Orlando Acevedo - Publications

Affiliations: 
Auburn University, Auburn, AL, United States 
Area:
Biochemistry
Website:
http://www.auburn.edu/academic/cosam/faculty/chemistry/acevedo/research1/acevedo_group/people.html

53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Thakur A, Somai S, Yue K, Ippolito N, Pagan D, Xiong J, Ellis HR, Acevedo O. Substrate-Dependent Mobile Loop Conformational Changes in Alkanesulfonate Monooxygenase from Accelerated Molecular Dynamics. Biochemistry. PMID 32881481 DOI: 10.1021/Acs.Biochem.0C00633  0.39
2020 Velez C, Doherty B, Acevedo O. Accurate Diels-Alder Energies and Selectivity in Ionic Liquids Using the OPLS-VSIL Force Field. International Journal of Molecular Sciences. 21. PMID 32054023 DOI: 10.3390/Ijms21041190  0.507
2019 Thakur A, Hevel JM, Acevedo O. Examining Product Specificity in Protein Arginine Methyltransferase 7 (PRMT7) using QM/MM Simulations. Journal of Chemical Information and Modeling. PMID 31033288 DOI: 10.1021/Acs.Jcim.9B00137  0.391
2018 Doherty B, Acevedo O. OPLS Force Field for Choline Chloride-Based Deep Eutectic Solvents. The Journal of Physical Chemistry. B. PMID 30125108 DOI: 10.1021/Acs.Jpcb.8B06647  0.428
2018 Nath C, Badavath VN, Thakur A, Ucar G, Acevedo O, Mohd Siddique MU, Jayaprakash V. Curcumin-based pyrazoline analogues as selective inhibitors of human monoamine oxidase A. Medchemcomm. 9: 1164-1171. PMID 30109004 DOI: 10.1039/C8Md00196K  0.342
2018 Doherty B, Zhong X, Acevedo O. A Virtual Site OPLS Force Field for Imidazolium-Based Ionic Liquids. The Journal of Physical Chemistry. B. PMID 29473749 DOI: 10.1021/Acs.Jpcb.7B11996  0.428
2018 Caceres T, Thakur A, Price OM, Ippolito N, Li J, Qu J, Acevedo O, Hevel JM. Phe 71 in type III Trypanosomal protein arginine methyltransferase 7 (TbPRMT7) restricts the enzyme to monomethylation. Biochemistry. PMID 29378138 DOI: 10.1021/Acs.Biochem.7B01265  0.349
2016 Allen CR, Ghebreab R, Doherty B, Li B, Acevedo O. Examining Ionic Liquid Effects on Mononuclear Rearrangement of Heterocycles using QM/MM Simulations. The Journal of Physical Chemistry. B. PMID 27690447 DOI: 10.1021/Acs.Jpcb.6B07205  0.515
2016 Gathiaka S, Boykin B, Cáceres T, Hevel JM, Acevedo O. Understanding protein arginine methyltransferase 1 (PRMT1) product specificity from molecular dynamics. Bioorganic & Medicinal Chemistry. PMID 27545444 DOI: 10.1016/J.Bmc.2016.08.009  0.321
2015 McCann BW, McFarland S, Acevedo O. Benchmarking Continuum Solvent Models for Keto-Enol Tautomerizations. The Journal of Physical Chemistry. A. 119: 8724-33. PMID 26202336 DOI: 10.1021/Acs.Jpca.5B04116  0.41
2015 Allen C, McCann BW, Acevedo O. Ionic liquid effects on nucleophilic aromatic substitution reactions from QM/MM simulations. The Journal of Physical Chemistry. B. 119: 743-52. PMID 25011571 DOI: 10.1021/Jp504967R  0.49
2014 Acevedo O, Jorgensen WL. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions. Wiley Interdisciplinary Reviews. Computational Molecular Science. 4: 422-435. PMID 25431625 DOI: 10.1002/Wcms.1180  0.607
2014 Acevedo O. Simulating chemical reactions in ionic liquids using QM/MM methodology. The Journal of Physical Chemistry. A. 118: 11653-66. PMID 25329366 DOI: 10.1021/Jp507967Z  0.485
2014 Armacost K, Musila J, Gathiaka S, Ellis HR, Acevedo O. Exploring the catalytic mechanism of alkanesulfonate monooxygenase using molecular dynamics. Biochemistry. 53: 3308-17. PMID 24798142 DOI: 10.1021/Bi5002085  0.411
2014 Gui S, Gathiaka S, Li J, Qu J, Acevedo O, Hevel JM. A remodeled protein arginine methyltransferase 1 (PRMT1) generates symmetric dimethylarginine. The Journal of Biological Chemistry. 289: 9320-7. PMID 24478314 DOI: 10.1074/Jbc.M113.535278  0.34
2014 Armacost K, Acevedo O. Exploring the aldol reaction using catalytic antibodies and "on water" organocatalysts from QM/MM calculations. Journal of the American Chemical Society. 136: 147-56. PMID 24344918 DOI: 10.1021/Ja405614P  0.43
2013 McCann BW, Acevedo O. Pairwise Alternatives to Ewald Summation for Calculating Long-Range Electrostatics in Ionic Liquids. Journal of Chemical Theory and Computation. 9: 944-50. PMID 26588737 DOI: 10.1021/Ct300961E  0.388
2013 Allen C, Sambasivarao SV, Acevedo O. An ionic liquid dependent mechanism for base catalyzed β-elimination reactions from QM/MM simulations. Journal of the American Chemical Society. 135: 1065-72. PMID 23273322 DOI: 10.1021/Ja3098614  0.766
2012 McCann BW, Song H, Kocer HB, Cerkez I, Acevedo O, Worley SD. Inter- and intramolecular mechanisms for chlorine rearrangements in trimethyl-substituted N-chlorohydantoins. The Journal of Physical Chemistry. A. 116: 7245-52. PMID 22671993 DOI: 10.1021/Jp304610K  0.424
2012 Acevedo O, Ambrose Z, Flaherty PT, Aamer H, Jain P, Sambasivarao SV. Identification of HIV inhibitors guided by free energy perturbation calculations. Current Pharmaceutical Design. 18: 1199-216. PMID 22316150 DOI: 10.2174/138920012799362828  0.712
2012 Barr WJ, Yi T, Aga D, Acevedo O, Harper WF. Using electronic theory to identify metabolites present in 17α-ethinylestradiol biotransformation pathways. Environmental Science & Technology. 46: 760-8. PMID 22129464 DOI: 10.1021/Es201774R  0.334
2011 Vilseck JZ, Sambasivarao SV, Acevedo O. Optimal scaling factors for CM1 and CM3 atomic charges in RM1-based aqueous simulations. Journal of Computational Chemistry. 32: 2836-42. PMID 21732390 DOI: 10.1002/Jcc.21863  0.748
2011 Sambasivarao SV, Acevedo O. Computational insight into small molecule inhibition of cyclophilins. Journal of Chemical Information and Modeling. 51: 475-82. PMID 21194235 DOI: 10.1021/Ci1004114  0.731
2010 Acevedo O, Jorgensen WL. Exploring solvent effects upon the Menshutkin reaction using a polarizable force field. The Journal of Physical Chemistry. B. 114: 8425-30. PMID 20527873 DOI: 10.1021/Jp100765V  0.608
2010 Acevedo O, Armacost K. Claisen rearrangements: insight into solvent effects and "on water" reactivity from QM/MM simulations. Journal of the American Chemical Society. 132: 1966-75. PMID 20088521 DOI: 10.1021/Ja908680C  0.465
2010 Acevedo O, Jorgensen WL. Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Accounts of Chemical Research. 43: 142-51. PMID 19728702 DOI: 10.1021/Ar900171C  0.629
2010 Kocer HB, Worley SD, Broughton RM, Acevedo O, Huang TS. Effect of phenyl derivatization on the stabilities of antimicrobial N -chlorohydantoin derivatives Industrial and Engineering Chemistry Research. 49: 11188-11194. DOI: 10.1021/Ie101258S  0.306
2010 Vilseck JZ, Acevedo O. Computing free-energy profiles using multidimensional potentials of mean force and polynomial quadrature methods Annual Reports in Computational Chemistry. 6: 37-49. DOI: 10.1016/S1574-1400(10)06003-2  0.484
2009 Sambasivarao SV, Acevedo O. Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids. Journal of Chemical Theory and Computation. 5: 1038-50. PMID 26609613 DOI: 10.1021/Ct900009A  0.756
2009 Acevedo O. Role of water in the multifaceted catalytic antibody 4B2 for allylic isomerization and Kemp elimination reactions. The Journal of Physical Chemistry. B. 113: 15372-81. PMID 19860435 DOI: 10.1021/Jp9069114  0.402
2009 Acevedo O. Determination of local effects for chloroaluminate ionic liquids on Diels-Alder reactions. Journal of Molecular Graphics & Modelling. 28: 95-101. PMID 19419891 DOI: 10.1016/J.Jmgm.2009.04.003  0.489
2009 Sheppard AN, Acevedo O. Multidimensional exploration of valley-ridge inflection points on potential-energy surfaces. Journal of the American Chemical Society. 131: 2530-40. PMID 19193015 DOI: 10.1021/Ja803879K  0.438
2008 Acevedo O, Squillacote ME. A new solvent-dependent mechanism for a triazolinedione ene reaction. The Journal of Organic Chemistry. 73: 912-22. PMID 18161986 DOI: 10.1021/Jo7022153  0.518
2007 Akdag A, Worley SD, Acevedo O, McKee ML. Mechanism of 5,5-Dimethylhydantoin Chlorination:  Monochlorination through a Dichloro Intermediate. Journal of Chemical Theory and Computation. 3: 2282-9. PMID 26636219 DOI: 10.1021/Ct7001804  0.416
2007 Acevedo O, Jorgensen WL. Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology. Journal of Chemical Theory and Computation. 3: 1412-9. PMID 26633213 DOI: 10.1021/Ct700078B  0.605
2007 Gunaydin H, Acevedo O, Jorgensen WL, Houk KN. Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution. Journal of Chemical Theory and Computation. 3: 1028-35. PMID 26627421 DOI: 10.1021/Ct050318N  0.655
2007 Acevedo O, Jorgensen WL, Evanseck JD. Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations. Journal of Chemical Theory and Computation. 3: 132-8. PMID 26627159 DOI: 10.1021/Ct6002753  0.741
2007 Acevedo O, Jorgensen WL. Understanding rate accelerations for Diels-Alder reactions in solution using enhanced QM/MM methodology Journal of Chemical Theory and Computation. 3: 1412-1419. DOI: 10.1021/ct700078b  0.454
2007 Acevedo O, Jorgensen WL, Evanseck JD. Elucidation of rate variations for a diels-alder reaction in ionic liquids from QM/MM simulations Journal of Chemical Theory and Computation. 3: 132-138. DOI: 10.1021/ct6002753  0.696
2007 Gunaydin H, Acevedo O, Jorgensen WL, Houk KN. Computation of accurate activation barriers for methyl-transfer reactions of sulfonium and ammonium salts in aqueous solution Journal of Chemical Theory and Computation. 3: 1028-1035. DOI: 10.1021/ct050318n  0.458
2006 Tubert-Brohman I, Acevedo O, Jorgensen WL. Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations. Journal of the American Chemical Society. 128: 16904-13. PMID 17177441 DOI: 10.1021/Ja065863S  0.756
2006 Acevedo O, Jorgensen WL. Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations. The Journal of Organic Chemistry. 71: 4896-902. PMID 16776519 DOI: 10.1021/Jo060533B  0.583
2006 Acevedo O, Jorgensen WL. Cope elimination: elucidation of solvent effects from QM/MM simulations. Journal of the American Chemical Society. 128: 6141-6. PMID 16669683 DOI: 10.1021/Ja057523X  0.621
2006 Acevedo O, Jorgensen WL. Chapter 14 Solvent Effects on Organic Reactions from QM/MM Simulations Annual Reports in Computational Chemistry. 2: 263-278. DOI: 10.1016/S1574-1400(06)02014-7  0.609
2005 Acevedo O, Jorgensen WL. Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations. Journal of the American Chemical Society. 127: 8829-34. PMID 15954791 DOI: 10.1021/Ja051793Y  0.628
2005 Boger DL, Miyauchi H, Du W, Hardouin C, Fecik RA, Cheng H, Hwang I, Hedrick MP, Leung D, Acevedo O, Guimarães CR, Jorgensen WL, Cravatt BF. Discovery of a potent, selective, and efficacious class of reversible alpha-ketoheterocycle inhibitors of fatty acid amide hydrolase effective as analgesics. Journal of Medicinal Chemistry. 48: 1849-56. PMID 15771430 DOI: 10.1021/Jm049614V  0.443
2004 Acevedo O, Jorgensen WL. Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations. Organic Letters. 6: 2881-4. PMID 15330638 DOI: 10.1021/Ol049121K  0.602
2004 DeChancie J, Acevedo O, Evanseck JD. 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). Journal of the American Chemical Society. 126: 6043-7. PMID 15137769 DOI: 10.1021/Ja037702J  0.64
2004 Loccisano AE, Acevedo O, DeChancie J, Schulze BG, Evanseck JD. Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulations. Journal of Molecular Graphics & Modelling. 22: 369-76. PMID 15099833 DOI: 10.1016/J.Jmgm.2003.12.004  0.627
2004 Acevedo O, Evanseck JD. Transition States and Transition Structures Cheminform. 35. DOI: 10.1002/chin.200427286  0.549
2003 Acevedo O, Evanseck JD. The effect of solvent on a Lewis acid catalyzed Diels-Alder reaction, using computed and experimental kinetic isotope effects. Organic Letters. 5: 649-52. PMID 12605481 DOI: 10.1021/Ol027408G  0.68
2003 Acevedo O, Evanseck JD. 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 Acs Symposium Series. 856: 174-190.  0.665
2002 Dick TJ, Acevedo O, Dalal P, Madura JD, Evanseck JD, Mathews JP. Molecular Basis for Carbon Dioxide Sequestration in Coal Acs Division of Fuel Chemistry, Preprints. 47: 14-16.  0.668
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