computational biochemistry: Role of water in catalytic antibodies.
Acevedo, O.
Seminar, University of Alabama at Birmingham, Sept. 2008 (invited talk).
33. Development and validation of OPLS-AA force field parameters for ionic liquid simulations.
Acevedo, O.;* Sambasivarao, S.V.
Book of Abstracts, 236th ACS National Meeting, Philadelphia, PA August 17-22, 2008.
32. Systematic development of OPLS-AA force field parameters for ionic liquid simulations.
Sambasivarao, S.V.;* Acevedo, O.
Book of Abstracts, 236th ACS National Meeting, Philadelphia, PA August 17-22, 2008.
31. Advances in potentials of mean force methodology for organic and biological simulations.
Acevedo, O.
2008 Southeastern Theoretical Chemistry Association symposium, The University of Alabama, Tuscaloosa, Alabama, May 2008 (invited talk).
30. Advances in potentials of mean force methodology for organic and biological simulations.
Acevedo, O.
Book of Abstracts, 235th ACS National Meeting, New Orleans, LA April 6-10, 2008. (invited poster).
Presented with the 2008 Hewlett-Packard Outstanding Junior Faculty Award (ACS award)
29. The chemistry of carbon sequestration.
Acevedo, O.
Focus the Nation symposium, Auburn University, Auburn, Alabama, January 2008 (invited talk).
28. Advances in QM/MM simulations for computational biochemistry.
Acevedo, O.
Seminar, Armstrong Atlantic State University, Savannah, Georgia, November 2007 (invited talk).
27. Advances in QM/MM simulations for computational biochemistry.
Acevedo, O.
Seminar, Auburn University - Department of Physics, Auburn, Alabama, September 2007 (invited talk).
26. Elucidation of the mechanism of hydrolysis by fatty acid hydrolase (FAAH) from QM/MM simulations.
Tubert-Brohman, I.;* Acevedo, O.; Jorgensen, W.L.
Fall Meeting of the Swiss Chemical Society, �cole Polytechnique F�d�rale de Lausanne, September 2007.
25. Medium effects on organic reactions featuring elimination mechanisms in pure and mixed solvents from QM/MM simulations.
Acevedo, O.
Book of Abstracts, 233th ACS National Meeting, Chicago, IL March 25-29, 2007.
24. Theoretical investigation of ionic liquids in the catalysis of the Diels-Alder reaction.
Acevedo, O.;* Jorgensen, W.L.; Evanseck, J.D.
Book of Abstracts, 231th ACS National Meeting, Atlanta, GA March 26-30, 2006.
23. Disconnection of maximum stereoelectronic effects from the transition structure.
Plumley, J.A.;* Evanseck, J.D.; Acevedo, O.
Book of Abstracts, 231th ACS National Meeting, Atlanta, GA March 26-30, 2006.
22. Computational organic chemistry: Elucidation of solvent effects from water to ionic liquids.
Acevedo, O.
Seminar, Auburn University, Auburn, Alabama, January 2006 (invited talk).
21. Computational organic chemistry: Elucidation of solvent effects from water to ionic liquids.
Acevedo, O.
Seminar, Grinnell College, Grinnell, Iowa, December 2005 (invited talk).
20. Kemp decarboxylation: The influence of hydrogen bonding.
Acevedo, O.
Seminar, Hobart and William Smith Colleges, Geneva, NY, December 2005 (invited talk).
19. Exploring solvent effects and mechanisms for organic reactions using computational methods.
Acevedo, O.;* Jorgensen, W.L.
Book of Abstracts, 230th ACS National Meeting, Washington, D.C. August 28-September 1, 2005.
18. The influence of inter- and intramolecular hydrogen bonding on Kemp decarboxylations from QM/MM simulations.
Acevedo, O.;* Jorgensen, W.L.
Jorgensen Symposium - 30 years in the trenches, Yale University, New Haven, CT, April, 2005.
17. Understanding how ionic liquids influence the Diels-Alder reaction.
Acevedo, O.
Seminar, University of Washington, Seattle, WA, December 2004, (invited talk).
16. Understanding how ionic liquids influence the Diels-Alder reaction.
Acevedo, O.
Seminar, Florida State University, Tallahassee, FL, November 2004, (invited talk).
15. Understanding how external influences impact reaction rates and selectivity.
Acevedo, O.;* Jorgensen, W.L.
Book of Abstracts, 228th ACS National Meeting, Philadelphia, PA, August 22-26, 2004.
14. Advances in QM/MM simulations for organic reactions in solution.
Jorgensen, W.L.;* Guimaraes, C.R.W.; Acevedo, O.
Book of Abstracts, 227th ACS National Meeting, Anaheim, CA, March 28-April 1, 2004.
13. Understanding how ionic liquids impact the Diels-Alder reaction: An ab initio, semiempirical and QM/MM approach.
Acevedo, O.; Evanseck, J.D.*
Book of Abstracts, 227th ACS National Meeting, Anaheim, CA, March 28-April 1, 2004.
12. Density functional investigation of ionic liquid cation-anion ratios in the catalysis of Diels-Alder reactions.
Acevedo, O.;* Evanseck, J.D.
Book of Abstracts, 226th ACS National Meeting, New York, NY, September 7-11, 2003.
11. Varying Lewis acidity in ionic liquids with new force field parameters.
Acevedo, O.;* Evanseck, J.D.
Book of Abstracts, 226th ACS National Meeting, New York, NY, September 7-11, 2003.
10. Density functional theory study of the influences of the N-1-butylpyridinium and chloroaluminate ratios upon the rates and endo/exo selectivity of the Diels-Alder reaction.
Waligorski, A.M.;* Acevedo, O.; Evanseck, J.D.
Book of Abstracts, 226th ACS National Meeting, New York, NY, September 7-11, 2003.
9. Principles of chemical reactivity in ionic liquids using quantum and molecular mechanics.
Acevedo, O.;* Evanseck, J.D.
Book of Abstracts, 225th ACS National Meeting, New Orleans, LA, March 22-27, 2003.
8. A density-functional exploration of copper(II) aqua ion and chiral bis(oxazoline) copper(II) Diels-Alder transition structures.
Dechancie, J.;* Acevedo, O.; Evanseck, J.D.
Book of Abstracts, 225th ACS National Meeting, New Orleans, LA, March 22-27, 2003.
7. Perturbing the Diels-Alder transition structure.
Acevedo, O.;* Evanseck, J.D.
Book of Abstracts, 224th ACS National Meeting, Boston, MA, August 18-22, 2002.
6. Theoretical assessment on how ionic liquids influence chemical reactivity and stereoselectivity of organic reactions.
Evanseck, J.D.;* Acevedo, O.
Book of Abstracts, 224th ACS National Meeting, Boston, MA, August 18-22, 2002.
5. Transition structures and ionic cages in ionic liquids.
Acevedo, O.;* Evanseck, J.D.
Book of Abstracts, 224th ACS National Meeting, Boston, MA, August 18-22, 2002.
4. Models of bis(oxazoline)-Cu(II) complexes upon Diels-Alder reactions.
Dechancie, J.;* Acevedo, O.; Evanseck, J.D.
Book of Abstracts, 224th ACS National Meeting, Boston, MA, August 18-22, 2002.
3. Novel transition structure interactions in boron Lewis acid catalyzed Diels-Alder reactions.
Acevedo, O.;* Kong, S.; Evanseck, J.D.
Book of Abstracts, 223th ACS National Meeting, Orlando, FL, April 7-11 2002.
2. Molecular details of how ionic liquids influence chemical reactivity and stereoselectivity.
Acevedo, O.;* Evanseck, J.D.
Book of Abstracts, 223th ACS National Meeting, Orlando, FL, April 7-11 2002.
1. Theoretical assessment of catalytic and stereoselective influence of bis(oxazoline)-Cu(II) complexes upon Diels-Alder reactions.
Dechancie, J.;* Acevedo, O.; Evanseck, J.D.
Book of Abstracts, 223th ACS National Meeting, Orlando, FL, April 7-11 2002.
