Publications

Book Chapters

99. Fishman Jacob, T.; Singh, V.; Dixit, M.; Ginsburg-Shmuel, T.; Fonseca, B.; Pintor, J.; Youdim, M. B. H.; Major, D. T.; Weinreb, O.; Fischer, B. A Highly Promising Drug Candidate for the Treatment of Glaucoma Based on a P2Y6-Receptor Agonist. Purinergic Signal. Accepted. 2018.

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98. Ansbacher, T.; Freud, Y.; Major, D. T. Slow Starter Enzymes: Role of Active Site Architecture in the Catalytic Control in the Biosynthesis of Taxadiene by Taxadiene Synthase. Biochemistry Accepted 2018.

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97. Kim, U. -H.; Jun, D. W.; Park, K. -J.; Zhang, Q.; Kaghazchi, P.; Aurbach, D.; Major, D. T.; Goobes, G.; Dixit, M.; Leifer, N.; Wang, C. M.; Yan, P.; Ahn, D.; Kim, K. -H.; Yoon, C. S.; Sun, Y. -K. Pushing the limit of layered transition metal oxide cathodes for high-energy density rechargeable Li ion batteries. Energy Environ. Sci. 201811, 1271-1279.

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96. Das, S.; Nam, K.; Major, D. T. Rapid Convergence of Energy and Free Energy Profiles with QM Size in QM/MM Simulations of Proton Transfer in DNA. J. Chem. Theory Comp. 2018, 14, 1695-1705.

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95. Bauer, P.; Barrozo, A. H.; Amrein, B. A.; Purg, M.; Esguerra, M.; Wilson, P. B.; Major, D. T.; Åqvist, J.; Kamerlin, S. C. L. Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations. SoftwareX. Accepted 2018.

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94. Dixit, M.; Weitman, M.; Gao, J.; Major, D. T. Comment on “Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity”. ACS Catal. 2018, 8, 1371-1375. https://pubs.acs.org/doi/abs/10.1021/acscatal.7b02823

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93. Levy, N.; Shpilman, J. S.; Honig, H.; Major, D. T.; Elbaz, L. Surprising Substituent Effect in Corroles on the Electrochemical Activation of Oxygen Reduction. Chem. Comm. 201753, 12942-12945. http://pubs.rsc.org/en/content/articlelanding/2017/cc/c7cc06920k#!divAbstract

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92. Dixit, M.; Markovsky, B.; Schipper, F.; Aurbach, D.; Major, D. T. The Origin of Structural Degradation During Cycling and Low Thermal Stability of Ni-rich Layered Transition Metal-Based Electrode Materials. J. Phys. Chem. C. 2017, 121, 22628-22636. https://pubs.acs.org/doi/abs/10.1021/acs.jpcc.7b06122

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91. Freud, Y.; Ansbacher, T.; Major, D. T. Catalytic control in the facile proton transfer in taxadiene synthase. ACS Catal. 2017, 7, 7653-7657. https://pubs.acs.org/doi/abs/10.1021/acscatal.7b02824 

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90. Rozental, E.; Altus, E.; Major, D. T.; Hoz, S. Shaping Polyyne Rods by an Electric Field. ChemistryOpen 2017, 6, 733-738. http://onlinelibrary.wiley.com/doi/10.1002/open.201700132/abstract

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89. Schipper, F.; Bouzaglo, H.; Dixit, M.; Erickson, E. M.; Weigel, T.; Talianker, M.; Grinblat, J.; Burstein, L.; Schmidt, M.; Lampert, J.; Erk, C.; Markovsky, B.; Major, D. T.; Aurbach, D. From Surface ZrO₂ Coating to Bulk Zr Doping by High Temperature Annealing of Nickel Rich Materials and their Enhanced Electrochemical Performance in Lithium Ion Batteries. Adv. Ener. Mater. 2017, 1701682. https://onlinelibrary.wiley.com/doi/abs/10.1002/aenm.201701682

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88. Major, D. T. Electrostatic Control of Chemistry in Terpene Cyclases. ACS Catal20177, 5461-5465.

http://pubs.acs.org/doi/abs/10.1021/acscatal.7b01328

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87. Mhashal, A.; Vardi-Kilshtain, A.; Kohen, A.; Major, D. T. The Role of the M20 Loop in the Hydride Transfer in E. Coli Dihydrofolate Reductase. J. Biol. Chem. 2017, 292, 14229-14239. 

http://www.jbc.org/content/early/2017/06/15/jbc.M117.777136

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86. Schipper, F.; Nayak, P. K.; Erickson, E. M.; Amalraj, S. F.; Srur-Lavi, O.; Penki, T. R.; Talianker, M.; Grinblat, J.; Sclar, H.; Breuer, O.; Julien, C. M.; Munichandraiah, N.; Kovacheva, D.; Dixit, M.; Major, D. T.; Markovsky, B.; Aurbach, D. Study of cathode materials for Lithium-ion batteries: Recent progress and new challenges. Inorganics 2017, 5, 32. http://www.mdpi.com/2304-6740/5/2/32

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85. Dixit, M.; Markovsky, B.; Aurbach, D.; Major, D. T. Unraveling the Effects of Al Doping on the Electrochemical Properties of LiNi0.5Co0.2Mn0.3O2 Using First Principles. J. Electrochem. Soc. 2017, 164, A6359-6365. http://jes.ecsdl.org/content/164/1/A6359/F4.expansion.html 

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84. Dixit, M.; Weitman, M.; Gao, J.; Major, D. T. Chemical Control in the Battle Against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase. ACS Catal. 2017, 7, 812-818. http://pubs.acs.org/doi/abs/10.1021/acscatal.6b02584 

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83. Majhi, K.; Singh, V.; Rietwyk, K. J.; Keller, D. A.; Barad, H. N.; Ginsburg, A.; Yan, Z.; Anderson, A. Y.; Zaban, A.; Major, D. T. Electron-Hybridization Induced Enhancement of Photo Activity in Indium-Doped Co3O4. J. Phys. Chem. C 2016, 120, 28983-28991. http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.6b10673 

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82. de la Llave, E.; Talaie, E.; Levi, E.; Kumar, P.; Dixit, M.; Rao, P. T.; Hartmann, P.; Chesneau, F. F.; Major, D. T.; Greenstein, M.; Aurbach, D.; Nazar, L. F. Improving Energy Density and Structural Stability of Manganese Oxide Cathodes for Na-ion Batteries by Structural Lithium Substitution. Chem. Mater. 2016, 28, 9064-9076. http://pubs.acs.org/doi/abs/10.1021/acs.chemmater.6b04078 

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81. Schipper, F.; Dixit, M.; Kovacheva, D.; Talianker, M.; Haik, O.; Grinblat, Y.; Erikson, E. M.; Ghanty, C.; Major, D. T.; Markovsky, B.; Aurbach, D. Stabilizing Nickel-Rich Layered Cathode Materials by a High-Charge Cation Doping Strategy: Zirconium-Doped LiNi0.6Co0.2Mn0.2O2. J. Mater. Chem. A 2016, 4, 16073-16084. http://pubs.rsc.org/en/Content/ArticleLanding/2016/TA/c6ta06740a#!divAbstract 

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80. Salama, M.; Shtrenberg, I.; Gizbar, H.; Nitoker, N.; Kosa, M.; Adamsky, K. K.; Ari, M.; Shimon, L. J. W.; Gottilieb, H. E.; Major, D. T.; Gofer, Y.; Aurbach, D. Unique Behavior of dimethoxyethane (DME)/Mg(N(SO2CF3)2)2 Solutions. J. Phys. Chem. C 2016, 120, 19586-19594. http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.6b07733 

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79. Pshetitsky, Y.; Eitan, R.; Verner, G.; Kohen, A.; Major, D. T. Improved Sugar Puckering Profiles for Nicotinamide Ribonucleoside for Hybrid QM/MM Simulations. J. Chem. Theory Comp. 2016, 12, 5179-5189. http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00401 

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78. Das, S.; Dixit, M.; Major, D. T. First Principles Model Calculations of the Biosynthetic Pathway in Selinadiene Synthase. Bioorg. Med. Chem. 2016, 24, 4867-4870. http://www.sciencedirect.com/science/article/pii/S096808961630493X 

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77. Dixit, M.; Das, S.; Mhashal, A. R.; Eitan, R.; Major, D. T. Practical aspects of multiscale classical and quantum simulations of enzyme reactions. Methods in Enzymology 2016, 577, 251-286 (Invited review). http://www.sciencedirect.com/science/article/pii/S0076687916300817 

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76. Guo, Q.; Gakhar, L.; Wickersham, K.; Francis, K.; Vardi-Kilshtain, A.; Major, D. T.; Cheatum, C.; Kohen, A. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii. Biochemistry 2016, 55, 2760-2771. http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00181 

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75. Levi Hevroni, B.; Major, D. T.; Dixit, M.; Mhashal, A. R.; Das, S.; Fischer, B. Nucleoside-2’,3’/3’,5’-Bis(thio)phosphate are Zn(II)/Cu(II)-Chelators Capable of Disassembly of Amyloid Beta(1-42)–Zn(II)/Cu(II) Aggregates via Zn(II)/Cu(II)-chelation. Org. Biomol. Chem. 2016, 14, 4640-4653. http://pubs.rsc.org/en/Content/ArticleLanding/2016/OB/C6OB00613B 

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74. Dutta, P.; Pramanick, S.; Singh, V.; Major, D. T.; Das, D.; Chatterjee, S. Anomalous magnetotransport behavior in Fe doped MnNiGe alloys. Phys. Rev. B 2016, 93, 134408. http://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.134408 

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73. Singh. V.; Major, D. T. Electronic Structure and Bonding in Co-based Single and Mixed Valence Oxides: A Quantum Chemical Perspective. Inorg. Chem. 2016, 55, 3307-3315. http://pubs.acs.org/doi/abs/10.1021/acs.inorgchem.5b02426 

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72. Dixit, M.; Major, D. T.; Pal, S. Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study. Chem. Phys. Lett. 2016, 651, 178-182. http://www.sciencedirect.com/science/article/pii/S0009261416301397 

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71. Kosa, M.; Aurbach, D.; Major, D. T. First-principles evaluation of the inherent stabilities of pure LixMPO4 (M=Mn, Fe, Co,) and Mixed Binary LixFeyM'1-yPO4 (M'=Mn, Co) Olivine Phosphates. Mater. Chem. Phys. 2016, 174, 54-58. http://www.sciencedirect.com/science/article/pii/S0254058416300694 

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70. Singh, V.; Dixit, M.; Kosa, M.; Major, D. T.; Levi, E.; Aurbach, D. Is it true that the normal valence-length correlation is irrelevant for metal-metal bonds? Chem. Eur. J. 2016, 22, 5269-5276. http://onlinelibrary.wiley.com/doi/10.1002/chem.201504161/full 

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69. Dixit, M.; Kosa, M.; Srur Lavi, O.; Markovsky, B.; Aurbach, D.; Major, D. T. Thermodynamic and Kinetic Studies of LiNi0.5Co0.2Mn0.3O2 as a Positive Electrode Material for Li-ion Batteries using First Principles. Phys. Chem. Chem. Phys. 2016, 18, 6799-6812. http://pubs.rsc.org/en/Content/ArticleLanding/2016/CP/c5cp07128c#!divAbstract 

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68. Kosa, M.; Barad, H.; Singh, V.; Keller, D.; Shimanovich, K.; Rühle, S.; Anderson, A.; Zaban, A.; Major, D. T. A Combined Computational and Experimental Investigation of Mg Doped α-Fe2O3. Phys. Chem. Chem. Phys. 2016, 18, 781-791. http://pubs.rsc.org/en/Content/ArticleLanding/2016/CP/c5cp05987a#!divAbstract 

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67. Singh, V.; Gershinsky, Y.; Kosa, M.; Dixit, M.; Zitoun, D.; Major, D. T. Magnetism in olivine-type LiCo1-xFexPO4 cathode materials: Bridging theory and experiment. Phys. Chem. Chem. Phys. 2015, 17, 31202 - 31215. http://pubs.rsc.org/en/Content/ArticleLanding/2015/CP/c5cp04871k#!divAbstract 

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66. Azran, S.; Danino, O.; Förster, D.; Kenigsberg, S.; Reiser, R.; Dixit, M.; Singh, V.; Major, D. T.; Fischer, B. Identification of Highly Promising Anti-Oxidants / Neuroprotectants Based on Nucleoside 5’-Phosphorothioate Scaffold. Synthesis, Activity, and Mechanisms of Action. J. Med. Chem. 2015, 58, 8427-8443. http://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.5b00575 

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65. Levy, N.; Mahammed, A.; Kosa, M.; Major, D. T.; Gross, Z.; Elbaz, L. Metal-corroles as non-precious metal catalysts for oxygen reduction. Angew. Chem. Int. Ed. 2015, 54, 14080-14084. http://onlinelibrary.wiley.com/doi/10.1002/anie.201505236/abstract 

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64. Eizig, Z.; Major, D. T.; Kasdan, H. L.; Afrimzon, E.; Zurgil, N.; Deutsch, M. Analysis of the spectroscopic Aspects of the Cationic Dye Basic Orange 21. J. Phys. Chem. A 2015, 119, 9794-9804. http://pubs.acs.org/doi/10.1021/acs.jpca.5b07339 

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63. Dixit, M.; Engel, H.; Eitan, R.; Aurbach, D.; Levi, M.; Kosa, M.; Major, D. T. Classical and Quantum Modeling of Li and Na Diffusion in FePO4. J. Phys. Chem. C 2015, 119, 15801-15809. http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.5b00405

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62. Sayer, A. H.; Blum, E.; Major, D. T.; Vardi-Kilshtain, A.; Levi-Hevroni, B.; Fischer, B. Adenosine/Guanosine-3',5’-Bis-Phosphate as Biocompatible and Selective Zn2+-Ion Chelators. Characterization and Comparison with Adenosine/Guanosine-5’-Di-Phosphate. Dalton Trans. 2015, 44, 7305-7317. http://pubs.rsc.org/-/content/articlelanding/2015/dt/c5dt00080g#!divAbstract 

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61. Vardi-Kilshtain, A.; Nitoker, N.; Major, D. T. Nuclear Quantum Effects and Kinetic Isotope Effects in Enzyme Reactions. Arch. Biochem. Biophys. Invited Review. 2015 , 582, 18-27. http://www.sciencedirect.com/science/article/pii/S0003986115001101 

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60. Aurbach, D.; Srur-Lavi, O.; Ghanty, C.; Dixit, M.; Haik, O.; Talianker, M.; Grinblat, J.; Leifer, N.; Lavi, R.; Major, D. T.; Goobes, G.; Zinigrad, E.; Erickson, E.; Kosa, M.; Markovsky, B.; Lampert, J.; Volkov, A.; Shin, J.-Y.; Garsuch, A. Studies of Aluminum-Doped LiNi0.5Co0.2Mn0.3O2: Electrochemical Behavior, Aging, Structural Transformations, and Thermal Characteristics. J. Electrochem. Soc. 2015, 162, A1014-A1027. http://jes.ecsdl.org/content/162/6/A1014.abstract 

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59. Pariente-Cohen, N.; Weitman, M.; Major, D. T.; Gottlieb, H.; Hoz, S.; Nudelman, A. Acylation or Phosphorylation of Hydroxyurea Unexpectedly Take Place on N rather than on O, Leading to the Formation of Amides Instead of the Expected Esters. RCS Advances 2015, 5, 24038-24043. http://pubs.rsc.org/en/Content/ArticleHtml/2015/RA/c5ra01016k 

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58. Engel, H.; Eitan, R.; Azuri, A.; Major, D. T. Nuclear Quantum Effects in Chemical Reactions via Higher-Order Path-Integral Calculations. Chem. Phys. 2015, 450-451, 95-101. http://www.sciencedirect.com/science/article/pii/S0301010415000038 

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57. Nitoker, N.; Major, D. T. Understanding the Reaction Mechanism and Intermediate Stabilization in Serine Racemase Using Multiscale Quantum-Classical Simulations. Biochemistry 2015, 54, 516-527. http://pubs.acs.org/doi/abs/10.1021/bi500984m 

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56. Singh, V.; Kosa, M.; Majhi, K.; Major, D. T. Putting DFT to the test: A first principles study of electronic, magnetic and optical properties of Co3O4. J. Chem. Theory Comp. 2015, 11, 64-72. http://pubs.acs.org/doi/abs/10.1021/ct500770m 

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55. Doron, D.; Stojkovic, V.; Gakhar, L.; Kohen, A.; Major, D. T. Free Energy Simulations of Active-Site Mutants of Dihydrofolate Reductase. J. Phys. Chem. B 2015, 119, 906-916(Invited paper, Jorgensen Festschrift). http://pubs.acs.org/doi/abs/10.1021/jp5059963 

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54. Kosa, M.; Major, D. T. Structural Trends in Hybrid Perovskites, [Me2NH2] M [HCOO]3 (M=Mn, Fe, Co, Ni, Zn). Computational Assessment Based on Bader Charge Analysis. Crystal Eng. Comm. 2015, 17, 295-298. http://pubs.rsc.org/en/content/articlepdf/2014/ce/c4ce01387e 

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53. Toledano, T.; Sazan, H.; Barnea-Nehoshtan, L.; Mukhopadhyay, S.; Alon, H.; Lerman, K.; Bendikov, T.; Major, D. T.; Sukenik, C.; Vilan, A.; Cahen, D. Odd-Even Effect in Molecular Electronic Transport via an Aromatic Ring. Langmuir 2014, 30, 13596-13605. http://pubs.acs.org/doi/abs/10.1021/la503536f 

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52. Carvalho, A. T. P.; Barrozo, A.; Doron, D.; Vardi Kilshtain, A.; Major, D. T.; Kamerlin, S. C. L. Challenges in Computational Studies of Enzyme Structure, Function and Dynamics. J. Mol. Graph. Mod. 2014, 54, 62-79 (Invited paper). http://www.sciencedirect.com/science/article/pii/S1093326314001570

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51. Yeung, H. H.-M.; Kosa, M.; Griffin, J. M.; Grey, C. P.; Major, D. T.; Cheetham, A. K. Topotactic elimination of water across a C-C ligand bond in a dense 3-D metal-organic framework. Chem. Comm. 2014, 50, 13292-13295. http://pubs.rsc.org/en/content/articlehtml/2014/cc/c4cc06136e 

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50. Kovaliov, M.; Weitman, M.; Major, D. T.; Fischer, B. Phenyl-Imidazolo-Cytidine Analogues: Structure-Photophysical Activity Relationship and Ability to Detect Single DNA Mismatch. J. Org. Chem. 2014, 79, 7051-7062. http://pubs.acs.org/doi/abs/10.1021/jo5011944 

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49. Gat, Y.; Vardi-Kilshtain, A.; Grossman, I.; Major, D. T.; Fass, D. Enzyme structure captures four cysteines aligned for disulfide relay. Protein Sci. 2014, 23, 1102-1112. https://dx.doi.org/10.1002%2Fpro.2496 

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48. Roston, D.; Kohen, A.; Doron, D.; Major, D. T. Simulations of Remote Mutants of Dihydrofolate Reductase Reveal the Nature of a Network of Residues Coupled to Hydride Transfer. J. Comput. Chem. 2014, 35, 1411-1417. http://onlinelibrary.wiley.com/doi/10.1002/jcc.23629/abstract 

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47. Doron, D.; Kohen, A.; Nam, K.; Major, D. T. How accurate are transition states from simulations of enzymatic reactions? J. Chem. Theory Comput. 2014, 10, 1863-1871. http://pubs.acs.org/doi/abs/10.1021/ct5000742 

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46. Major, D. T.; Freud, Y.; Weitman, M. Catalytic Control in Terpenoid Cyclases: Multiscale Modeling of Thermodynamic, Kinetic, and Dynamic Effects. Curr. Opin. Chem. Biol. 2014, 21, 25-33 (Invited paper). http://www.sciencedirect.com/science/article/pii/S1367593114000349 

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45. Doron, D.; Weitman, M.; Vardi-Kilshtain, A.; Azuri, A.; Engel, H.; Major, D. T. Multi-scale quantum-classical simulations of enzymes. Isr. J. Chem. 2014, 54, 1108-1117 (Invited paper). http://onlinelibrary.wiley.com/doi/10.1002/ijch.201400026/abstract 

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44. Zilbershtein-Shklanovsky , L.; Weitman, M.; Major, D. T.; Fischer, B. Rules for the design of highly fluorescent nucleoside probes: 8-(substituted cinnamyl)-adenosine analogues. J. Org. Chem. 2013, 78, 11999-12008. http://pubs.acs.org/doi/abs/10.1021/jo402050x 

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43. Osnis, A.; Kosa, M.; Aurbach, D.; Major, D. T. Systematic first-principles investigation of mixed transition metal olivine phosphates LiM1-yM’yPO4 (M/M’=Mn, Fe, Co) as cathode materials. J. Phys. Chem. C 2013, 117, 17919–17926. http://pubs.acs.org/doi/abs/10.1021/jp402755r 

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42. Buhbut, S.; Clifford, J. N.; Kosa, M.; Anderson, A.; Shalom, M.; Major, D. T.; Palomares, E.; Zaban, A. Controlling dye aggregation, injection energetics, and catalytic recombination in organic sensitizer based dye cells using a single electrolyte additive. Energy Environ. Sci. 2013, 6, 3046-3053. http://pubs.rsc.org/en/content/articlepdf/2013/ee/c3ee41486h 

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41. Vardi-Kilshtain, A.; Doron, D.; Major, D. T. Quantum and classical simulations of orotidine monophosphate decarboxylase: Support for a direct decarboxylation mechanism. Biochemistry 2013, 52, 4382-4390. http://pubs.acs.org/doi/abs/10.1021/bi400190v 

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40. Pour, N.; Gofer, Y.; Major, D. T.; Keinan-Adamsky, K.; Gottlieb, H.; Aurbach, D. Multinuclear magnetic resonance spectroscopy and density function theory calculations for the identification of the equilibrium species in THF solutions of organo-metallic complexes suitable as electrolyte solutions for rechargeable Mg batteries. Organometallics 2013, 32, 3165-3173. http://pubs.acs.org/doi/abs/10.1021/om300865a 

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39. Major, D. T.; Weitmann, M. Electrostatically Guided Dynamics - the Root of Fidelity in a Promiscuous Terpene Synthase? J. Am. Chem. Soc. 2012, 134, 19454-19462. http://pubs.acs.org/doi/abs/10.1021/ja308295p 

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38. Vardi-Kilshtain, A.; Major, D. T.; Kohen, A.; Engel, H.; Doron, D. Hybrid Quantum and Classical Simulations of the Formate Dehydrogenase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface. J. Chem. Theory Comput. 2012, 8, 4786-4796. http://pubs.acs.org/doi/abs/10.1021/ct300628e

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37. Doron, D.; Kohen, A.; Major, D. T. Collective Reaction Coordinate for Hybrid Quantum and Molecular Mechanics Simulations: A Case Study of the Hydride Transfer in Dihydrofolate Reductase. J. Chem. Theory Comput. 2012, 8, 2484-2496. http://pubs.acs.org/doi/abs/10.1021/ct300235k

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36. Stern, N.; Major, D. T.; Gottlieb, H. E.; Weizman, D.; Fischer, B. Speciation and Characterization by Potentiometric Titrations, NMR, and Molecular Dynamics Simulations. J. Biol. Inorg. Chem. 2012, 17, 861-879. http://www.springerlink.com/content/0949-8257/10.1007/s00775-012-0903-2

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35. Engel, H.; Doron, D.; Kohen, A.; Major, D. T. Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase. J. Chem. Theory Comput. 2012, 8, 1223-1234.
http://pubs.acs.org/doi/abs/10.1021/ct200874q

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34. Osnis, A.; Sukenik, C. N.; Major, D. T. Structure of Carboxyl Acid Terminated Self-Assembled Monolayers from Molecular Dynamics Simulations and Hybrid Quantum Mechanics-Molecular Mechanics Vibrational Normal Mode Analysis. J. Phys. Chem. C 2012, 116, 770-782. http://pubs.acs.org/doi/abs/10.1021/jp208443u

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33. Vardi-Kilshtain, A.; Azuri, A.; Major, D. T. Path-Integral Calculations of Heavy Atom Kinetic Isotope Effects in Condensed Phase Reactions Using higher order trotter factorizations. J. Comp. Chem. 2012, 33, 435-441. http://onlinelibrary.wiley.com/doi/10.1002/jcc.21986/abstract

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32. Doron, D.; Major, D. T.; Kohen, A.; Thiel, W.; Wu, X. Hybrid quantum and classical simulations of the dihydrofolate reductase catalyzed hydride transfer reaction on an accurate semi-empirical potential energy surface. J. Chem. Theory Comput. 2011, 7, 3420-3437. http://pubs.acs.org/doi/abs/10.1021/ct2004808

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31. Lin, Y. L.; Gao, J.; Rubinstein, A.; Major, D. T. Molecular Dynamics Simulations of the Intramolecular Proton Transfer and Carbanion Stabilization in the Pyridoxal 5-phosphate Dependent Enzymes L-Dopa Decarboxylase and Alanine Racemase. Invited review. BBA Proteins and Proteomics 2011, 1814, 1438-1446. http://dx.doi.org/10.1016/j.bbapap.2011.05.002

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30. Margulis-Goshen, K.; Weitman, M.; Major, D. T.; Magdassi, S. Inhibition of Crystallization and Growth of Celecoxib nanoparticles formed from volatile microemulsions. J. Pharm Sci. 2011, 100, 4390-4400. http://onlinelibrary.wiley.com/doi/10.1002/jps.22623/abstract

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29. Pour, N.; Gofer, Y. Major, D. T.; Aurbach, D. Structural Analysis of Electrolyte Solutions for Rechargeable Mg Batteries Comprising Magnesium-Aluminate Chloro-Phenyl Complexes by Electrochemical, Spectroscopic, Diffractometric means and DFT Calculations. J. Am. Chem. Soc. 2011, 133, 6270-6278. http://pubs.acs.org/doi/abs/10.1021/ja1098512

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28. Azuri, A.; Engel, H.; Doron, D.; Major, D. T. Path-Integral Calculations of nuclear quantum effects in model systems, small molecules, and enzymes via gradient-based forward corrector algorithms. J. Chem. Theory Comput. 2011, 7, 1273-1286. http://pubs.acs.org/doi/abs/10.1021/ct100716c

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27. Weitman, M.; Lerman, K.; Nudelman, A.; Major D. T.; Hizi, A.; Herschhorn, A. Structure-Activity Relationship Studies of 1-(4-Chloro-2,5-dimethoxyphenyl)-3-(3-propoxypropyl)thiourea, a Non-nucleoside Reverse Transcriptase Inhibitor of Human Immunodeficiency Virus Type-1. Eur. J. Med. Chem. 2011, 46, 447-467. http://dx.doi.org/10.1016/j.ejmech.2010.11.003

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26. Stern, N.; Major, D. T.; Gottlieb, H. E.; Weizman, D.; Fischer, B. What is the Conformation of Physiologically-Active Dinucleoside Polyphosphates in an Aqueous Solution? Conformational Analysis of Free Dinucleoside Polyphosphates by NMR and Molecular Dynamics Simulations. Org. Biomol. Chem. 2010, 8, 4637-3652. http://pubs.rsc.org/en/content/articlehtml/2010/ob/c005122e

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25. Rubinstein, A.; Major, D. T. Understanding catalytic specificity in alanine racemase from Quantum Mechanical and Molecular Mechanical simulations of the arginine 219 mutant. Biochemistry 2010, 49, 3957-3964. http://pubs.acs.org/doi/abs/10.1021/bi1002629

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24. Weitman, M.; Major, D. T. Challenges posed to bornyl diphosphate synthase: Diverging reaction mechanisms in monoterpenes. J. Am. Chem. Soc. 2010, 132, 6349-6360. http://pubs.acs.org/doi/abs/10.1021/ja910134x

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23. Gabashvili, A.; Major, D. T.; Perkas, N.; Gedanken, A. The sonochemical synthesis and characterization of mesoporous chiral titania using a chiral inorganic precursor. Ultrason. Sonochem. 2010, 17, 605-609. http://dx.doi.org/10.1016/j.ultsonch.2009.10.019

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22. Weitman, M.; Lerman, L.; Nudelman, A.; Major, D. T.; Gottlieb, H. E. Facile structural elucidation of imidazoles and oxazoles based on NMR spetroscopy and quantum mechanical calculations. Tetrahedron 2010, 66, 1465-1471. http://dx.doi.org/10.1016/j.tet.2009.12.019

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21. Margulis-Goshen, K.; Netivi, H.; Major, D. T.; Gradzielski, M.; Raviv, U.; Magdassi, S. Formation of organic nanoparticles from volatile microemulsions. J. Colloid Interface Sci. 2010, 342, 283-292. http://dx.doi.org/10.1016/j.jcis.2009.10.024

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20. Major, D. T.; Heroux, A.; Orville, A. M.; Valley, M. P.; Fitzpatrick, P. F.; Gao, J. Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction. Proc. Nat. Acad. Sci. U.S.A. 2009, 106, 20734-20739. http://www.pnas.org/content/106/49/20734.full

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19. Rubinstein, A.; Major, D. T. Catalyzing racemizations in the absence of a cofactor: The reaction mechanism in proline racemase. J. Am. Chem. Soc. 2009, 131, 8513-8521. http://pubs.acs.org/doi/abs/10.1021/ja900716y

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18. Nizri, G.; Lagerge, S.; Kamyshny, A.; Major, D. T.; Magdassi, S. Polymer-Surfactant Interactions: Binding Mechanism of Sodium Dodecyl Sulfate to Poly(diallyldimethylammonium chloride). J. Colloid Interface Sci. 2008, 320, 74-81. http://dx.doi.org/10.1016/j.jcis.2008.01.016

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17. Gao, J.; Wong, K.-Y.; Major, D. T. Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. J. Comput. Chem. 2008, 29, 514-522. http://onlinelibrary.wiley.com/doi/10.1002/jcc.20810/abstract

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16. Braverman, S.; Pechenick-Azizi, T.; Major, D. T.; Sprecher, M. b-Halo-a,b-Unsaturated g-Sultones. J. Org. Chem. 2007, 72, 6824-6831. http://pubs.acs.org/doi/abs/10.1021/jo071085q

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15. Major, D.T.; Gao, J. An Integrated Path Integral and Free Energy Perturbation-Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solutions and in Enzymes. J. Chem. Theory Comput. 2007, 3, 949-960. http://pubs.acs.org/doi/abs/10.1021/ct600371k

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14. Major, D.T.; Gao, J. A Combined QM/MM Study of the Reaction Mechanism and a-Amino Acidity in Alanine Racemase. J. Am. Chem. Soc. 2006, 128, 16345-16357. http://pubs.acs.org/doi/abs/10.1021/ja066334r

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13. Major, D.T.; Nam, K.; Gao, J. Transition State Stabilization and a-Amino Acidity in Alanine Racemase. J. Am. Chem. Soc. 2006, 128, 8114-8115. http://pubs.acs.org/doi/abs/10.1021/ja062272t

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12.  Gao, J.; Ma, S.; Major, D.T.; Nam, K.; Pu, J.; Truhlar, D. G. Mechanism and Free Energies of Enzymatic Reactions. Chem. Rev. 2006, 106, 3188-3209 (Invited paper). http://pubs.acs.org/doi/abs/10.1021/cr050293k

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11.  Major, D.T.; Garcia-Viloca, M.; Gao, J. Path-integral simulations of proton transfer reactions in aqueous solution using a combined QM/MM potential. J. Chem. Theory Comput. 2006, 2, 236-245. http://pubs.acs.org/doi/abs/10.1021/ct050257t

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10. Major, D.T.; York, D. M.; Gao, J. Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction.  J. Am. Chem. Soc. 2005, 127, 16374-16375. http://pubs.acs.org/doi/abs/10.1021/ja055881u

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9. Major, D.T.; Gao, J. Implementation of the bisection sampling method in path-integral simulations. J. Mol. Graph. Mod. 2005, 24, 121-127 (Invited paper for special issue in honor of Prof. Ian Hillier). http://dx.doi.org/10.1016/j.jmgm.2005.04.002

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8. Major, D. T.; Nahum, V.; Wang, Y. F.; Reiser, G.; Fischer, B. Molecular recognition in purinergic receptors. 2. Diastereoselectivity of the h-P2Y(1)-receptor. J. Med. Chem. 2004, 47, 4405-4416. http://pubs.acs.org/doi/abs/10.1021/jm049771u

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7. Major, D. T.; Fischer, B. Molecular recognition in purinergic receptors. 1. A comprehensive computational study of the h-P2Y(1)-receptor. J. Med. Chem. 2004, 47, 4391-4404. http://pubs.acs.org/doi/abs/10.1021/jm049772m

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6. Major, D. T.; Fischer, B. Theoretical study of the pH-dependent photophysics of N1,N6-ethenoadenine and N3,N4-ethenocytosine. J. Phys. Chem. A. 2003, 107, 8923-8931. http://pubs.acs.org/doi/abs/10.1021/jp0340515

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5. Major, D. T.; Laxer, A.; Fischer, B. Protonation studies of modified adenine and adenine nucleotides by theoretical calculations and 15N NMR. J. Org. Chem. 2002, 67, 790-802. http://pubs.acs.org/doi/abs/10.1021/jo0107554

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4. Laxer, A.; Major, D. T.; Gottlieb, H. E.; Fischer, B. (15N (5))-labeled adenine derivatives: Synthesis and studies of tautomerism by 15N NMR spectroscopy and theoretical calculations. J. Org. Chem. 2001, 66, 5463-5481. http://pubs.acs.org/doi/abs/10.1021/jo010344n

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3.  Major, D. T.; Halbfinger, E.; Fischer, B. Molecular Recognition of Modified Adenine Nucleotides by the P2Y1-Receptor. Part II. A Computational Approach. J. Med. Chem. 1999, 42, 5338-5347. http://pubs.acs.org/doi/abs/10.1021/jm9901576

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2. Fischer, B.; Halbfinger, E.; Major, D. T.; Ritzmann, M.; Ubl, J. J.; Reiser, G.; Boyer, J. L.; Harden, K. T. Molecular recognition of modified adenine nucleotides by the P2Y1-receptor. Part I. A synthetic, biochemical and NMR approach. J. Med. Chem. 1999, 42, 5325-5337. http://pubs.acs.org/doi/abs/10.1021/jm990156d

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1. Fischer, B.; Yefidoff, R.; Major, D. T.; Rutman-Halili, I.; Shneyvays, V.; Zinman, T.; Jacobson, K. A.; Shainberg A. Characterization of ‘mini-nucleotides’ as P2X-receptor agonists in rat cardiocytes culture. An integrated synthetic, biochemical and theoretical study. J. Med. Chem. 1999, 42, 2685-2696. http://pubs.acs.org/doi/abs/10.1021/jm990085i

 

The Major Group 

Computational Chemistry • Chemical Biology • Materials Science