Theoretical Chemistry Purdue
Slipchenko Group
Publications
2020
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
Link to article
Predictive First-Principles Modeling of a Photosynthetic Antenna Protein: The Fenna–Matthews–Olson Complex
Yongbin Kim, Sergei Savikhin, Lyudmila Slipchenko, etal.
J. Phys. Chem. Lett. 11, XXX, 1636-1643 (2020)
Link to article
The Unusual Symmetry of Hexafluoro-o-xylene-A Microwave Spectroscopy and Computational Study
Yongbin Kim, Timothy Zwier, Lyudmila Slipchenko, etal.
J. Chem. Phys. 152, 064302 https://doi.org/10.1063/1.5142169 (2020)
Link to article
2019
FMOxFMO: Elucidating Excitonic Interactions in the Fenna–Matthews–Olson Complex with the Fragment Molecular Orbital Method
Danil S. Kaliakin, Yongbin Kim, Lyudmila Slipchenko, etal.
J. Chem. Theory Comput. 16,2, 1175-1187 https://doi.org/10.1021/acs.jctc.9b00621 (2019)
Link to article
The Effects of Site Asymmetry on Near-Degenerate State-to-State Vibronic Mixing in Flexible Bichromophores
Zwier, Timothy; Slipchenko, Lyudmila; etal.
J. Chem. Phys. 151, 084313 doi.org/10.1063/1.5107423 (2019)
Link to article
Polarizable Embedding for Simulating Redox Potentials of Biomolecules
Gurunathan, Pradeep Kumar; Kim, Yongbin; Slipchenko, Lyudmila; etal.
Physical Chemistry Chemical Physics, 22 (2019)
Link to article
2018
Exchange-Repulsion Energy in QM/EFP
C. Viquez Rojas, J. Fine, L. Slipchenko
J. Chem. Phys. 149, Issue 9, 094103, DOI:10.1063/1.5043107 (2018)
Link to article
Crystallization Inhibition Properties of Cellulose Esters and Ethers for a Group of Chemically Diverse Drugs: Experimental and Computational Insight
L.I. Mosquera-Giraldo , C.H. Borca , A.S. Parker, Y.Dong, K.J. Edgar , S.P. Beaudoin, L.V. Slipchenko , and L.S. Taylor
Biomacromolecules, 19 (12), pp 4593–4606
DOI: 10.1021/acs.biomac.8b01280 (2018)
Link to article
Analysis of crystallographic structures and DFT calculations reveal a new structural arrangement in proteins involving lysine NН3 group and carbonyl
N. R. Skrynnikov, S. A. Izmailov, L. V. Slipchenko and O. N. Rogacheva
Acta Cryst. A74,a175 (2018)
Link to article
Triplet-triplet coupling in chromophore dimers: Theory and experiment
D.A. Hartzler, L.V. Slipchenko, S. Savikhin
J. Phys. Chem. A, Article ASAP (2018)
Link to article
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
N. Mugheirbi, L. Mosquera-Giraldo, C. Borca, L.V. Slipchenko, L. Taylor
Mol. Pharmaceutics 15 (8), 3236–3251 (2018)
Link to article
2017
To Be or Not To Be Symmetric: That Is the Question for Potentially Active Vibronic Modes
S. Tyler, E. Judkins, D. Morozov, C. Borca, L.V. Slipchenko, D. McMillin
J. Chem. Educ. 94 (9), 1232–1237 (2017)
Link to article
Effective Fragment Potential Method for H-Bonding: How To Obtain Parameters for Nonrigid Fragments
N. Dubinets, L.V.Slipchenko
J. Phys. Chem. A 121 (28), 5301–5312 (2017)
Link to article
Effective Fragment Potential method: Past, present and future
L.V. Slipchenko and P.K. Gurunathan
in book “Fragmentation: Toward Accurate Calculations on Complex Molecular Systems” edited by M.S. Gordon, Wiley, pp. 183-208 (2017)
Link to article
Dispersion interactions in QM/EFP
L.V. Slipchenko, K. Ruedenberg, M.S. Gordon
J. Phys. Chem. A 121 (49), 9495–9507 (2017)
Link to article
A new structural arrangement in proteins involving lysine NH3+ group and carbonyl
O.N. Rogacheva, S.A. Izmailov, L.V. Slipchenko, N.R. Skrynnikov
Sci. Reports 7, 16402 (2017)
Link to article
Multipole Moments in the Effective Fragment Potential Method
Bertoni, L.V. Slipchenko, A.J. Misquitta, and M.S. Gordon
J. Phys. Chem. A 121(9), 2056-2067 (2017)
Link to article
2016
A Comparison of the Crystallization Inhibition Properties of Bile Salts
N. Li, L.I. Mosquera-Giraldo, C.H. Borca, J.D. Ormes, M. Lowinger, J.D. Higgins, L.V. Slipchenko, and L.S. Taylor
Cryst. Growth Des. 16(12), 7286-7300 (2016)
Link to article
Ground-state charge transfer: Lithium-benzene and the role of Hartree-Fock exchange
C. Borca, L.V. Slipchenko*, A. Wasserman
J. Phys. Chem. A 120(41), 8190-8198 (2016)
Link to article
Mechanistic Design of Chemically Diverse Polymers with Applications in Oral Drug Delivery
L.I. Mosquera-Giraldo, C.H. Borca, X. Meng, K.J. Edgar, L.V. Slipchenko, and L.S. Taylor
Biomacromolecules 17(11), 3659-3671 (2016)
Link to article
The acid-catalyzed hydrolysis of an α-pinene-derived organic nitrate: kinetics, products, reaction mechanisms, and atmospheric impact
J.D. Rindelaub, C.H. Borca, M.A. Hostetler, J.H. Slade, M.A. Lipton, L.V. Slipchenko, and P.B. Shepson
Atmos. Chem. Phys. 16, 15425-15432 (2016)
Link to article
The Extension of the Effective Fragment Potential Method to Macromolecules
P.K. Gurunathan, A. Acharya, D. Ghosh, D. Kosenkov, I. Kaliman, Y. Shao, A.I. Krylov, L.V. Slipchenko
J. Phys. Chem. B 120, 6562-6574 (2016)
Link to article
Radical damage in lipids investigated with the fragment molecular orbital method
M.C. Green, H. Nakata, D. Fedorov, L.V. Slipchenko
Chem. Phys. Lett. 651, 56-61 (2016)
Link to article
Photochemical Degradation of Isoprene-derived 4,1-Carbonyl Nitrate
Xiong, C. H. Borca, L. V. Slipchenko and P. B. Shepson
Atmos. Chem. Phys. 16, 5595-5610 (2016)
Link to article
Impact of Short-range Forces on Defect Production from High-energy Collisions
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
J. Chem. Theory Comp. 12, 2871–2879 (2016)
Link to article
Thermodynamics and kinetics for the free radical oxygen protein oxidation pathway in a model for β-structured peptides
M. C. Green, L.J. Dubnicka, A.C. Davis, H.A. Rypkema, J.S. Francisco, and L.V. Slipchenko
J. Phys. Chem. A 120, 2493-2503 (2016)
Link to article
2015
Thermal Isomerizations of Diethynyl Cyclobutadienes and Implications for Fullerene Formation
B. J. Esselman, F.L. Emmert III, A.J. Wiederhold, S.J. Thompson, L.V. Slipchenko, R.J. McMahon
J. Org. Chem. 80, 11863-11868 (2015)
Link to article
Assessing Cholesterol Metabolism, Storage, and Transport in Live Cells and C. elegans by SRS Imaging of Phenyl-Diyne Cholesterol
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
Scientific Reports 5, 7930 (2015)
Link to article
Hybrid MPI/OpenMP parallelization of the Effective Fragment Potential method in the libefp software library
Kaliman and L.V. Slipchenko
J. Comp. Chem. 36, 129-135 (2015)
Link to article
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package
Y. Shao, Z. Gan, E. Epifanovsky, A.T.B. Gilbert, and 153 others
Mol. Phys. 113, 184 (2015)
Link to article
2014
Vibronic Coupling in Asymmetric Bichromophores: Theory and Application to Diphenylmethane-d5
B. Nebgen and L.V. Slipchenko
J. Chem. Phys. 141, 134119 (2014)
Link to article
Excited states of OH-(H2O)n clusters for n = 1-4: An ab initio study
G. Hoffman, P.K. Gurunathan, J. Francisco, and L.V. Slipchenko
J. Chem. Phys. 141, 104315 (2014)
Link to article
Vibronic Coupling in Asymmetric Bichromophores: Experimental Investigation of Diphenylmethane-d5
N. Pillsbury, N. Kidwell, B. Nebgen, L.V. Slipchenko, K. Douglass, J. Cable, D. Plusquellic, and T. Zwier
J. Chem. Phys. 141, 064316 (2014)
Link to article
2013
The Atmospheric Significance of Water Clusters and Ozone-Water Complexes
J. Anglada, G. Hoffman, L.V. Slipchenko, M. Martins-Costa, M.F. Ruiz-Lopez, J. Francisco
J. Phys. Chem. A 117 (40), 10381-10396 (2013)
Link to article
Jet-cooled Spectroscopy of the a-Methylbenzyl Radical: Probing the State-Dependent Effects of Methyl Rocking Against a Radical Site
N. Kidwell, N. Reilly, B. Nebgen, D. Mehta-Hurt, R. Hoehn, D. Kokkin, M. McCarthy, L.V. Slipchenko, T. Zwier
J. Phys. Chem. A 117 (50), 13465-13480 (2013)
Link to article
LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library
I.A. Kaliman and L.V. Slipchenko
J. Comp. Chem. 34 (26), 2284-2292 (2013)
Link to article
Accurate First Principles Model Potentials for Intermolecular Interactions
M.S. Gordon, Q.A. Smith, P. Xu, L.V. Slipchenko
Annu. Rev. Phys. Chem. 64, 553-78 (2013)
Link to article
Open-Shell Pair Interaction Energy Decomposition Analysis (PIEDA): Formulation and Application to the Hydrogen Abstraction in Tripeptides
M.C. Green, D.G. Fedorov, K. Kitaura, J.S. Francisco, and L.V. Slipchenko
J. Chem. Phys. 138, 074111 (2013)
Link to article
Effective Fragment Potential method in Q-Chem: A guide for users and developers
D. Ghosh, D. Kosenkov, V. Vanovschi, J.C. Flick, I. Kaliman, Y. Shao, A.T.B. Gilbert, A.I. Krylov, and L.V. Slipchenko
J. Comp. Chem. 34 (12), 1060-1070 (2013)
Link to article
2012
Non-covalent interactions in extended systems described by the Effective Fragment Potential method: Theory and application to nucleobase oligomers
D. Ghosh, D. Kosenkov, V. Vanovschi, C.F. Williams, J.M. Herbert, M.S. Gordon, M.W. Schmidt, L.V. Slipchenko, and A.I. Krylov
J. Phys. Chem. A, 114 (48), 12739-12754 (2010)
Link to article
Vibronic Coupling in Asymmetric Bichromophores: Theory and Application to Diphenylmethane
B. Nebgen, F.E. Emmert III, L.V. Slipchenko
J. Chem. Phys. 137, 084112 (2012)
Link to article
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.C. Flick, D. Kosenkov, E.G. Hohenstein, C.D. Sherrill, and L.V. Slipchenko
J. Chem Theory Comp. 8 (8), 2835-2843 (2012)
Link to article
The dispersion interaction between quantum mechanics and effective fragment potential molecules
Q.A. Smith, K. Ruedenberg, M.S. Gordon, L.V. Slipchenko
J. Chem. Phys. 136, 244107 (2012)
Link to article
Interactions Between Halide Anions and a Molecular Hydrophobic Interface
B.M. Rankin, M. D. Hands, D. S. Wilcox, L.V. Slipchenko, and D. Ben-Amotz
Faraday Disc., 160, 255-270 (2013)
Link to article
Conformationally Locked Chromophores as Models of Excited-State Proton Transfer in Fluorescent Proteins
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
J. Am. Chem. Soc., 134 (13), 6025-6032 (2012)
Link to article
Effects of Ethynyl Substituents on Electronic Structure of Cyclobutadiene
S.J. Thompson, F.L. Emmert III, L.V. Slipchenko
J. Phys. Chem. A, 116, 3194-3201 (2012)
Link to article
Intermolecular Interactions in Complex Liquids: Effective Fragment Potential Investigation of Water-tert-Butanol Mixtures
M. Hands and L.V. Slipchenko
J. Phys. Chem. B, 116, 2775-2786 (2012)
Link to article
2011
pi-Hydrogen Bonding in Liquid Water
K.P. Gierszal, J.G. Davis, M.D. Hands, D.S. Wilcox, L.V. Slipchenko, and D. Ben-Amotz
J. Phys. Chem. Lett., 2 (22), 2930-2933 (2011)
Link to article
Evolution of Amide Stacking in Larger γ-Peptides: Triamide H-Bonded Cycles
W. James, E. Buchanan, C. Mueller, J. Dean, D. Kosenkov, L.V. Slipchenko, L. Guo, A. Reidenbach, S. Gellman, T. Zwier
J. Phys. Chem. A, 115, 13783-13798 (2011)
Link to article
Effective Fragment Potential Study of the Interaction of DNA Bases
Q.A. Smith, M.S. Gordon, and L.V. Slipchenko
J. Phys. Chem. A, 115, 11269-11276 (2011)
Link to article
Fragmentation Methods: A Route to Accurate Calculations on Large Systems
M.S. Gordon, S. Pruitt, D. Fedorov, L.V. Slipchenko
Chem. Rev., 112 (1), 632-672 (2011)
Link to article
Modeling solvent effects on electronic excited states
A. DeFusco, N. Minezawa, L.V. Slipchenko, F. Zahariev, and M.S. Gordon
J. Phys. Chem. Lett., 2 (17), 2184-2192 (2011)
Link to article
Computational Investigation of Amine-Oxygen Exciplex Formation
L.M. Haupert, G.J. Simpson, and L.V. Slipchenko
J. Phys. Chem. A, 115, 10159-10165 (2011)
Link to article
Benzene-Pyridine Interactions Predicted by the Effective Fragment Potential Method
Q.A. Smith, M.S. Gordon, and L.V. Slipchenko
J. Phys. Chem. A, 115 (18), 4598-4609 (2011)
Link to article
Effect of Solvation on Vertical Ionization Energy of Thymine: From Microhydration to Bulk
D. Ghosh, O. Isayev, L.V. Slipchenko, and A.I. Krylov
J. Phys. Chem. A, 115 (23), 6028-6038 (2011)
Link to article
Solvent Effects on the Electronic Transitions of p-Nitroaniline: A QM/EFP Study
D. Kosenkov and L.V. Slipchenko
J. Phys. Chem. A, 115 (4), 392-401 (2011)
Link to article
2010
Solvent Induced frequency shifts: Configuration Interaction Singles combined with the Effective Fragment Potential Method
P. Arora, L.V. Slipchenko, S.P. Webb, A. Defusco, M.S. Gordon
J. Phys. Chem. A, 114 (25), 6742-6750 (2010)
Link to article
Solvation of the excited states of chromophores in polarizable environment: orbital relaxation versus polarization
L.V. Slipchenko
J. Phys. Chem. A, 114 (33), 8824-8830 (2010)
Link to article
Systematic study of the embedding potential description in the Fragment Molecular Orbital method
D.G. Fedorov, L.V. Slipchenko, K. Kitaura
J. Phys. Chem. A, 114 (33), 8742-8753 (2010)
Link to article
2009
Intramolecular Amide Stacking and Its Competition with Hydrogen Bonding in a Small Foldamer
W.H. James III, C.W. Mueller, E.G. Buchanan, M.G.D. Nix, L. Guo, L. Roskop, M.S. Gordon, L.V. Slipchenko, S.H. Gellman and T.S. Zwier
J. Am. Chem. Soc., 131(40), 14243 (2009)
Link to article
Accurate methods for large molecular systems
M.S. Gordon, J.M. Mullin, S.R. Pruitt, L.B. Roskop, L.V. Slipchenko, and J. A. Boatz
J. Phys. Chem. B, 113(29), 9646-9663 (2009)
Link to article
The binding of Ag+ and Au+ to ethane
N.J. Barnett, L.V. Slipchenko, and M.S. Gordon
J. Phys. Chem. A, 113(26), 7474-7481(2009)
Link to article
Double spin-flip approach within equation-of-motion coupled cluster and configuration interaction formalisms: Theory, implementation and examples
D. Casanova, L.V. Slipchenko, A.I. Krylov, M. Head-Gordon
J. Chem. Phys. 130, 044103 (2009)
Link to article
Water-Benzene Interactions: An Effective Fragment Potential and Correlated Quantum Chemistry Study
L.V. Slipchenko and M.S. Gordon
J. Phys. Chem. A 113 (10), 2092-2102 (2009)
Link to article
Damping functions in the effective fragment potential method
L.V. Slipchenko and M.S. Gordon
Mol. Phys., 107(8-12), 999-1016 (2009)
Link to article
Coarse-grained intermolecular potentials derived from the effective fragment potential: application to water, benzene, and carbon tetrachloride
G. Pranami, L.V. Slipchenko, M.H. Lamm, and M.S. Gordon
in Book "Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications" edited by T.-S. Lee and D. M. York, Springer Verlag (2009)
Link to article
2008
Modeling π–π Interactions with the Effective Fragment Potential Method: The Benzene Dimer and Substituents
T. Smith, L.V. Slipchenko, and M.S. Gordon
J. Phys. Chem. A, 112 (23), 5286-5294 (2008)
Link to article
2007
The effective fragment potential: a general method for predicting intermolecular forces
M.S. Gordon, L.V. Slipchenko, H. Li, and J.H. Jensen
Ann. Rep. Comp. Chem., 3, 177-193 (2007)
Link to article
Breaking the curse of the non-dynamical correlation problem: the Spin-Flip method
A.I. Krylov, L.V. Slipchenko, and S.V. Levchenko
ACS Symposium Series, 958, 89-102 (2007)
Link to article
2006
Electrostatic energy in the effective fragment potential (EFP) method: theory and application to benzene dimer
L.V. Slipchenko and M.S. Gordon
J. Comp. Chem., 28, 276-292 (2006)
Link to article
Advances in methods and algorithms in a modern quantum chemistry program package
Y. Shao, L. F. Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. Brown, A. T. B. Gilbert, L. V. Slipchenko, and 59 others
Phys. Chem. Chem. Phys., 8, 3172-3191 (2006)
Link to article
Efficient strategies for accurate calculations of electronic excitation and ionization energies: theory and application to the dehydro-meta-xylylene anion
L.V. Slipchenko and A.I. Krylov
J. Phys. Chem. A, 110, 291 - 298 (2006)
Link to article
2005
Spin-conserving and spin-flipping equation-of-motion coupled-cluster method with triple excitations
L.V. Slipchenko and A.I. Krylov
J. Chem. Phys. 123, 84107-84120 (2005)
Link to article
2004
Reactivity and structure of the 5-dehydro-m-xylylene anion
T.E. Munsch, L.V. Slipchenko, A.I. Krylov, and P.G. Wenthold
J. Org. Chem. 69, 5735-5741 (2004)
Link to article
5-dehydro-1,3-quinodimethane: a hydrocarbon with an open-shell doublet ground state
L.V. Slipchenko, T.E. Munsch, P.G. Wenthold, and A.I. Krylov
Angew. Chem. Int. Ed. 43, 742 (2004). highlighted in Chemical & Engineering News and Science Daily, 2004
Link to article
2003
Electronic structure of the 1,3,5-tridehydrobenzene triradical in its ground and excited states
L.V. Slipchenko and A.I. Krylov
J. Chem. Phys. 118, 9614-9622 (2003)
Link to article
Electronic structure of the trimethylenemethane diradical in its ground and electronically excited states: bonding, equilibrium structures and vibrational frequencies
L.V. Slipchenko and A.I. Krylov
J. Chem. Phys. 118, 6874-6883 (2003)
Link to article
2002
Singlet-triplet gaps in diradicals by the Spin-Flip approach: a benchmark study
L.V. Slipchenko and A.I. Krylov
J. Chem. Phys. 117, 4694-4708 (2002)
Link to article