Publications

Yang, Z.; Alexandrova, A. N.; Sautet, P. Modeling CO2 Hydrogenation to Methanol on an Ensemble of Inverse ZrO2 on Cu Catalytic Sites: […]

Ihiri, F.; Garcia-Garibay, M. A.; Alexandrova, A. N. Quantum-Chemically Informed Representation Learning for Molecular Crystals Property Prediction via Multimodal Graph Neural Networks. 2026, submitted.

Laderer, W. T.; Alexandrova, A. N. Prospect to Boost Catalytic Activity of Precious Metals by Adsorption Atop Topological Insulators. 2026, submitted.

Gericke, A.; Erbez, J.; Chen, X.; Khan, A.; Chen, Z.; Lee, Y.; Hong, S. ; Heinlein, J.; Schroeder, E.; Bac,

Ihiri, F.; Balan, H.; Sureshan, K.; Alexandrova, A.; García-Garibay, M. A. Machine Learning Prediction of Topochemical Azide-Alkyne Cycloaddition in Molecular

Wan, C.; Zhang, Z.; Weng, Zheng; Sun, S.; Huang, W.-H.; Liu, E.; Chen, Z.; Wang, Y.; Zhang, A.; Lin, Y.; Yeh,

Sun, S.; Hao, Y.; Huang, C.-J.; Chen, C. A.; Green, J.; Roshandel, H.; He, J.; Laderer, W.; Tran, M.; Diaconescu,

Ajmera, P.; Guion, D.; Barnes, S.; Sadun, A. A.; Alexandrova, A. N. Molecular Mechanism of Mitochondrial Complex I Disruption by

Biswas, S.; Isakov, A.; Dias, N.; Finn, M.; Cokas, J.; Epshteyn, A.; Alexandrova, A. N.; Ahmed, M.; Kaiser, R. Low

Marino, S.; Han, Y.; Samira, S.; Berry, R.; Gordon, M.; Alexandrova, A. N.; Christopher, P. Turnovers drive supported metal nanoparticle

Cabezas-Escares, J.; Echeverri, A.; Muñoz, F.; Alexandrova, A. N. Phonon-induced electronic degeneracy breaking: a SSAdNDP interpretation. 2026, submitted.

Lewis, L.; Badve, P.; Vaca, I.; Ajmera, P.; Lee, Y.; Alexandrova, A. N.; Meier, K.; Shafaat, H.A protein-based model of

Sola, M.; Ottosson, H.; Radenkovic, S.; Alexandrova, A. N. Conceptual inflation in (anti)aromaticity: The need for a unified taxonomy. 2025, submitted.

Ajmera, P.; Farley, L.; Minnetian, N.; King, R. P.; Jayasekara, H.; Chaturvedi, S. S.; Yang, J.; Alexandrova, A. N.; Rovis, T.

Ghoshal, S.; Ezeakunne, C.; Lee, Y.; Alexandrova, A. N.; Kattel, S. The Crucial Role of Hydrogen Ligation on the Stability

Zhou, H.; Wojcik, P.; Zhu, G.-Z.; Lao, G.; Khvorost, T.; Caram, J. R.; Campbell, W. C.; Alexandrova, A. N.; Krylov,

Wei, Y.; Alexandrova, A. N. What can Raman spectroscopy really say about the adsorbed CO on roughened Cu electrodes in

Weng, G.; Alexandrova, A. N. Bulk-Boundary Correspondence of Semimetal Ru3Sn7 and Topological Surface States on Chemically Realistic Terminations. Adv. Mater. Interf. 2025, 60,

Chaturvedi, S. S.; Goswami, A.; Qian, J.; Petersen, A.; Ajmera, P.; Alexandrova, A. N. Distinct Electric Fields Enable Common Catalytic Function

Wojcik, P.; Zhou, H.; Khvorost, T.; Zhu, G.-Z.; Lao, G.; Caram, J. R.; Alexandrova, A. N.; Hudson, E. R.; Campbell,

Wei, Y.; Sautet, P.; Alexandrova, A. N. Temperature-Dependent Adsorbate-Induced Surface Roughening Onset in Electrochemical CO2 Reduction on Copper. 2025, J. Phys. Chem.

Isenberg, N.; Lee, Y.; Colombo Tedesco, C.; Chen, Z.; Alexandrova, A. N.; Tassone, C.; Rallo, R. Ripening of Rh nanoparticle catalysts

Masubuchi, T.; Rublev, P.; Han, Y.; Perez, P. J.; Boebinger, M.; Hwang, S.; Saravanan, L.; Belnap, D. M.; Alexandrova, A.

Choi J.; Banerjee, A.; Ross, R. D.; Chiu, S.; Zhang, Z.; Sacci, R.; Veith, G.; Hahn, C.; Alexandrova, A. N.;

Isakov, A.; Poths, P.; Cummings, E.; Alexandrova, A. N. Role of Sn content in the activity and selectivity of PtSn/SiO2 clusters for

Chen, X.; Lee, Y.; Hong, S.; Schroeder, E.; Gericke, S.; Greg, B.; Chen, Z.; Hesse, S.; Tassone, C.; Rioux, R.;

Han, Y.; Wei, Y.; Goswami, A.; Alexandrova, A. N. Uncovering the true Active Sites in Ni-N-C Catalysts for CO₂ Electroreduction. 2025, J.

 Lu, J.; Sawaya, M. R.; Chaturvedi, S. S.; Guion, D.; Lutter, L.; Ge, P.; Hou, K.; Murrali, M. G.; Cooper,

Ross, R.; Han, Y.; Jeong, H.-Y.; Ynzunza, J.; Lavroff, R. H.; Banerjee, A.; Prajapati, A.; Morales-Giuo, C.; Velazquez, J.; Alexandrova,

Vargas, S.; Gee, W.; Doyle, A.; Alexandrova, A. N. Multi-level QTAIM-Enriched Graph Neural Networks for Resolving Properties of Transition Metal Complexes. 2025,

Mir, A.; Banerjee, A.; Ihiri, F.; Chiu, S.; Alexandrova, A. N.; Morales-Guio, C.; Yang, J. Optimizing CO2-Loaded Aqueous Amine Solutions for

Wei, J.; Zhang, Z.; Wei, Y.; Gee, W.; Zhou, Y.-W.; Herran, M.; Sautet, P.; Alexandrova, A. N.; Roldan Cuenya, B.;

Goswami, A.; Zhang, Z.; Alexandrova, A. N. CO2 Electroreduction on Borated Copper Surfaces: Boron Active Sites, not Copper. 2025, submitted.

Baidun, M.; Kolganov, A.; Alexandrova, A. N.; Pidko, E. Hydride Accessibility and Reactivity in the Configurational and Stoichiometric Space of β-Ga2O3 for

Biswas, S.; Cokas, J.; Paul, D.; Dias, N.; Finn, M. T.; Hudak, B. M.; Epshteyn, A.; Alexandrova, A. N.; Ahmed,

Kareem, H.; Lee, Y.; Saqib, M.; Tran, D.; Alexandrova, A. N.; Wachsman, E.; Baker, D. Bimetallic-GDC Nanowire Catalyst as a Cathode

Lao, G.; Khvorost, T.; Macias, Jr., A.; Morgan, H. W. T.; Lavroff, R. H.; Choi, R.; Zhou, H.; Usvyat, D.;

Shah, A. H.; Poths, P.; Wan, C.; Wang, S.; Liu, Y.; Alexandrova, A. N.; Huang, Y.; Duan, X. Specific adsorption of

Kogan, S.; Alexandrova, A. N.; Morgan, H. W. T. 5d orbital covalency controls the high-pressure polymorphism of BaO. 2025, Chem. Eur. J.,

Morgan, H. W. T.; Terhune, J. E. S.; Elwell, R.; Tan, H. B. T.; Perera, U. C.; Derevianko, A.; Hudson,

Laderer, W. T.; Jiang, X.; Vlcek, V.; Morgan, H. W. T.; Alexandrova, A. N. Topological perturbation to a standard dehydrogenation catalyst,

Morgan, H. W. T.; Tran Tran, H. B.; Elwell, R.; Alexandrova, A. N.; Hudson, E. R.; Derevianko, A. Theory of internal

Alexandrova, A. N.; Christopher, P. Heterogeneous catalysis: Optimal performance at a phase boundary? 2025, Matter, 102209. Download

Morgan, H. W. T.; Tan, H. B. T.; Derevianko, A.; Elwell, R.; Terhune, J. E. S.; Hudson, E. R.; Alexandrova,

Terhune, J. E. S; Elwell, R.; Tran Tan, H. B. et. al. Photoinduced quenching of the 229Th isomer in a solid-state host. 2025,

Chiu, S.; Alexandrova, A. N. Cation Effects on CO2 Delivery to Cu Electrode in Reactive Capture of CO2. 2025, J. Phys. Chem. Lett.,

Weng, G.; Alexandrova, A. N. Unraveling the Surface Termination and Evolution of Surface States for Electrocatalyst PtSn4 in Alkaline HER. 2025, ACS Catal.,

Brower, R. S.; Wuille Bille, B.; Chiu, S.; Perryman, J. T.; Yao, L.; Agboola, F.; Nagasaka, C. A.; Xie, Y.;

Li, G.; Chiu, S.; Morgan, H. W. T.; Fuchs, A. T.; Isakov, A.; Poths, P.; Zhang, Z.; Alexandrova, A. N.;

Cheng, D.; Nguyen, K.-L. C.; Sumaria, V.; Wei Z.; Zhang, Z.; Gee, W.; Li, Y.; Morales-Guio, C. G.; Heyde, M.;

Yang, Z.; Kumari, S.; Alexandrova, A. N.; Sautet, P. Catalytic Activity of Ensemble of Sites for CO2 Hydrogenation to Methanol on a

Lee, Y.; Chen, X.; Gericke, S.; Li, M.; Zakharov, D.; Head, A.; Yang, J.; Alexandrova, A. N. Machine-Learning-Driven Exploration of Surface

Ajmera, P.; Vargas, S.; Chaturvedi, S. S.; Hennefarth, M. R.; Alexandrova, A. N. PyCPET – Computing Heterogeneous 3D Protein Electric Fields

Zhou, H.; Khvorost, T.; Alexandrova, A. N. Caram. J. R. Vibronic Engineering for Quantum Functional Groups. 2025, Acc. Chem. Res., i58, 1181-1191 Download.

Prajapati, A.; Hahn, C.; Weidinger, I.; Shi, Y.; Lee, Y.; Alexandrova, A. N.; Thompson, D.; Bare, S. R.; Chen, S.;

Wan, C.; Zhang, Z.; Wang, S.; Sun, Q.; Liu, E.; Pu, H.; Zhang, A.; Chen, Z.; Shah, A. H.; Alexandrova,

Halder, A.; Warburton, R. E.; Sun, G.; Cheng, L.; Assary, R. S.; Seifert, S.; Homer, M.; Greeley, J.; Alexandrova, A.

Morgan, H. W. T.; Elwell, R.; Terhune, J. E. S; Tran Tan, H. B.; Perera, U. C. Derevianko, A.; Alexandrova,

Eberhart, M. E.; Alexandrova, A. N.; Ajmera, P.; Bím, D.; Chaturvedi, S.; Vargas, S.; Wilson, T Methods for Theoretical Treatment of

Green, J.; Morgan, H. W. T.; Mandigo-Stoba, M.; Gutierez, C.; Alexandrova, A. N.; Ni, N. Mapping the fermiology of the triangular

Pineda, S.V.; Chhetri, P.; Bara, S.; Elskens, Y.; Casci, S.; Alexandrova, A.N.; Au, M.; Athanasakis-Kaklamanakis, M.; Bartokos, M.; Beeks, K.;

Wojcik, P.; Khvorost, T.; Lao, G.; Zhu, G.-Z.; Macias Jr., A.; Caram, J. R.; Campbell, W. C.; Garcia-Garibay, M. A.;

Elwell, R.; Terhune, J. E. S.; Morgan, H. W. T.; Alexandrova, A. N.; Tran Tan, H. B.; Derevianko, A.; Hudson,

Zhang, Z.; Gee, W.; Lavroff, R. H.; Alexandrova, A. N. GOCIA: Global Optimizer for Clusters, Interfaces, and Adsorbates. 2025, Phys. Chem. Chem.

Lavroff, R. H.; Kats, D.; Maschio, L.; Bogdanov, N.; Alavi, A.; Alexandrova, A. N.; Usvyat, D. Aperiodic fragments in periodic solids:

Weng, G.; Alexandrova, A. N. Understanding the Finite Size and Suface Relaxation Effects on the Surface States of Bi2Se3 Family Topological Insulator. 2024,

Lavroff, R. H.; Cummings, E.; Sawant, K.; Zhang, Z.; Sautet, P.; Alexandrova, A. N. Cu-supported ZnO in Conditions of CO2 Reduction to

Eberhart, M. E.; Wilson, T. R.; Jones, T.; Alexandrova, A. N. Electric fields imbue enzyme reactivity by aligning active site fragment

Vargas, S.; Chaturvedi, S.; Alexandrova, A. N. Machine-learning prediction of protein function from the portrait of its intramolecular electric field. 2024, J.

Urwin, D. J.; Tran, E.; Alexandrova, A. N. Relative Genotoxicity of Polycyclic Aromatic Hydrocarbons via Free Energy Perturbation Approaches. 2024, Proc. Natl.

Shin, A. J.; Zhao, C.; Shen, Y.; Dickerson, C. E.; Li, B.; Bím, D.; Alson, L. K.; Atallah, T. L.;

Choi, J.; Chiu, S.; Banerjee, A.; Sacci, R. L.; Veith, G. M.; Stieber, C.; Hahn, C.; Alexandrova, A. N.; Morales-Guio,

Li, B. Y.; Duong, T.; Neuhauser, D.; Alexandrova, A. N.; Caram, J. R. Simple Algorithm for Converting Random Number Generator Outputs

Elwell, R.; Schneider, C.; Jeet, J.; Terhune, J. E. S.; Morgan, H. W. T.; Alexandrova, A. N.; Tan, H. B.

Li, B. Y.; Dickerson, C. E.; Shin, A. J.; Zhao, C.; Shen, Y.; He, Y.; Diaconescu, P. L.; Alexandrova, A.

Chaturvedi, S. S.; Vargas, S.; Ajmera, P.; Alexandrova, A. N. Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field. 2024, J. Am.

Zhang, Z.; Gee, W.; Sautet, P; Alexandrova, A. N. H and CO Co-induced Surface Roughening on Cu in CO2 Electroreduction Conditions. 2024, J. Am.

Green, J.; Emmanouilidou, E.; Morgan, H. W. T.; Laderer, W. T.; Hu, C.; Loera, J.; Alexandrova, A. N.; Ni, N. Fermiology

Qie, B.; Wang, Z.; Jiang, J.; Zhang, Z.; Jacobse, P.; Lu, J.; Li, X.; Liu, F.; Alexandrova, A. N.; Louie,

Khvorost, T.; Wojcik, P.; Chang, C.; Calvillo, M.; Dickerson, C. E.; Krylov, A. I.; Alexandrova, A. N. Dual optical cycling centers

Cabezas-Escares, J.; Barrera, N. F.; Lavroff, R. H.; Alexandrova, A. N. Cardenas, C.; Munoz, F. Electronic Structure and Vibrational Stability of

Vargas, S.; Gee, W.; Alexandrova, A. N. High-throughput Quantum Theory of Atoms in Molecules (QTAIM) for Geometric Deep Learning of Molecular

Poths, P.; Vargas, S.; Sautet, P.; Alexandrova, A. N. Thermodynamic equilibrium versus kinetic trapping: thermalization of cluster catalyst ensembles can extend

Shah, A. H.; Zhang, Z.; Wan, C.; Wang, S.; Wang, L.; Alexandrova, A. N.; Huang, Y.; Duan, X. The platinum-surface water

Akopov, G.; Hu, S.; Shumilov, K.; Hamilton, S.; Pangilinan, L.; Mehmedović, Z.; Yin, H.; Robinson, P. J.; Roh, I.; Kavner,

Weng, G.; Laderer, W.; Alexandrova, A. N. Understanding the Adiabatic Evolution of Surface States in Tetradymite Topological Insulators under Electrochemical Conditions. 2024,

Salcedo, A.; Alexandrova, A. N.; Loffreda, D.; Michel, C. The Role of Oxidizing Conditions in the Dispersion of Supported Platinum Nanoparticles

White, K. E.; Avery, E. M.; Cummings, E.; Hong, X.; Langecker, J.; Vetushka, A.; Dusek, M.; Machacek, J.; Visnak, J.;

Cheng, D.; Alexandrova, A. N.; Sautet, P. H-induced restructuring on Cu(111) triggers CO electro-reduction in acidic electrolyte. 2024, J. Phys. Chem. Lett.,

Lavroff, R. H.; Munarriz, J.; Dickerson, C. E.; Munoz, F.; Alexandrova, A. N. Chemical Bonding Dictates Drastic Critical Temperature Difference in

Zhu, G.-Z.; Lao, G.; Dickerson, C. E.; Caram, J. R.; Campbell, W. C.; Alexandrova, A. N. Hudson, E. R. Extending the

Morgan, H. W. T.; Laderer, W.; Alexandrova, A. N. δ-bonding and spin-orbit coupling make SrAg4Sb2 a topological insulator. 2023, Chem. Eur. J., DOI: 10.1002/chem.202303679.

Zelevinski, T.; Izmaylov, A. F.; Alexandrova, A. N. Physical Chemistry of Quantum Information Science. J. Phys. Chem. A 2023, 127, 10357-10359.

Kumari, S.; Alexandrova, A. N.; Sautet, P. Nature of Zirconia on Copper Inverse Catalyst under CO2 Hydrogenation Conditions. 2023, J. Am. Chem. Soc.,

Cendejas, M. C.; Mellone, O. A. P.; Kurumbail, U.; Zhang, Z.; Jansen, J. H.; Ibrahim, F.; Dong, S.; Vinson, J.;

Alexandrova, A. N.; Biteen, J. S.; Coriani, S.; Geiger, F. M.; Gewirth, A. A.; Goward, G. R.; Guo, H.; Huang,

Yu, Y.; Koh, H.; Zhang, Z.; Yang, Z.; Alexandrova, A. N.; Stach, E. A.; Xie, J. Kinetic Pathways of Fast Lithium

Sun, Q.; Dickerson, C. E.; Dai, J.; Pope, I.; Cheng, L.; Neuhauser, D.; Alexandrova, A. N.; Mitra, D.; Zelevinsky, T. Probing

Dickerson, C. E.; Alexandrova, A. N.; Narang, P.; Philbin, J. P. Single molecule superradiance for optical cycling. 2024, submitted.

Roshandel, H.; Vargas, S.; Lai, A.; Alexandrova, A. N.; Diaconescu, P. L. Prediction of Reaction Orthogonality using Machine Learning. 2025, submitted.

Fuller, J. T.; Barnes, S.; Sadun, L.; Ajmera, P.; Alexandrova, A. N.; Sadun, A. Coenzyme Q10 trapping in mitochondrial Complex I

Zhang, Z.; Hermans, I.; Alexandrova, A. N. Off-stoichiometric Restructuring and Sliding Dynamics of Hexagonal Boron Nitride Edges in Conditions of Oxidative

Wan, C.; Zhang, Z.; Dong, J.; Xu, M.; Pu, H.; Baumann, D.; Lin, Z.; Wang, S.; Huang, J.; Shah, A.

Zito, A. M.; Clarke, L. E.; Barlow, J.; Bím, D.; Zhang, Z.; Ripley, K.; Li, C.; Kummeth, A.; Leonard, M.

Nguen, H. M.; Morgan, H. W. T.; Chantarojsiri, T.; Kerr, T. A.; Yang, J. Y.; Alexandrova, A. N.; Leonard, N.

Chaturvedi, S. S.; Bim, D.; Christov, C. Z.; Alexandrova, A. N. From Random to Rational: Improving Enzyme Design through Electric Fields,

Morgan, H. W. T.; Alexandrova, A. N. Structures of LaH10, EuH9, and UH8 superhydrides rationalized by electron counting and Jahn-Teller distortions in

Lavroff, R. H.; Wang, J.; White, M. G.; Sautet, P.; Alexandrova, A. N. Mechanism of Stoichiometrically Governed Titanium Oxide Brownian Tree

Cheng, D.; Wei, Z.; Zhang, Z.; Broekmann, P.; Alexandrova, A. N.; Sautet, P. Restructuring and activation of Cu (111) under electrocatalytic

Zhang, Z.; Masubuchi, T.; Sautet, P.; Anderson, S. L.; Alexandrova, A. N. Hydrogen Evolution on FTO-Supported Ptn Clusters: Ensemble of Hydride States

Poths, P.; Morgan, H. W. T.; Li, G.; Fuchs, A.; Anderson, S. L.; Alexandrova, A. N. Promoter-Poison Partnership Protects Platinum Performance

Kumari, S.; Masubuchi, T.; White, H.; Alexandrova, A. N.; Anderson, S. L.; Sautet, P. Electrocatalytic hydrogen evolution at full atomic utilization

Poths, P.; Zandkarimi, B.; Alexandrova, A. N.; Jiminez-Izal, E. Pt:Ge ratio as a lever of activity and selectivity control of supported

Li, G.; Poths, P.; Morgan, H. W. T.; Masubuchi, T.; Alexandrova, A. N.; Anderson, S. L. Got Coke? Self-Limiting Poisoning Makes

Eberhart, M. E.; Wilson, T. R.; Johnston, N.; Alexandrova, A. N. Geometry of charge density as a reporter on the role

Poths, P.; Hong, Z.; Li, G.; Anderson, S. L.; Alexandrova, A. N. “Magic” sinter-resistant cluster sizes of Ptn Supported on Alumina. 2022, J.

Lao, G.; Zhu, G.-Z.; Dickerson, C. E.; Augenbraun, B. L.; Alexandrova, A. N.; Caram, J. R.; Hudson, E. R.; Campbell,

Wilson, T. R.; Morgenstern, A.; Alexandrova, A. N.; Eberhart, M. E. Bond bundle analysis of ketosteroid isomerase. 2022, J. Phys. Chem. B.

Munarriz, J.; Zhang, Z.; Sautet, P.; Alexandrova, A. N. Graphite-supported Ptn Cluster Electrocatalysts: Major Change of Active Sites as a Function of

Morgan, H. W. T.; Alexandrova, A. N. Electron Counting and High-Pressure Phase Transformations in Metal Hexaborides. 2022, Inorg. Chem., 61, 18701-18709. Download. ArXiv

Ramey, G.; Vargas, S.; De Alwis, D.; Alexandrova, A. N.; Distefano III, J.; Bloomingdale, P. An Artificial Intelligence Framework for Optimal

Shah, A. H.; Zhang, Z.; Huang, Z.; Wang, S.; Zhong, G.; Wan, G.; Alexandrova, A. N.; Huang, Y.; Duan, X. Unriddling

Zhang, Z.; Wei, Z.; Sautet, P.; Alexandrova, A. N. Hydrogen-Induced Restructuring of a Cu(100) Electrode in Electroreduction Conditions. 2022, J. Am. Chem.

Barlow, J. M.; Clarke, L.; Zhang, Z.; Bím, D.; Ripley, K.; Zito, A.; Brushett, F.; Alexandrova, A. N.; Yang, J.

Dickerson, C. E.; Chang, C.; Guo, H.; Alexandrova, A. N. Fully saturated hydrocarbons as hosts of optical cycling centers. 2022, J. Phys.

Zito, A. M.; Bím, D.; Vargas, S.; Alexandrova, A. N.;Yang, J. Y. Computational and Experimental Design of Quinones for Electrochemical CO2 Capture

Hassan, I.; Fuller, J. T.; Dippon, V.; Ta, A.; Danneman, M.; McNaughton, B.; Alexandrova, A. N.; Rovis, T. Improved Rh(III)-Catalysis by

Mitra, D.; Lasner, Z.; Zhu, G.-Z.; Dickerson, C. E.; Augenbraun, B. L.; Alexandrova, A. N.; Campbell, W. C.; Caram, J.

Zhu, G.-Z.; Augenbraun, B. L.; Dickerson, C. E.; Frim, M.; Lao, G.; Lasner, Z.; Mitra, D.; Alexandrova, A. N.; Campbell,

Zhang, Z.; Kummeth, A. L.; Yang, J. Y.; Alexandrova, A. N. Inverse Molecular Design of Alkoxides and Phenoxides for Aqueous Direct

Lavroff, R. H.; Morgan, H. W. T.; Zhang, Z.; Poths, P.; Alexandrova, A. N. Ensemble representation of catalytic interfaces: soloists, orchestras,

Zhang, Z.; Zandkarimi, B.; Munarriz, J.; Dickerson, C. E.; Alexandrova, A. N. Fluxionality of Subnano Clusters Reshapes the Activity Volcano of

Poths, P.; Alexandrova, A. N. Theoretical perspective on operando spectroscopy of fluxional nano-catalysts. 2022, J. Phys. Chem. Lett., 13, 4321-4334. Download

Singh, S.; Romero, A. H.; Mella, J. D.; Eremeev, V. Munoz, E.; Alexandrova, A. N.; Rabe, K. M.; Vanderbilt, D;

Xian, W.; Hennefarth, M. R.; Lee, M. W.; Do, T.; Lee, E. Y.; Alexandrova, A. N.; Wong, G. C. L. Histidine

Poths, P.; Sun, G.; Sautet, P.; Alexandrova, A. N. Interpreting operando XANES of supported Cu and CuPd clusters in conditions of

Bím, D.; Navráti, M.; Gutten, O.; Konvalinka, J.; Kutil, Z.; Navráti, V.; Alexandrova A. N.; Barinka, C.; Rulisek, L. Predicting Effects

163. Guo, H.; Poths, P.; Sautet, P.; Alexandrova, A. N. Oxidation Dynamics of Supported Catalytic Cu Clusters: Coupling to Fluxionality. 2022, ACS

Wilson, T. R.; Alexandrova, A. N.; Eberhart, M. E. Electron Density Geometry and the Quantum Theory of Atoms in Molecules. 2021, J.

Lavroff, R. H.; Pennington, D. L.; Hua, A. S.; Li, B. Y.; Williams, J. A.; Alexandrova, A. N. Recent Innovations in

Ortiz, J. V.; Alexandrova, A. N.; Simons, J. Tribute to Alexander I. Boldyrev. 2021 J. Phys. Chem. A, 125, 9261-9263. View Alexander I. Boldyrev

Deng, J.; Lin, S-.C.; Fuller, J. T.; Zandkarimi, B.; Chen, H. M.; Alexandrova, A. N.; Liu, C. Electrocatalytic Methane Functionalization with

Vargas, S.; Hennefarth, M. R.; Liu, Z.; Alexandrova, A. N. Machine Learning to Predict Reaction Barriers from the Reactant State Electron

Reilley, D. J.; Arraf, Z.; Alexandrova, A. N. Contrasting Effects of Inhibitors Li+ and Be2+ on Catalytic Cycle of Glycogen Synthase Kinase-3β. 2021 J. Phys.

Alexandrova, A. N.; Hartland, G. V. Revising Manuscripts: Trying to Make Everyone Happy. 2021, J. Phys. Chem. A/B/C, DOI: 10.1021/acs.jpca.1c07066, 10.1021/acs.jpcb.1c07067, 10.1021/acs.jpcc.1c07068.

Alexandrova, A. N.; Hartland, G. V. The Art of Reviewing Manuscripts. Viewpoint. 2021, J. Phys. Chem. A/B/C, DOI: 10.1021/acs.jpca.1c06146, 10.1021/acs.jpcb.1c06147, 10.1021/acs.jpcc.1c06148.

Bím, D.; Alexandrova, A. N. Electrostatic Regulation of Blue Copper Sites. 2021, Chem. Sci.,12, 11406-11413. Download

Hennefarth, M. R.; Alexandrova, A. N. Advances in Optimizing Enzyme Electrostatic Preorganization. 2022, Curr. Opin. Struct. Biol., 72, 1-8. Download

Alexandrova, A. N.; Hartland, G. V. Suggesting Reviewers to Improve Your Manuscript. Viewpoint. 2021, J. Phys. Chem. A/B/C, DOI: 10.1021/acs.jpca.1c05521, 10.1021/acs.jpcb.1c05522, 10.1021/acs.jpcc.1c05523.

Reilley, D. J.; Wang, J.; Dokholyan, N. V.; Alexandrova, A. N. Titr-DMD – A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics

Mehta, R.; Rivera, D. D.; Reilley, D. J.; Thomas, P. W.; Hinojosa, A.; Tan, D.; Stewart, A. C.; Crowder, M.

Bím, D.; Alexandrova, A. N. Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity. 2021 ACS Catal.,11, 6534-6546. Download, ChemRxiv

Urwin, D. J.; Alexandrova, A. N. Regularization of Least Squares Problems in CHARMM Parameter Optimization by Truncated Singular Value Decompositions. 2021, J.

Shumilov, K. D.; Mehmedovic, Z.; Yin, H.; Poths, P.; Nuryyeva, S.; Liepuoniute, I.; Jang, C.; Alexandrova, A. N. Understanding hardness of

Dickerson, C. E.; Guo, H.; Zhu, G.; Hudson, E. R.; Caram, J. R.; Campbell, W. C.; Alexandrova, A. N. Optical Cycling

Dickerson, C. E.; Guo, H.; Shin, A. J.; Augenbraun, B. L.; Caram, J. R.; Campbell, W. C.; Alexandrova, A. N. Franck-Condon

Zandkarimi, B.; Poths, P.; Alexandrova, A. N. When Fluxionality Beats Size Selection: Acceleration of Ostwald Ripening of Sub-Nano Clusters. 2021, Angew. Chem.

Hennefarth, M. R.; Alexandrova, A. N. Heterogeneous Intramolecular Electric Field as a Descriptor of Diels-Alder Reactivity. 2021, J. Phys. Chem. A, 125,

Sun, G.; Fuller, J. T.; Alexandrova, A. N.; Sautet, P. Reaction induced catalyst restructuring as a major player for methane dissociaiton

Zhang, R.; AthariBorojeny, M.; Collinge, G.; Iablokov, V.; Shumilov, K.; Alexandrova, A. N.; Kruse, N.; McEwen, J.-S. Promoting the cleavage of

Zhang, Z.; Cui, Z.; Jimenez-Izal, E.; Sautet, P.; Alexandrova, A. N. Hydrogen Evolution on Restructured B-rich WB: Metastable Surface States and

Munarriz, J.; Robinson, P. J.; Alexandrova, A. N. Towards a Single Chemical Model to Understand Lanthanide Hexaborides. 2020, Angew. Chem. Int. Ed.,

Guo, H.; Dickerson, C. E.; Shin, A. J.; Zhao, C.; Atallah, T. L.; Caram, J. R.; Campbell, W. C.; Alexandrova,

Li, Y. L.; Zee, C.-T.; Lin, J. B.; Basile, V. M.; Muni, M.; Flores, M. D.; Munarriz, J.; Kaner, R.

Zandkarimi, B.; Gorey, T. J.; Li, G.; Munarriz, J.; Anderson, S. L.; Alexandrova, A. N. Alloying with Sn Suppresses Sintering of

Zandkarimi, B.; Alexandrova, A. N. Can Fluxionality of Subnanometer Cluster Catalysts Solely Cause Non-Arrhenius Behavior in Catalysis? 2020, J. Phys. Chem. C,

Hennefarth, M. R.; Alexandrova, A. N. Direct Look at the Electric Field in Ketosteroid Isomerase and its Variants. 2020, ACS Catal., 10,

Deng, J.; Iniguez, J. A.; Fuller, J.; Lin, S.-C.; Yang, D.; Chan, G.; Chen, H. M. Alexandrova, A. N.; Liu,

Goronzy, D. P.; Stanek, J.; Avery, E.; Guo, H.; Bastl, Z.; Dusek, M.; Gallup, N. M.; Gun, S.; Kucerakova, M.;

Alexandrova, A. N.; Liu, Z.-P.; Schmidt, J. R.; Schneider, W. F.; Solomon, G. Characteristics of Impactful Computational Contributions to The Journal

Venegas, J.; Zhang, Z.; Agbi, T.; McDermott, W.; Alexandrova, A. N.; Hermans, I. Why Boron Nitride is such a Selective Catalyst

Reilley, D. J.; Fuller, J. T.; Nechay, M. R.; Victor, M.; Li, W.; Rubbery, J. D.; Mujika, J. I.; Lopez,

Fuhr, A.; Alexandrova, A. N.; Sautet, P. Stoichiometry-Controllable Optical Defects in CuxIn2-xSy Quantum Dots for Energy Harvesting. 2020, J. Mater. Chem. A., 8,

Zandkarimi, B.; Sun, G.; Halder, A.; Seifert, S.; Vajda, S.; Sautet, P.; Alexandrova, A. N. Interpreting operando XANES of Surface-Supported Subnanometer

Sun, G.; Alexandrova, A. N.; Sautet, P. Structural rearrangements of subnanometer Cu clusters govern catalytic oxidation. 2020, ACS Catal., 10, 5309-5317. Download

Liu, G.; Poths, P.; Zhang, X.; Zu, Z.; Marshall, M.; Alexandrova, A. N.; Bowen, K. H. CO2 Hydrogenation to Formate and Formic

Guo, H.; Sautet, P.; Alexandrova, A. N. Reagent Triggers Isomerisation of Fluxional Cluster Catalysts via Dynamic Coupling. 2020, J. Phys. Chem. Lett.,

Robinson, P. J.; Munarriz, J.; Valentine, M. E.; Granmore, A.; Drichko, N.; Chamorro, J. R.; Rosa, P. F.; McQueen, T.

Gorey, T. J.; Zandkarimi, B.; Li, G.; Baxter, E. T.; Alexandrova, A. N.; Anderson, S. L. Coking-Resistant Sub-Nano Dehydrogenation Catalysts: Ptn/SiO2 vs.

Liu, J.-Y.; Gong, X.-Q.; Li, X.-Q.; Shi, H.; Cronin, S. B.; Alexandrova, A. N. (Photo)electrocatalytic CO2 reduction at the defective anatase TiO2 surface. 2020,

Zhang, Z.; Zandkarimi, B.; Alexandrova, A. N. Ensembles of metastable states govern heterogeneous catalysis on dynamic interfaces. 2020, Acc. Chem. Res., 53,

Reilley, D. J.; Hennefarth, M. R.; Alexandrova, A. N. The Case for Enzymatic Competitive Metal Affinity Methods. 2020, ACS Catal., View Point

Li, G.; Zandkarimi, B.; Cass, A. C.; Gorey, T. J.; Allen, B. J.; Alexandrova, A. N.; Anderson, S. L. Sn-modification of

Sun, G.; Alexandrova, A. N.; Sautet, P. Pt8 Cluster on Alumina under a Pressure of Hydrogen: Support-dependent Reconstruction from First-principles Global Optimization. 2019,

Wang, S.; Chiang, N.; Guo, H.; Wattanatom, N.; Barr, K.; Alexandrova, A. N.; Weiss, P. S. Photoinduced Carrier Distribution in Titanyl

Halder, A.; Ha, M.-A.; Zhai, H.; Alexandrova, A. N.; Vajda, S. Oxidative Dehydrogenation of Cyclohexane on Pd vs. Cu Clusters: Selectivity

Zhai, H.; Sautet, P.; Alexandrova, A. N. Global Optimization of Adsorbate Covered Supported Cluster Catalysts: the Case of Pt7H10CH3 on alpha-Al2O3. 2020, ChemCatChem,

Kang, K.; Fuller, J.; Reath, A. H.; Ziller, J. W.; Alexandrova, A. N.; Yang, J. Y. Installation of an Oriented Electric

Axtell, J.;Messina, M.; Liu, J.-Y.; Galaktionova, D.; Schwan, L. J.; Porter, T.; Savage, M.; Wixtron, A.; Rheingold, A.; Kubia, C.;

Jimenez-Izal, E.; Gates, B.; Alexandrova, A. N. The messy story of clusters in catalysis. 2019 Physics Today, 72, 38-43. Invited Article

Zhai, H.; Munoz, F.; Alexandrova, A. N. Strain to Alter the Covalency and Superconductivity in Transition Metal Diborides. 2019, J. Mater. Chem.

Gorey, T.; Zandkarimi, B.; Li, G.; Baxter, E.; Alexandrova, A. N.; Anderson, S. L. Preparation of Size and Composition-controlled PtnSnx/SiO2 (n =

Zandkarimi, B.; Alexandrova, A. N. Surface-supported cluster catalysis: ensembles of metastable states run the show. 2019, WIRES, advanced review, DOI: 10.1002/wcms.1420. Download

Jimenez-Izal, E.; Liu, J.-Y.; Alexandrova, A. N. Germanium as key dopant to boost the catalytic performance of platinum for alkane dehydrogenation. 2019,

Reilley, D. J.; Popov, K.; Dokholyan, N. V.; Alexandrova, A. N. Uncovered Allosteric Pathway Resolves the Ambiguous Mechanism of Phenylalanine Hydrolase. 2019,

Aubry, T. J.; Axtell, J. C.; Basile, V. M.; Winchell, K. J.; Lindmut, J. R.; Porter, T. M.; Liu, J.-Y.;

Fuller, J.; Wilson, T. R.; Eberhart, M. E.; Alexandrova, A. N. Charge Density in Enzyme Active Site as a Descriptor of

Hou, B.; Shen, L.; Shi, H.; Chen, J.; Zhao, B.; Li, K.; Wang, Y.; Shen, G.; Ha, M-.A.; Liu, F.;

Fuhr, A.; Sautet, P.; Alexandrova, A. N. Heterogeneity in Local Chemical Boding Explains Spectral Broadening in Quantum Dots with Cu Impurities. 2019,

Liu, J.-Y.; Gong, X.-Q.; Alexandrova, A. N. Mechanism of the Catalytic Conversion of CO2 to Methane and Methanol on Defected Anatase TiO2. 2019,

Zandkarimi, B.; Alexandrova, A. N. Dynamics of subnanometer Pt clusters can break the scaling relationships in catalysis. 2019, J. Phys. Chem. Lett.,

Zhang, Z.; Jimenez-Izal, E.; Hermans, I.; Alexandrova, A. N. Dynamic Phase Diagram of Catalytic Surface of Hexagonal Boron Nitride in Conditions

Lai, A.; Alexandrova, A. N.; Diaconescu, P. L. Geomtry change in a series of zirconium cmpounds during lactide ring opening polymerization. 2018,

Jimenez-Izal, E.; Zhai, H.; Liu, J.; Alexandrova, A. N. Nanoalloying MgO-Deposited Pt Clusters with Si for Controlling the Selectivity of Alkane

Popov, I. A.; Jimenez-Izal, E.; Alexandrova, A. N.; Boldyrev, A. I. Multicenter Bonding Effects in Oxygen Vacancy in the Bulk and

Zhai, H.; Alexandrova, A. N. Local Fluxionality of Surface-Deposited Cluster Catalysts: the Case of Pt7 on Al2O3. 2018, J. Phys. Chem. Lett., 9,

Jimenez-Izal, E.; Alexandrova, A. N. Computational Design of Clusters for Catalysis. 2018, Ann. Rev. Phys. Chem., invited article, 69, 377-400. Download

Lei, J.; Yeung, M. T.; Robinson, P. J.; Mohammedi, R.; Turner, C. L.; Yan, J.; Kavner, A.; Alexandrova, A. N.;

Thomas, J. C.; Goronzy, D. P.; Serino, A. C.; Auluck, H. S.; Irving, O. R.; Jimenez-Izal, E.; Sautet, P.; Alexandrova,

Baxter, E. T.; Ha, M.-A.; Cass, A. C.; Zhai, H.; Alexandrova, A. N.; Anderson, S. L. Diborane Interactions with Pt7/alumina: Preparation

Robinson, P. J.; Liu, G.; Ciborowski, S.; Martinez-Martinez, C.; Chamorro, J. R.; McQueen, T. M.; Bowen, K. H.; Alexandrova, A.

Alexandrova, A. N. Divide-and-Conquer Chemical Bonding Models for Materials: a Tool for Materials Design at the Electronic Level. 2017, Chem. Mater., 29,

Dyck, O.; Kim, S.; Jimenez-Izal, E.; Alexandrova, A. N.; Kalinin, S. V.; Jesse, S. Building Structures Atom-by-Atom via Electron Beam Manipulation. 2018,

Ha, M.-A.; Baxter, E. T.; Cass, A. C.; Anderson, S. L.; Alexandrova, A. N. Boron Switch for Selectivity of Catalytic Dehydrogention

Morgenstern, A.; Jaszai, M.; Eberhart, M. E.; Alexandrova, A. N. Quantified Electrostatic Preorganization in Enzymes Using the Geometry of the Electron

Baxter, E. T.; Ha, M.-A.; Cass, A. C.; Alexandrova, A. N.; Anderson, S. L. Ethylene Dehydrogenation on Pt4,7,8 clusters on Al2O3: Strong

Cui, Z.; Jimenez-Izal, E.; Alexandrova, A. N. Prediciton of Two-dimensional Phase of Boron with Anisotropic Electric Conductivity. 2017, J. Phys. Chem. Lett.,

Robinson, P. J.; Zhang, X.; McQueen, T. M.; Bowen, K. H.; Alexandrova, A. N. SmB6– Cluster Anion: Covalency Involving f-Orbitals. 2017, J. Phys.

Zhai, H.; Alexandrova, A. N. Fluxionality of Catalytic Clusters: When It Matters and How to Address It. 2017, ACS Catal, 7, 1905-1911. Download

Ugalde, J. M.; Bultinck, P.; Bickelhaupt, F. M.; Alexandrova, A. N. The 4th International Conference on Chemical Bonding. 2016 J. Phys. Chem. A, 120,

Zhai, H.; Alexandrova, A. N. Ensemble-Average Representation of Pt Clusters in Conditions of Catalysis Accessed through GPU Accelerated Deep Neural Network

Jimenez-Izal, E.; Saeys, M.; Alexandrova, A. N. Metallic and Magnetic 2D Materials Containing Planar Tetracoordinated C and N. 2016, J. Phys. Chem.

Zhang, X.; Ganrefoer, G.; Alexandrova, A. N.; Bowen, K. Photoelectron Spectroscopic and Computational Study of the PtMgH3,5– Cluster Anions. 2016, Phys. Chem. Chem.

Gallup, N. M.; Alexandrova, A. N. Use of QM/DMD as a Multiscale Approach to Modelling Metalloenzymes. 2016, Methods in Enzymology, 577, 319-399. Download

Messina, M.; Axtell, J.; Wang, Y.; Chong, P.; Wixtrom, A.; Kirlikovali, K.; Upton, B.; Hunter, B.; Shaafat, O.; Khan, S.;

Nechay, M. R.; Gallup, N. M.; Morgenstern, A.; Smith, Q. A.; Eberhart, M. E.; Alexandrova, A. N. Histone Deacetylase 8: Characterization

Robinson, P. J.; Alexandrova, A. N.* Assessing the bonding properties of individual molecular orbitals. 2015, J. Phys. Chem. A, 119, 12862-12867. Download.

Qiu, Z.; Zeng, G.; Ha, M.-A.; Hou, B.; Mechlenburg, M.; Shi, H.; Alexandrova, A. N.; Cronin, S. B. Microscopic study of

Moise, G.; Gallup, N. M.; Alexandrova, A. N.; Hengge, A. C.;* Johnson, S. J.* Conservative tryptophan mutants of the protein-tyrosine phosphatase

Valdez, C. E.; Morgenstern, A.; Eberhart, M. E.; Alexandrova, A. N. Predictive Methods for Computational Metalloenzyme Redesign – A Test Case

Jimenez-Izal, E.; Alenxadrova, A. N.* sigma-aromaticity in polyhydride complexes of Ir, Os, and Pt. 2016, Phys. Chem. Chem. Phys., 18, 11644-11652. Invited article

Zhang, X.; Robinson, P. J.; Alexandrova, A. N.*; Bowen, K. H.* Photoelectron Spectroscopic and Theoretical Study of the [HPd(nu2-H2]– Cluster Anion. 2015, J.

Dadras, J.; Jimenez-Izal, E.; Alexandrova, A. N.* Alloying Pt Sub-Nano-Clusters with Boron: Sintering Preventative and Coke Antagonist? 2015, ACS Catal., 5, 5719-5727. Download.

Qiu, J.; Zeng, G.; Ha, M.-A.; Ge, M.; Lin, Y.; Hettick, M.; Alexandrova, A. N.; Javery, A.; Cronin, S. B.* Artificial

Ha, M.-A.; Alexandrova, A. N. Oxygen Vacancies of Anatase 101: Extreme Sensitivity to the Density Functional Theory Method. 2016, J. Chem. Theor.

Zhai, H.; Ha, M.-A.; Alexandrova, A. N.* AFFCK: Adaptive Force Field-Assisted ab initio Coalescent Kick Method for Global Minimum Search. 2015, J.

Nechay, M. R.; Valdez, C. E.; Alexandrova, A. N.* Computational treatment of metalloproteins., 2015, J. Phys. Chem. B., 119, 5945-5956. Feature Article. Journal

Nandula, A.; Trinh, Q. T.; Saeys, M.;* Alexandrova, A. N.* Origin of Extraordinary Stability of Square Planar Carbon in Surface Carbides

Dadras, J.; Shen, L.; Alexandrova, A. N.* Pt-Zn Clusters on MgO(100) and TiO2(110): Dramatically Different Sintering Behavior. 2015, J. Phys. Chem. C,

Nedd, S.; Redler, R. L.; Proctor, E. A.; Dokholyan, N. V.;* Alexandrova, A. N.* Cu,Zn-Superoxide Dismutase without Zn is Folded but

Li, Z.; Gibson, R.; Le, T.; Poddar, T.; Smith, Q. A.; Santsiero, B. D.; Czernin, J.; Alexandrova, A. N.; Jung,

Valdez, C. E.; Smith, Q. A.; Nechay, M. R.; Alexandrova, A. N.* Mysteries of metals in metalloenzymes. 2014, Acc. Chem. Res., 47,

Alexandrova, A. N.;* Bouchard, L.-S. Sub-nano clusters: the last frontier of inorganic chemistry. 2015 Adv. Chem. Phys., 156, pp. 73-100. Eds.: S. A.

Ha, M.-A.; Dadras, J.; Alexandrova, A. N.* Rutile-deposited Pt-Pd clusters: a hypothesis regarding the stability at 50/50 ratio. 2014, ACS Catal., 4,

Nedd, S.; Alexandrova, A. N.* Pd-catalyzed formation of coumarine. A theoretical study. 2015, Phys. Chem. Chem. Phys., 17, 1347-1353. Download

Valdez, C. E.; Gallup, N. M.; Alexandrova, A. N.* Co2+ Acireductone Dioxygenase: Fe2+ Mechanism, Ni2+ Mechanism, or Something Else? 2014, Chem. Phys. Lett., 604, 77-82. Download

Shen, L.; Dadras, J.; Alexandrova, A. N.* Pure and Zn-Doped Pt Clusters Go Flat and Upright on MgO(100). 2014, Phys. Chem. Chem.

Zhang, X.; Bowen, K. H.;* Alexandrova, A. N.* PtAl– and PtAl22– Ions: Theoretical and Photoelectron Spectroscopic Characterization. 2014, J. Chem. Phys., 140, 164316. Download

Zhang, X.; Liu, G.; Gantefoer, G.; Bowen, K. H.;* Alexandrova, A. N.* ZnPtH5–, a sigma-Aromatic Cluster. 2014, J. Phys. Chem. Lett., 4,

Alexandrova, A. N.;* Nechay, M. R.; Lydon, B. R.; Buchan, D. P.; Yeh, A. J.; Tai, M.-H.; Kostrikin, I. P.;

Alexandrova, A. N.;* Huber, S.;* Tavassoli, A.* The 3rd Transatlantic Frontiers in Chemistry Symposium 2013 Chem. Eur. J., 19, 15777-15783. Invited Article Download

Sparta, M.; Valdez, C. E.; Alexandrova, A. N.* Metal-dependent activity of Fe and Ni acireductone dioxygenases: how two electrons reroute the

Murphy, J. M.; Armijo, A. L.; Lee, C. H.; Campbell, D. O.; Li, Z.; Liao, H.-I.; Lee, J. T.; Nathanson,

Zhang, J.; Alexandrova, A. N.* The Golden Crown: How a Single Gold Atom Boosts the CO Oxidation Catalyzed by Palladium Cluster

Baraldi, C.; Freguglia, G.; Tinti, A.; Sparta, M.; Alexandrova, A. N.; Gamberini, M. C.* IR, Raman and SERS spectra of propantheline

Valdez, C. E.; Sparta, M.; Alexandrova, A. N.* The role of the flexible L43-S54 protein loop of the CcrA metallo-beta-lactamase in

Schmidt, N. W.; Lis, M.; Alexandrova, A. N.;* Tew, G. N. ;* Wong, G. L.* Engineering principles of peptide induced me

Sparta, M.; Alexandrova, A. N.* How metal substitution affects the enzymatic activity of COMT. 2012 PLoS ONE, 7, e47172. Download

Ramachandran, S.; Temple, B.; Alexandrova, A. N.; Chaney, S. G.; Dokholyan, N. V.* Recognition of Platinum-DNA adducts by HM GB1a. 2012 Biochemistry, 51,

Sparta, M.; Ding, F.; Shirvanyants, D.; Dokholyan, N. V.;* Alexandrova, A. N.* Hybrid dynamics simulation engine for metalloproteins. 2012 Biophys. J. 103, 767-776. Download

Valdez, C. E.; Alexandrova, A. N.* Why Urease is a di-Nickel Enzyme, whereas the CcrA beta-Lactamase is a di-Zinc Enzyme. 2012 J. Phys.

Kuznetsov, V. I.; Alexandrova, A. N.;* Hengge, A. C.* Metavanadate at the active site of the phosphatase VHZ. 2012 J. Am. Chem. Soc.

Alexandrova, A. N.;* Nayhouse, M. J.; Huynh, M. T.; Kuo, J. L.; Melkonian, A. V.; Chavez, G. De J.; Hernando,

Zhang, J.;* Sergeeva, A. P.; Sparta, M.; Alexandrova, A. N.* Photo-driven Molecular Wankel Engine B13 +. 2012 Angew. Chem. Int. Ed. 51, 8512-8515. Designated as

Alexandrova, A. N.* Tug of war between AO-hybridization and aromaticity in dictating structures of Li-doped alkali clusters. 2012, Chem. Phys. Lett., 533,

Zhang, J.; Alexandrova, A. N.* Double Sigma-Aromaticity in a Surface Deposited Cluster: Pd4 on TiO2 (110). 2012, J. Phys. Chem. Lett., 3, 751-754. Download.

Zhang, J.; Alexandrova, A. N.* Structure, stability, and mobility of small Pd clusters on stoicheometric and defective TiO2 (110) surfaces. 2011, J. Chem.

Alexandrova, A. N.* Quantum Mechanical Insights into Biological Processes at the Electronic Level. In Computational Modeling of Biological Systems: From Moleucles

Alexandrova, A. N.;* Jorgensen, W. L. On the Mechanism and Rate of Spontaneous Decomposition of Amino Acids. 2011, J. Phys. Chem. B,

Huynh, M.; Alexandrova, A. N.* Persistent Covalency and Planarity in the BnAl6-n2- and LiBnAl6-n– (n=1-6) Cluster Ions. 2011, J. Phys. Chem. Lett., 2, 2046-2051. Download

Shirvanyants, D.; Alexandrova, A. N.; Dokholyan, N. V.* Rigid substructure search. 2011, Bioinformatics, 27, 1327-1329. Download

Sparta, M.; Alexandrova, A. N.* Computational design and characterization of artificial enzymes for Kemp elimination. 2011, Molecular Simulation (Recent Advances in Molecular

Alexandrova, A. N.;* Boldyrev, A. L.; Li, X.; Sarkas, H. W.; Hendricks, J. H.; Arnold , S. T.; Bowen, K.

Alexandrova, A. N.* H(H2O)n Clusters – Microsolvation of Hydrogen Atom via Molecular ab initio Gradient Embedded Genetic Algorithm (GEGA). 2010, J. Phys. Chem.

Alexandrova, A. N.* Promiscuous DNA Alkyladenine Glycosylase Dramatically Favors a Bound Lesion Over Undamaged Adenine. 2010, Biophys. Chem., 152, 118-127. Download

Alexandrova, A. N.;* Tully, J. C.; Granucci, G. Photochemistry of DNA Fragments via Semiclassical Nonadiabatic Dynamics. 2010, J. Phys. Chem. B 114,

Bopp, J. C.; Alexandrova, A. N.; Elliott, B. M. Herden, T.; Johnson, M. A. Infrared vibrational spectra of On– n = 3-10,12

Alexandrova, A. N.;* Jorgensen, W. L. Origin of the Activity Drop with the E50D Variant of Catalytic Antibody 34E4 for Kemp

Alexandrova, A. N.; Roethlisberger, D.; Baker, D.; Jorgesen, W. L. Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination. J.

Jorgensen, W. L.; Jensen, K. P.; Alexandrova, A. N. Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water. J. Chem. Theor.

Alexandrova, A. N.; Jorgensen, W. L. Why Urea Eliminates Ammonia Rather Than Hydrolyzes in Aqueous Solution. J. Phys. Chem. B 111, 720-730, 2007. Download

Alexandrova, A. N.; Boldyrev, A. I.; Zhai, H.-J.; Wang, L.-S. All-Boron Aromatic Clusters as Potential New Inorganic Ligands and Building Blocks

Zubarev, D. Yu.; Alexandrova, A. N.; Boldyrev, A. I.; Cui, L.-F.; Li, X.; Wang, L.-S. Alteration of Si62- Structure upon Na+ Coordination in

Alexandrova, A. N.; Koyle, E.; Boldyrev, A. I. Theoretical Study of Hydrogenation of Doubly-Aromatic B7– . J. Mol. Model., 2006, 12, 569-576. Download

Alexandrova, A. N.; Boldyrev, A. I. Search for the Lix0/+1/-1 Lowest Energy Structures Using Ab Initio Gradient Embedded Genetic Algorithm (GEGA). Elucidation

Alexandrova, A. N.; Boldyrev, A. I.; Zhai, H.-J.; Wang, L.-S. Doubly-Antiaromatic All-Boron Ligand B62- in the LiB6– molecule. Ab Initio and Photoelectron Spectroscopic

Alexandrova, A. N.; Boldyrev, A. I.; Zhai, H.-J.; Wang, L.-S. Cu3C4– – a New Sandwich Molecule with Two Revolving C22–Units. J. Phys. Chem.

Alexandrova, A. N.; Boldyrev, A. I.; Fu, Y.-J.; Yang, X.; Wang, X.-B.; Wang, L.S. Structure of the NaxClx+1– (x=1-4) Clusters via Ab

Alexandrova, A. N.; Zhai, H.-J.; Wang, L.-S.; Boldyrev, A. I. Molecular Wheel B82- as a New Inorganic Ligand: Photoelectron Spectroscopy and Ab

Alexandrova, A. N.; Boldyrev, A. I. Arachno-, Nido- and Closo-Aromatic Isomers of the Li6B6H6 Molecul. Inorg. Chem., 43, 3588, 2004. Download

Alexandrova, A. N.; Boldyrev, A. I.; Zhai, H.-J.; Wang, L.-S. Electronic Structure, Isomerism, and Chemical Bonding in B7– and B7 J. Phys. Chem.

Zhai, H.-J.; Alexandrova, A. N.; Wang, L.-S.; Boldyrev, A. I. Hepta- and Octacoordinate Boron in Molecular Wheels of Eight- and Nine-Atom

Zhai, H.-J.; Wang, L.-S.; Alexandrova, A. N.; Boldyrev, A. I.; Zakzewski, V. G. Photoelectron Spectroscopy and Ab Initio Study of B3– and

Alexandrova, A. N.; Birch, K. A.; Boldyrev, A. I. Flattening the B6H62- Octahedron. Ab Initio Prediction of the New Family of Planar

Alexandrova, A. N.; Boldyrev, A. I.; Zhai, H.-J.; Wang, L.-S.; Steiner, E.; Fowler, P. W. Structure and Bonding in B6– and B6:

Elliott, B. M.; Alexandrova A. N.; Boldyrev, A. I. Hydrogen Trioxide Anion: A Possible Atmospheric Intermediate and Path of Oxygen-Rich Molecules. J.

Alexandrova, A. N.; Boldyrev, A. I. sigma-Aromaticity and sigma-Antiaromaticiy in Alkaline Metal and Alkaline Earth Metal Small Clusters. J. Phys. Chem. A,

Zhai, H.-J.; Wang, L.-S.; Alexandrova, A. N.; Boldyrev, A. I. Electronic Structure and Chemical Bonding of B5– and B5 by Photoelectron Spectroscopy and