Publications
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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