Theoretical Chemistry Purdue

Slipchenko Group

Publications

2020

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)
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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)
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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)
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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)
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Polarizable Embedding for Simulating Redox Potentials of Biomolecules
Gurunathan, Pradeep Kumar; Kim, Yongbin; Slipchenko, Lyudmila; etal.
Physical Chemistry Chemical Physics, 22 (2019)
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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)
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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)
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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)
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Triplet-triplet coupling in chromophore dimers: Theory and experiment
D.A. Hartzler, L.V. Slipchenko, S. Savikhin
J. Phys. Chem. A, Article ASAP (2018)
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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)
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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)
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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)
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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)
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Dispersion interactions in QM/EFP
L.V. Slipchenko, K. Ruedenberg, M.S. Gordon
J. Phys. Chem. A 121 (49), 9495–9507 (2017)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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2014

Vibronic Coupling in Asymmetric Bichromophores: Theory and Application to Diphenylmethane-d5
B. Nebgen and L.V. Slipchenko
J. Chem. Phys. 141, 134119 (2014)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Damping functions in the effective fragment potential method
L.V. Slipchenko and M.S. Gordon
Mol. Phys., 107(8-12), 999-1016 (2009)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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
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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)
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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)
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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)
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