.. _research: Research ========== We develop theoretical and computational approaches targeting the electronic structure and interactions in extended systems, such as photosynthetic and fluorescent proteins, molecular solids, polymers, and bulk liquids. With these tools, we investigate fundamental aspects of non-covalent interactions and the effect of the environment on electronic structure. This page highlights our recent work in these exciting areas. .. _photosynthesis: Energy and electron transfer in photosynthesis ----------------------------------------------- Efficiency and rates of energy transfer in photosystems are controlled by the protein environment. Geometries and relative orientations of chromophores, chlorophylls and carotenoids, are determined by the shapes of protein cavities, whereas electronic excited states of the chromophores is affected by non-uniform electric fields due to the protein. Can we understand and predict the protein effects on the optical spectroscopy and energy transfer in photosynthetic proteins? See below... .. container:: image-text-block .. image:: _static/research_images/fmo_mutant.jpeg :alt: fmo_mutant :width: 50% :align: left | `Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic Proteins from First Principles: The Fenna-Matthews-Olson Complex Example `_ | Yongbin Kim, Zach Mitchell, Jack Lawrence, Dmitry Morozov, Sergei Savikhin, Lyudmila V. Slipchenko | J. Phys. Chem. Lett. 2023, 14, 31, 7038-7044 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/fmo_wt.jpeg :alt: fmo_wt :width: 50% :align: left | `Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna-Matthews-Olson Complex `_ | Yongbin Kim, Dmitry Morozov, Valentyn Stadnytskyi, Sergei Savikhin, Lyudmila V. Slipchenko | J. Phys. Chem. Lett. 2020, 11, 5, 1636-1643 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/fmo_fmo.jpeg :alt: fmo_fmo :width: 50% :align: left | `FMOxFMO: Elucidating Excitonic Interactions in the Fenna–Matthews–Olson Complex with the Fragment Molecular Orbital Method `_ | Danil S. Kaliakin, Hiroya Nakata, Yongbin Kim, Qifeng Chen, Dmitri G. Fedorov, Lyudmila V. Slipchenko | J. Chem. Theory Comput. 2020, 16, 2, 1175-1187 .. raw:: html
.. _vibronic: Excitonic and vibronic interactions ------------------------------------ Theoretical description of energy transfer in a multi-chromophore systme requires two components, namely: - accurate description of the electronic structure of photoactive pigments - ability to model electronic and vibronic couplings that enable efficient energy transfer between the pigments The excited-state QM/EFP and FMO methods address the former - see :ref:`photosynthesis` and :ref:`method development`. To target the second aspect, we develop vibronic models of the Fulton-Gouterman type. Our vibronic model can efficiently treat multiple vibrational modes in multi-chromophore systems. .. container:: image-text-block .. image:: _static/research_images/wscp_vibronic.jpeg :alt: wscp_vibronic :width: 50% :align: left | `Controlling Vibronic Coupling in Chlorophyll Proteins: The Effects of Excitonic Delocalization and Vibrational Localization `_ | Galina Grechishnikova, Jacob H. Wat, Nicolas de Cordoba, Ethan Miyake, Amala Phadkule, Amit Srivastava, Sergei Savikhin, Lyudmila Slipchenko, Libai Huang, Mike Reppert | J. Phys. Chem. Lett. 2024, 15, 37, 9456-9465 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/tt_transfer.jpeg :alt: triplet-triplet et :width: 50% :align: left | `Triplet-Triplet Coupling in Chromophore Dimers: Theory and Experiment `_ | Daniel A. Hartzler, Lyudmila V. Slipchenko, Sergei Savikhin | J. Phys. Chem. A 2018, 122, 33, 6713-6723 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/dpm.png :alt: dpm :width: 50% :align: left | `Vibronic coupling in asymmetric bichromophores: Theory and application to diphenylmethane-d5 `_ | Benjamin Nebgen and Lyudmila V. Slipchenko | J. Chem. Phys. 141, 134119 (2014) .. raw:: html
.. _non-covalent: Ubiquitous non-covalent interactions -------------------------------------- Non-covalent interactions govern the structure and functions of biological macromolecules such as DNA and proteins, the properties of condensed phase species like liquids and colloids, and adsorption processes of molecules on surfaces and interfaces. We investigate the nature of non-covalent interactions in molecular clusters, heterogeneous liquids, molecular interfaces, and biological systems. In many systems we consider the non-covalent interactions of different types (e.g., electrostatic and dispersive forces) compete with each other. While these situations are challenging for theory and require a balanced description of different non-covalent forces, they provide a rich variety of structural and bonding patterns that exhibit themselves in complicated spectroscopic observables. .. container:: image-text-block .. image:: _static/research_images/tba_microheterogeneity.jpeg :alt: tba microheterogeneity :width: 50% :align: left | `Quantifying the Nearly Random Microheterogeneity of Aqueous tert-Butyl Alcohol Solutions Using Vibrational Spectroscopy `_ | Andres S. Urbina, Lyudmila V. Slipchenko, and Dor Ben-Amotz | J. Phys. Chem. Lett. 2023, 14, 50, 11376-11383 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/cd2k.png :alt: cd2k :width: 50% :align: left | `Rationalizing Protein-Ligand Interactions via the Effective Fragment Potential Method and Structural Data from Classical Molecular Dynamics <>` | Andres S. Urbina and Lyudmila V. Slipchenko | J. Chem. Phys, in press .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/xylene.jpeg :alt: xylene :width: 50% :align: left | `The unusual symmetry of hexafluoro-o-xylene—A microwave spectroscopy and computational study `_ | Sven Herbers; Sean M. Fritz; Piyush Mishra; Yongbin Kim; Lyudmila Slipchenko; Timothy S. Zwier | J. Chem. Phys. 152, 064302 (2020) .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/pyrimidine_co2.jpeg :alt: Pyrimidine_co2 :width: 50% :align: left | `Capturing CO2 in Quadrupolar Binding Pockets: Broadband Microwave Spectroscopy of Pyrimidine-(CO2)n, n = 1,2 `_ | Blair A. Welsh, Andres S. Urbina, Tuan A. Ho, Susan L. Rempe, Lyudmila V. Slipchenko, Timothy S. Zwier | J. Phys. Chem. A 2024, 128, 6, 1124-1133 .. raw:: html
.. _method development: Method and software development -------------------------------- Calculations in the condensed phase still remain a major challenge to the theoretical community. The increased number of nuclear and electronic degrees of freedom makes accurate *ab initio* calculations of a condensed phase system unfeasible long before the system can approach the bulk. One general approach is then to separate a system into two parts, such that one (active) part is treated by quantum mechanical (QM) techniques, and the other, usually larger, part is calculated by using classical (molecular) mechanics (MM), which is referred to as QM/MM. However, the accuracy of QM/MM models might suffer both from inaccurate force field parameters and intrinsic limitations of the MM force field functional form. In order to overcome this problem, we utilize the Effective Fragment Potential (EFP) method, which is the *ab initio*-based polarizable force field. .. image:: _static/research_images/libefp_logo.png :alt: libefp logo :width: 50% :align: left Our EFP and QM/EFP methods are available in the GAMESS, Q-Chem and Psi4 electronic structure packages, and in our own LibEFP software library. .. note:: Check out our `EFP website `_ that provides up-to-date information on the EFP development, documentation and tutorials! .. container:: image-text-block .. image:: _static/research_images/ani_efp.jpeg :alt: ani-efp :width: 50% :align: left | `ANI/EFP: Modeling Long-Range Interactions in ANI Neural Network with Effective Fragment Potentials `_ | Shahed Haghiri, Claudia Viquez Rojas, Sriram Bhat, Olexandr Isayev, Lyudmila Slipchenko | J. Chem. Theory Comput. 2024, 20, 20, 9138-9147 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/qmefp_pieda.jpeg :alt: qmefp_pieda :width: 50% :align: left | `Detangling Solvatochromic Effects by the Effective Fragment Potential Method `_ | Lyudmila_Slipchenko | J. Phys. Chem. A 2024, 128, 3, 656-669 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/flex_efp.jpeg :alt: flex_efp :width: 50% :align: left | `Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database `_ | Yongbin Kim, Yen Bui, Ruslan N. Tazhigulov, Ksenia B. Bravaya, Lyudmila V. Slipchenko | J. Chem. Theory Comput. 2020, 16, 12, 7735-7747 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/exrep_exstates.jpeg :alt: qmefp exrep exstates :width: 50% :align: left | `Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding `_ | Claudia I. Viquez Rojas, Lyudmila V. Slipchenko | J. Chem. Theory Comput. 2020, 16, 10, 6408-6417 .. raw:: html
.. container:: image-text-block .. image:: _static/research_images/qmefp_disp.jpeg :alt: qmefp disp :width: 50% :align: left | `Dispersion Interactions in QM/EFP `_ | Lyudmila V. Slipchenko, Mark S. Gordon, Klaus Ruedenberg | J. Phys. Chem. A 2017, 121, 49, 9495-9507 .. raw:: html