Acevedo Research Group at Auburn University

Publications

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, (in press).

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.
2010, (submitted).

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. Download.

Presentations

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, École Polytechnique Fédérale 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.