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    The core of this program is the design of new functional materials (artificial metalloenzymes, heterogeneous catalysis, alloys, molecular motors), guided by insights into chemical bonding, and accompanied by the development of the modern theory of chemical bonding. Since we are interested in materials' functions, we model materials and interfaces in a maximally relastic way, often playing with metastable structures and their ensembles emerging only in conditions of pratical use. We develop the necessary multi-scale modeling methods, which combine quantum mechanics, statistical mechanics, sometimes empyrical approaches, and are powered by algorithms of artificial intellegence and machine learning. Both applied and method-development efforts are prominent in the group, and we are a warm home for students of many different backgrounds, from chemistry and biochemistry, to physics, computer science, and applied mathematics.



    Over the years, this research has been powered by:
    1. Design of artificial enzymes

    We aim at designing catalysts that mimic natural enzymes in catalytic strategies, but catalyze reactions that interest humankind. This effort is presently fundamental. However, eventually, it might lead to unprecidented catalytic processes, green, efficient, and inexpensive, used at an industrial scale. The philosophy of this area of research is that the effort is largely done in silico, and experiment is envoked only at the end of the workflow to check theoretical predictions. Modeling of enzymes is done with atomistic and electronic insight. We develop fast techniques for mixed quantum-classical simulations and design. A particular interest is in metalloenzymes, which may containin non-physiological metals of the highest catalytic potency. At the moment we are particularly ponder the quenstion of electrostatic preorganization as one of the major driving forces behind the catalytic power of enzymes, and ways to incorportae it in our design protocols.

    Selected References:

    Morgensetern, A.; Jaszai, M.; Eberhart, M. E.; Alexandrova, A. N. Quantifying Electrostatic Preorganization in Enzymes Using the Geometry of Charge Density. 2017, Chem. Sci., 8, 5010-5018.

    Valdez, C. E.; Morgenstern, A.; Eberhart, M. E.; Alexandrova, A. N. Predictive Methods for Computational Metalloenzyme Reddesign - A Test Case with Carboxypeptidase A. 2016, Phys. Chem. Chem. Phys., 18, 31744-31756.

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

    Valdez, C. E.; Smith, Q. A.; Nechay, M. W.; Alexandrova, A. N.* Mysteries of metals in metalloenzymes. 2014, Acc. Chem. Res., 47, 3110-3117.

    Sparta, M.; Valdez, C. E.; Alexandrova, A. N.* Metal-dependent activity of Fe and Ni acireductone dioxygenases: how two electrons reroute the catalytic pathway. 2013 J. Mol. Biol., 245, 3007-3018. Featured on the Cover

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

    Valdez, C. A.; Alexandrova, A. N.* Why Urease is a di-Nickel Enzyme, whereas the CcrA beta-Lactamase is a di-Zinc Enzyme. 2012 J. Phys. Chem. B., DOI: 10.1021/jp302771n. PDF

    Shirvanyants, D.; Alexandrova, A. N.; Dokholyan, N. V.* Rigid substructure search, 2011, Bioin formatics, 27, 1327-1329. PDF

    2. Realistic heterogeneous catalytic interfaces

    We study a variety of heterogeneous catalytic interfaces, approaching in modeling the realistic representation of catalytic conditions. In particular, semiconductor supports decorated with sub-nano clusters of transition metals are of interest. We find that clusters in the presence of adsorbates and at increased temperatures are dynamic, fluxional, and adopt a variety of shapes. Hence, the catalytic activity, which is known to be a function of cluster size and composition, is an ensemble average property. It is additionally often likely that not the most stable, but the less stable and yet thermally accessible cluster isomers are responsible for the majority of the catalytic effect. Other types of functional surfaces where this new paradigm holds up include electrocatalytic interfaces, corroding surfaces, and any kind of surface prone to the formation of defects, and reconstructions in conditions of practical use. We describe such interfaces using novel state-of-the-art algorithms that include electronic structure calculations, statistical mechanics, and elements of machine learning (such as Neural Networks). Of a great current interest are quesitons of dynamics, dynamic coupling of fluxionality to the reaction, thermodynamics and kinetics of the ensembles of surface states.

    Selected References:

    Ha, M.-A.; Baxter, E. T.; Cass, A. C.; Anderson, S. L.; Alexandrova, A. N. Boron Switch for Selectivity of Catalytic Dehydrogenation on Size-Selected Pt clusters on Al2O3. 2017, J. Am. Chem. Soc., 139, 11568-11575.

    Baxter, E. T.; ha, M.-A.; Cass, A. C.; Alexandrova, A. N.; Anderson, S. L. Ethylene Dehydrogenaiton of Pt4,7,8 clusters on Al2O3: Strong Cluster-Size Dependence Linked to Preferred Catalyst Morphologies. 2017, ACS Catal, 7, 3322-3335.

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

    Zhai, H.; Alexandrova, A. N. Ensemble-Average Representaiton of Pt Clusters in Conditions of Catalysis Accessed through GPU Accelerated Deep Neural Network Fitting Globa Optimization. 2016, J. Chem. Theor. Comput., 12, 6213-6226.

    Ha, M.-A.; Dadras, J.; Alexandrova, A. N.* Rutile-supported Pt-Pd clusters: a hypothesis regarding the stability at 50/50 ratio. 2014, ACS Catal., Special issue on computational catalysis, 4, 3570-3580.

    Zhang, J.; Alexandrova, A. N.* Structure, stability, and mobility of small Pd clusters on stoicheomet ric and defective TiO2 (110) surfaces. 2011, J. Chem. Phys., 135, 174702


    3. Chemical bonding in materials, and materials design

    We develop the fundamental theory of chemical bonding for materials, both in 2-D and in 3-D, with the aim of rationalizaiton of their structures and properties, and eventual design that would not involve screenings or machine learning, but rather would be guided by the principles of electronic structure. Of interest are ultra-hard alloys (collaboraiton with Profs. Sarah Tolbert, Richard Kaner in UCLA), strongly-correlated materials (collaboration with Profs. McQueen and Bowen in Hopkins), new 2-D materials with interesting electronic and magnetic properties.

    Selected References:

    Robinson, P. J.; Liu, G.; Ciborowski, S.; Martinez-Martinez, C.; Chamorro, J.; McQueen, T. M.; Bowen, K. H.; Alexandrova, A. N. Mystery of Three Borides: Differential Metal-Boron Bonding Governing Superhard Structures. 2017, Chem. Mater., DOI: 10.1021/acs.chemmater.7b04378.

    Alexandrova, A. N. Divide-and-Conquer Chemical Bonding Models for Materials: a Tool for Materials Design at the Electronic Level. 2017, Chem. Mater., 29, 8555-8565.

    Cui, Z.; Jimenez-Izal, E.; Alexandrova, A. N. Prediciton of Two-Dimensional Phase of Boron with Anisotropic Electric Conductivitiy. 2017, J. Phys. Chem. Lett., 8, 1224-1228.

    Jimenez-Izal, E.; Saeys, M.; Alexandrova, A. N. Metallic and Magnetic 2D Materials Containing Planar Tetracoordinated C and N. 2016, J. Phys. Chem. C., 120, 21685-21690.

    Nandula, A.; Trinh, Q. T.; Saeys, M.; Alexandrova, A. N. Origin of Extraordinary Stability of Square Planar Carbon in Surface Carbides of Co, Ni, and Beyond. 2015, Angew. Chem. Int. Ed., VIP paper, 54,5312-5316.

    Some Regalia:
We are on the cover of JMB 2013

We are on the cover of CPL 2012

We are on the cover of JPC A 2005

We are on the inside cover of PCCP 2012



C&E News, 2013





C&E News, 2005



We are highlighted in Nat. Nanotech 2012

We are in UCLA Today

UCLA Today again

In NY Times

Jin is in Departmental News

In Chemistry World 2014

UCLA Today on Crystal's Lindau Award

ICCB 2014 on cover of C&E News!

We are on the cover of PCCP, 2014

We are on the cover of JPC B, 2015