Publications ============ `Google Scholar page `_ 2024 ---- * Mike Reppert, Rajesh Dutta, Lyudmila Slipchenko, The interplay of excitonic delocalization and vibrational localization in optical lineshapes: A variational polaron approach J. Chem. Phys. 161, 154109 (2024) `Link `_ * Shahed Haghiri, Claudia Viquez Rojas. Sriram Bhat, Olexandr Isayev, Lyudmila Slipchenko*, ANI/EFP: Modeling Long-Range Interactions in ANI Neural Network with Effective Fragment Potentials J. Chem. Theory Comput. 2024, 20, 20, 9138–9147 `Link `_ * Galina Grechishnikova, Jacob H. Wat, Nicolas de Cordoba, Ethan Miyake, Amala Phadkule, Amit Srivastava, Sergei Savikhin, Lyudmila Slipchenko, Libai Huang, and Mike Reppert*, Controlling Vibronic Coupling in Chlorophyll Proteins: The Effects of Excitonic Delocalization and Vibrational Localization J. Phys. Chem. Lett. 2024, 15, 37, 9456–9465 `Link `_ * Roadmap on methods and software for electronic structure based simulations in chemistry and materials Electron. Struct. 6 (2024) 042501 `Link `_ * Lujun Luo , Antoine P. Martin, Elijah K. Tandoh, Andrei Chistoserdov, Lyudmila V. Slipchenko, Sergei Savikhin*, and Wu Xu*, Impact of Peripheral Hydrogen Bond on Electronic Properties of the Primary Acceptor Chlorophyll in the Reaction Center of Photosystem IInt. J. Mol. Sci. 2024, 25(9), 4815 `Link `_ * Blair A. Welsh, Andres S. Urbina, Tuan A. Ho, Susan L. Rempe, Lyudmila V. Slipchenko, and Timothy S. Zwier*, Capturing CO2 in Quadrupolar Binding Pockets: Broadband Microwave Spectroscopy of Pyrimidine-(CO2)n, n = 1,2, J. Phys. Chem. A 2024 128 (6), 1124-1133 `Link `_ * Lyudmila V. Slipchenko*, Detangling Solvatochromic Effects by the Effective Fragment Potential Method, J. Phys. Chem A 2024 128 (3), 656-669 `Link `_ * Andres S. Urbina, Lyudmila V. Slipchenko, and Dor Ben-Amotz*, Quantifying the Nearly Random Microheterogeneity of Aqueous tert-Butyl Alcohol Solutions Using Vibrational Spectroscopy, J. Phys. Chem. Lett. 2023 14 (50), 11376-11383 `Link `_ 2023 ---- * Early-Career and Emerging Researchers in Physical Chemistry Volume 2, J. Phys. Chem. B 2023 127 (43), 9211-9214 `Link `_ * Yongbin Kim, Zach Mitchell, Jack Lawrence, Dmitry Morozov, Sergei Savikhin, and Lyudmila V. Slipchenko*, Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic Proteins from First Principles: The Fenna–Matthews–Olson Complex Example, J. Phys. Chem. Lett. 2023 14 (31), 7038-7044 `Link `_ * Patrick K. Wise, Lyudmila V. Slipchenko, and Dor Ben-Amotz*, Ion-Size Dependent Adsorption Crossover on the Surface of a Water Droplet, J. Phys. Chem. B 2023 127 (20), 4658-4665 `Link `_ 2022 ---- * West, C.P., Mesa Sanchez, D., Morales, A.C., Hsu, Y.J., Ryan, J., Darmody, A., Slipchenko, L.V., Laskin, J. and Laskin, A.*, Molecular and Structural Characterization of Isomeric Compounds in Atmospheric Organic Aerosol Using Ion Mobility-Mass Spectrometry, J. Phys. Chem. A, 127(7), 1656-1674 `Link `_ * Watanabe Y, Washer BM, Zeller M, Savikhin S, Slipchenko LV, Wei A. Copper (I)–Pyrazolate Complexes as Solid-State Phosphors: Deep-Blue Emission through a Remote Steric Effect. J. Amer. Chem. Soc. 144(23):10186-92 `Link `_ * A.J. Bredt, Y. Kim, D. Mendes de Oliveira, A.S. Urbina, L.V. Slipchenko, D. Ben-Amotz*, Expulsion of Hydroxide Ions from Methyl Hydration Shells, J. Phys. Chem. B, 126, 4, 869–877 `Link `_ 2021 ---- * Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package, J. Chem Phys 155(8) `Link `_ * A.J. Bredt, D. Mendes de Oliveira, A.S. Urbina, L.V. Slipchenko, D. Ben-Amotz*, Hydration and seamless integration of hydrogen peroxide in water, J. Phys. Chem. B 125(25) 6986-6993 `Link `_ 2020 ---- * Yongbin Kim, Yen Bui, Ruslan N. Tazhigulov, Ksenia B. Bravaya, Lyudmila V. Slipchenko*, Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database, J. Chem. Theory Comput. 16(12) 7735–7747 `Link `_ * Sven Herbers, Sean M Fritz, Piyush Mishra, Yongbin KimG, Lyudmila Slipchenko, Timothy S Zwier*, The unusual symmetry of hexafluoro-o-xylene—A microwave spectroscopy and computational study, J. Chem. Phys. 152(6) 064302 `Link `_ * James RW Ulcickas, Ziyi Cao, Jiayue Rong, Charles A Bouman, Lyudmila V Slipchenko, Gregery T Buzzard, Garth J Simpson*, Multi-Agent Consensus Equilibrium (MACE) In Molecular Structure Determination, J. Phys. Chem. A 124 (43) 9105-9112 `Link `_ * Recent developments in the general atomic and molecular electronic structure system, J. Chem. Phys. 152 (15) 154102 `Link `_ * Yongbin Kim, Dmitry Morozov, Valentyn Stadnytskyi, Sergei Savikhin, Lyudmila V Slipchenko*, Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna–Matthews–Olson Complex, J. Phys. Chem. Lett. 11(5) 1636-1643 `Link `_ * Claudia I Viquez Rojas, Lyudmila V Slipchenko*, Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding, J. Chem. Theory Comput. 16(10) 8408-6417 `Link `_ 2019 ---- * Danil S Kaliakin, Hiroya Nakata, Yongbin Kim, Qifeng Chen, Dmitri G Fedorov, Lyudmila V Slipchenko*, FMOxFMO: Elucidating Excitonic Interactions in the Fenna–Matthews–Olson Complex with the Fragment Molecular Orbital Method, J. Chem. Theory Comput. 16 (2), 1175-1187 `Link `_ * Nathanael M Kidwell, Benjamin Nebgen, Lyudmila V Slipchenko, Timothy S Zwier*, The effects of site asymmetry on near-degenerate state-to-state vibronic mixing in flexible bichromophores, J. Chem. Phys. 151 (8), 084313 `Link `_ * R. Tazhigulov, P.K. Gurunathan, Y. Kim, L.V. Slipchenko, K.B. Bravaya*, Polarizable Embedding for Simulating Redox Potentials of Biomolecules, Phys. Chem. Chem. Phys., 21 (22) 11642-11650 `Link `_ 2018 ---- * L.I. Mosquera-Giraldo, C.H. Borca, A.S. Parker, Y. Dong, K.J. Edgar, S.P. Beaudoin, L.V. Slipchenko, L.S. Taylor*, Crystallization Inhibition Properties of Cellulose Esters and Ethers for a Group of Chemically Diverse Drugs: Experimental and Computational Insight, Biomacromolecules, 19 (12), 4593–4606 `Link `_ * D.A. Hartzler, L.V. Slipchenko*, S. Savikhin*, Triplet-triplet coupling in chromophore dimers: Theory and experiment, J. Phys. Chem. A, 122, 6713-6723 `Link `_ * Viquez-Rojas, J. Fine, L.V. Slipchenko*,Exchange-Repulsion Energy in QM/EFP, J. Chem. Phys., 149(9) 094103 `Link `_ * N. Mugheirbi, L. Mosquera-Giraldo, C. Borca, L.V. Slipchenko, L. Taylor*, Phase Behavior of Drug-Hydroxypropyl Methylcellulose Amorphous Solid Dispersions Produced from Various Solvent Systems: Mechanistic Understanding of the Role of Polymer using Experimental and Theoretical Methods, Mol. Pharmaceutics, 15 (8), 3236–3251 `Link `_ 2017 ---- * N. Dubinets, L.V.Slipchenko*, Effective Fragment Potential method for H-bonding: How to obtain parameters for non-rigid fragments, J. Phys. Chem. A, 121 (28), 5301–5312 `Link `_ * S. Tyler, E. Judkins, D. Morozov, C. Borca, L.V. Slipchenko, D. McMillin*, To Be or Not to Be Symmetric: That is the Question for Potentially Active Vibronic Modes, J. Chem. Educ., 94 (9), 1232–1237 `Link `_ * L.V. Slipchenko*, K. Ruedenberg, M.S. Gordon, Dispersion interactions in QM/EFP, J. Phys. Chem. A, 121 (49), 9495–9507 `Link `_ * O.N. Rogacheva, S.A. Izmailov, L.V. Slipchenko, N.R. Skrynnikov*, A new structural arrangement in proteins involving lysine NH3+ group and carbonyl, Sci. Reports, 7, 16402 `Link `_ * Bertoni, L.V. Slipchenko, A.J. Misquitta, and M.S. Gordon*, Multipole Moments in the Effective Fragment Potential Method, J. Phys. Chem. A 121 (9), 2056–2067 `Link `_ 2016 ---- * N. Li, L.I. Mosquera-Giraldo, C.H. Borca, J.D. Ormes, M. Lowinger, J.D. Higgins, L.V. Slipchenko, and L.S. Taylor*, A Comparison of the Crystallization Inhibition Properties of Bile Salts, Cryst. Growth Des. 16 (12), 7286–7300 `Link `_ * L.I. Mosquera-Giraldo, C.H. Borca, X. Meng, K.J. Edgar, L.V. Slipchenko, and L.S. Taylor*, Mechanistic Design of Chemically Diverse Polymers with Applications in Oral Drug Delivery, Biomacromolecules 17 (11), 3659–3671 `Link `_ * J.D. Rindelaub, C.H. Borca, M.A. Hostetler, J.H. Slade, M.A. Lipton, L.V. Slipchenko, and P.B. Shepson*, The acid-catalyzed hydrolysis of an α-pinene-derived organic nitrate: kinetics, products, reaction mechanisms, and atmospheric impact, Atmos. Chem. Phys., 16, 15425-15432 `Link `_ * M. C. Green, L.J. Dubnicka, A.C. Davis, H.A. Rypkema, J.S. Francisco, and L.V. Slipchenko*, Thermodynamics and kinetics for the free radical oxygen protein oxidation pathway in a model for β-structured peptides, J. Phys. Chem. A, 120, 2493-2503 `Link `_ * P.K. Gurunathan, A. Acharya, D. Ghosh, D. KosenkovP, I. KalimanP, Y. Shao, A.I. Krylov*, L.V. Slipchenko*, The Extension of the Effective Fragment Potential Method to Macromolecules, J. Phys. Chem. B, 120, 6562-6574 `Link `_ * C. Borca, L.V. Slipchenko*, A. Wasserman*, Ground-state charge transfer: Lithium-benzene and the role of Hartree-Fock exchange, J. Phys. Chem A, 120(41), 8190-8198 `Link `_ * Xiong, C. H. Borca, L. V. Slipchenko and P. B. Shepson*, Photochemical Degradation of Isoprene-derived 4,1-Carbonyl Nitrate, ACP, 16, 5595-5610 `Link `_ * M.C. Green, H. Nakata, D. Fedorov, L.V. Slipchenko, Radical damage in lipids investigated with the fragment molecular orbital method, Chem. Phys. Lett., 651, 56-61 `Link `_ * R.E. Stoller, A. Tamm, L.K. Beland, G. D. Samolyuk, G. M. Stocks, A. Caro, L.V. Slipchenko, Yu.N. Osetsky, A. Aabloo, M. Klintenberg, and Y. Wang, Impact of Short-range Forces on Defect Production from High-energy Collisions, J. Chem. Theory Comp. 12, 2871–2879 `Link `_ 2015 ---- * B. J. Esselman, F.L. Emmert, A.J. Wiederhold, S.J. Thompson, L.V. Slipchenko, R.J. McMahon*, Thermal Isomerizations of Diethynyl Cyclobutadienes and Implications for Fullerene Formation, J. Org. Chem. 80, 11863-11868 `Link `_ * H.J. Lee, W. Zhang, D. Zhang, Y. Yang, B. Liu, E.L. Barker, K.K. Buhman, L.V. Slipchenko, M. Dai, J.-X. Cheng*, Assessing Cholesterol Metabolism, Storage, and Transport in Live Cells and C. elegans by SRS Imaging of Phenyl-Diyne Cholesterol, Scientific Reports 5, 793 `Link `_ * Advances in molecular quantum chemistry contained in the Q-Chem 4 program package, Mol. Phys. 113, 184 `Link `_ * Kaliman and L.V. Slipchenko, Hybrid MPI/OpenMP parallelization of the Effective Fragment Potential method in the libefp software library, J. Comp. Chem. 36, 129-135 `Link `_ 2014 ---- * Nebgen and L.V. Slipchenko*, Vibronic Coupling in Asymmetric Bichromophores: Theory and Application to Diphenylmethane-d5, J. Chem. Phys., 141, 134119 `Link `_ * N. Pillsbury, N. Kidwell, B. Nebgen, L.V. Slipchenko, K. Douglass, J. Cable, D. Plusquellic, and T. Zwier, Vibronic Coupling in Asymmetric Bichromophores: Experimental Investigation of Diphenylmethane-d5, J. Chem. Phys. 141, 064316 `Link `_ * G. Hoffman, P.K. Gurunathan, J. Francisco, and L.V. Slipchenko*, Excited states of OH-(H2O)n clusters for n = 1-4: An ab initio study, J. Chem. Phys., 141, 104315 `Link `_ 2013 ---- * N.M. Kidwell, N.J. Reilly, B. NebgenG, D.N. Mehta-Hurt, R.D. Hoehn, D.L. Kokkin, M.C. McCarthy, L.V. Slipchenko, and T.S. Zwier*, Jet-Cooled Spectroscopy of the α-Methylbenzyl Radical: Probing the State-Dependent Effects of Methyl Rocking Against a Radical Site, J. Phys. Chem. A, 117 (50), 13465–13480 `Link `_ * J. Anglada, G. Hoffman, L.V. Slipchenko, M. Martins-Costa, M.F. Ruiz-Lopez, J. Francisco*, Atmospheric Significance of Water Clusters and Ozone-Water Complexes, J. Phys. Chem. A, 117 (40), 10381–10396 `Link `_ * I.A. Kaliman and L.V. Slipchenko, LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library, J. Comp. Chem. 34(26), 2284-2292 `Link `_ * M.C. Green, D.G. Fedorov, K. Kitaura, J.S. Francisco, and L.V. Slipchenko*, Open-Shell Pair Interaction Energy Decomposition Analysis (PIEDA): Formulation and Application to the Hydrogen Abstraction in Tripeptides, J. Chem. Phys. 138, 074111 `Link `_ * D. Ghosh, D. Kosenkov, V. Vanovschi, J.C. Flick, I. Kaliman, Y. Shao, A.T.B. Gilbert, A.I. Krylov*, and L.V. Slipchenko*, Effective Fragment Potential method in Q-Chem: A guide for users and developers, J. Comp. Chem., 34(12), 1060-1070 `Link `_ * M.S. Gordon*, Q.A. Smith, P. Xu, L.V. Slipchenko, Accurate First Principles Model Potentials for Intermolecular Interactions, Annu. Rev. Phys. Chem., 64, 553-78 `Link `_ * B.M. Rankin, M. D. HandsG, D. S. Wilcox, L.V. Slipchenko, and D. Ben-Amotz*, Interactions Between Halide Anions and a Molecular Hydrophobic Interface, Faraday Disc., 160, 255-270 `Link `_ 2012 ---- * B. NebgenG, F.E. Emmert, L.V. Slipchenko*, Vibronic Coupling in Asymmetric Bichromophores: Theory and Application to Diphenylmethane, J. Chem. Phys. 137, 084112 (12 pages) `Link `_ * J.C. FlickU, D. Kosenkov, E.G. Hohenstein, C.D. Sherrill, and L.V. Slipchenko*, Accurate Prediction of Non-covalent Interaction Energies with the Effective Fragment Potential method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set, J. Chem Theory Comp., 8 (8), 2835–2843 `Link `_ * Q.A. Smith, K. Ruedenberg, M.S. Gordon*, L.V. Slipchenko, The dispersion interaction between quantum mechanics and effective fragment potential molecules, J. Chem. Phys. 136, 244107 (12 pages) `Link `_ * M.S. Baranov, K. A. Lukyanov, A.O. Borissova, J. Shamir, D. Kosenkov, L.V. Slipchenko, L.M. Tolbert, I.V. Yampolsky*, and K.M. Solntsev*, Conformationally Locked Chromophores as Models of Excited-State Proton Transfer in Fluorescent Proteins, J. Am. Chem. Soc., 134 (13), 6025–6032 `Link `_ * S.J. Thompson, F.L. Emmert, L.V. Slipchenko*, Effects of Ethynyl Substituents on Electronic Structure of Cyclobutadiene, J. Phys. Chem. A, 116, 3194-3201 `Link `_ * M. Hands and L.V. Slipchenko*, Intermolecular Interactions in Complex Liquids: Effective Fragment Potential Investigation of Water-tert-Butanol Mixtures, J. Phys. Chem. B, 116, 2775-2786 `Link `_ 2011 ---- * K.P. Gierszal, J.G. Davis, M.D. HandsG, D.S. Wilcox, L.V. Slipchenko, and D. Ben-Amotz*, π-Hydrogen Bonding in Liquid Water, J. Phys. Chem. Lett., 2 (22), 2930–2933 `Link `_ * W. James, E. Buchanan, C. Mueller, J. Dean, D. Kosenkov, L.V. Slipchenko, L. Guo, A. Reidenbach, S. Gellman, T. Zwier*, Evolution of Amide Stacking in Larger γ-Peptides: Triamide H-Bonded Cycles, J. Phys. Chem. A, 115, 13783–13798 `Link `_ * Q.A. Smith, M.S. Gordon*, and L.V. Slipchenko, Effective Fragment Potential Study of the Interaction of DNA Bases, J. Phys. Chem. A, 115, 11269–11276 `Link `_ * A. DeFusco, N. Minezawa, L.V. Slipchenko, F. Zahariev, and M.S. Gordon*, Modeling solvent effects on electronic excited states, J. Phys. Chem. Lett., 2 (17), 2184–2192 `Link `_ * M.S. Gordon*, S. Pruitt, D. Fedorov, L.V. Slipchenko, Fragmentation Methods: A Route to Accurate Calculations on Large Systems, Chem. Rev., 112 (1), 632–672 `Link `_ * L.M. Haupert, G.J. Simpson, and L.V. Slipchenko*, Computational Investigation of Amine–Oxygen Exciplex Formation, J. Phys. Chem. A, 115, 10159–10165 `Link `_ * D. Ghosh, O. Isayev, L.V. Slipchenko*, and A.I. Krylov*, Effect of Solvation on Vertical Ionization Energy of Thymine: From Microhydration to Bulk, J. Phys. Chem. A, 115 (23), 6028–6038 `Link `_ * Q.A. Smith, M.S. Gordon*, and L.V. Slipchenko, Benzene-Pyridine Interactions Predicted by the Effective Fragment Potential Method, J. Phys. Chem. A, 115 (18), 4598–4609 `Link `_ * D. Kosenkov and L.V. Slipchenko*, Solvent Effects on the Electronic Transitions of p-Nitroaniline: A QM/EFP Study, J. Phys. Chem. A, 115 (4), 392-401 `Link `_ 2010 ---- * D. Ghosh, D. KosenkovP, V. Vanovschi, C.F. Williams, J.M. Herbert, M.S. Gordon, M.W. Schmidt, L.V. Slipchenko*, and A.I. Krylov*, Non-covalent interactions in extended systems described by the Effective Fragment Potential method: Theory and application to nucleobase oligomers, J. Phys. Chem. A, 114 (48), 12739-12754 `Link `_ * L.V. Slipchenko*, Solvation of the excited states of chromophores in polarizable environment: orbital relaxation versus polarization, J. Phys. Chem. A, 114 (33), 8824-8830 `Link `_ * . D.G. Fedorov*, L.V. Slipchenko, K. Kitaura, Systematic study of the embedding potential description in the Fragment Molecular Orbital method, J. Phys. Chem. A, 114 (33), 8742-8753 `Link `_ * P. Arora, L.V. Slipchenko, S.P. Webb, A. Defusco, M.S. Gordon*, Solvent Induced frequency shifts: Configuration Interaction Singles combined with the Effective Fragment Potential Method, J. Phys. Chem. A, 114 (25), 6742–6750 `Link `_ Earlier Publications -------------------- * L.V. Slipchenko and M.S. Gordon*, Damping functions in the effective fragment potential method, Mol. Phys., 107(8-12), 999-1016 `Link `_ * L.V. Slipchenko and M.S. Gordon*, Water−Benzene Interactions: An Effective Fragment Potential and Correlated Quantum Chemistry Study, J. Phys. Chem. A, 113 (10), 2092-2102 `Link `_ * N.J. Barnett, L.V. Slipchenko, and M.S. Gordon*, The binding of Ag+ and Au+ to ethane, J. Phys. Chem. A, 113(26), 7474-7481 `Link `_ * T. Smith, L.V. Slipchenko, and M.S. Gordon*, Modeling π-π interactions by the effective fragment potential method: the benzene dimer and substituents, J. Phys. Chem. A, 112 (23), 5286-5294 `Link `_ * M.S. Gordon*, L.V. Slipchenko, H. Li, and J.H. Jensen, The effective fragment potential: a general method for predicting intermolecular forces, Ann. Rep. Comp. Chem., 3, 177-193 `Link `_ * L.V. Slipchenko and M.S. Gordon*, Breaking the curse of the non-dynamical correlation problem: the Spin-Flip method, ACS Symposium Series, 958, 89–102 `Link `_ * L.V. Slipchenko and M.S. Gordon*, Electrostatic energy in the effective fragment potential (EFP) method: theory and application to benzene dimer, J. Comp. Chem., 28, 276-292 `Link `_ * Advances in methods and algorithms in a modern quantum chemistry program package, Phys. Chem. Chem. Phys., 8, 3172–3191 `Link `_ * L.V. Slipchenko and A.I. Krylov*, Spin-conserving and spin-flipping equation-of-motion coupled-cluster method with triple excitations, J. Chem. Phys., 123, 84107-84120 `Link `_ * T.E. Munsch, L.V. Slipchenko, A.I. Krylov*, and P.G. Wenthold*, Reactivity and structure of the 5-dehydro-m-xylylene anion, J. Org. Chem., 69, 5735-5741 `Link `_ * L.V. Slipchenko, T.E. Munsch, P.G. Wenthold*, and A.I. Krylov*, 5-dehydro-1,3-quinodimethane: a hydrocarbon with an open-shell doublet ground state, Angew. Chem. Int. Ed., 43, 742 `Link `_ * L.V. Slipchenko and A.I. Krylov*, Electronic structure of the 1,3,5-tridehydrobenzene triradical in its ground and excited states, J. Chem. Phys., 118, 9614-9622 `Link `_ * L.V. Slipchenko and A.I. Krylov*, Electronic structure of the trimethylenemethane diradical in its ground and electronically excited states: bonding, equilibrium structures and vibrational frequencies, J. Chem. Phys., 118, 6874-6883 `Link `_ * L.V. Slipchenko and A.I. Krylov*, Singlet-triplet gaps in diradicals by the Spin-Flip approach: a benchmark study, J. Chem. Phys., 117, 4694-4708 `Link `_