prof. Ing. Pavel Hobza, DrSc., FRSC
Tel: 58 563 4760, E-mail: pavel.hobza@upol.cz, Room: 3.006
Research interests- Quantum chemistry and computational chemistry
- Noncovalent interactions
- Structure and dynamics of molecular and biomolecular clusters and biomolecules
- Hydrogen-bonding and improper
- Blue-shifting hydrogen-bonding
- Halogen and σ-hole bonding
- In silico drug design
- M.Sc. - Faculty of Technical and Nuclear Physics, Czech Technical University, Prague, chemistry
- Ph.D. - Institute of Physical Chemistry, Czechoslovak Academy of Sciences, Prague, C.Sc.
- 1973,1986 - Institute of Hygiene and Epidemiology
- 1979,1982 - Postdoctoral Fellow at the Universite de Montreal, Canada
- 1984,1986 - Visiting Professor at the Universite de Montreal, Canada
- 1986,1987, 1988,1989, 1990 - Research Associate at Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany and Technische Universität München, Germany
- 1990-1991 - DFG-visiting professor, Technische Universität München, Germany
- 1991-2003 - J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague
- 2000-2004 - Research Centre for Complex Molecular Systems and Biomolecules, head
- 2005-2011 - Research Centre for Biomolecules and Complex Molecular Systems, head
- 2012-now - Centre of Excellency: Controlling the Structure and Function of Biomolecules at the molecular level, head
- 2002-now - Professor of Physical Chemistry, Charles University, Prague
- 2005-now - Research Centre for Biomolecules and Complex Molecular Systems, head
- 2003-now - Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Department of Molecular Modelling, head
- 2005-now - Professor of Physical Chemistry, Palacký University, Olomouc
- 1979,1982 - Postdoctoral Fellow at the Universite de Montreal, Canada
- 1984,1986 - Visiting Professor at the Universite de Montreal, Canada
- 1986,1987, 1988,1989, 1990 - Research Associate at Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany and Technische Universität München, Germany
- 1990-1991 - DFG-visiting professor, Technische Universität München, Germany
Publications
2020
- Manna D, Lo R, Hobza P: Spin modification of iron(ii) complexes via covalent (dative) and dispersion guided non-covalent bonding with N-heterocyclic carbenes: DFT, DLPNO-CCSD(T) and MCSCF studies. Dalton Trans., 49(1), 164-170, 2020. (DOI)
2019
- Eyrilmez SM, Kopruluoglu C, Řezáč J, Hobza P: Impressive Enrichment of Semiempirical Quantum Mechanics-Based Scoring Function: HSP90 Protein with 4541 Inhibitors and Decoys. ChemPhysChem, 20(21), 2759-2766, 2019. (DOI)
- Gallardo A, Fanfrlik J, Hobza P, Jelínek P: Nature of Binding in Planar Halogen-Benzene Assemblies and Their Possible Visualization in Scanning Probe Microscopy. J. Phys. Chem. C, 123(13), 8379-8386, 2019. (DOI)
- Hobza P: In My Element: Hydrogen Chem. Eur. J., 25(6), 1367-1368, 2019. (DOI)
- Lo R, Manna D, Zbořil R, Nachtigallová D, Hobza P: Spin Crossover in Iron(II) Porphyrazine Induced by Noncovalent Interactions Combined with Hybridization of Iron(II) Porphyrazine and Ligand's Orbitals: CASPT2, CCSD(T), and DFT Studies. J. Phys. Chem. C, 123(37), J. Phys. Chem. C, 2019. (DOI)
- Miriyala VM, Lo R, Haldar S, Sarmah A, Hobza P: Structure and Properties of Double-Sandwich Complexes at Graphene Surface: A Theoretical Study. J. Phys. Chem. C, 123(23), 14712-14724, 2019. (DOI)
- Sarmah A, Hobza P: Computational Approach To Understand the Adsorption Behavior of Iron(II) Phthalocyanine on the Doped Graphene Surface. J. Phys. Chem. C, 123(11), 6717-6724, 2019. (DOI)
2018
- Ajani H, Jansa J, Kopruluoglu C, Hobza P, Kryštof V, Lycka A, Lepšík M: Imidazo[1,2-c]pyrimidin-5(6H)-one as a novel core of cyclin-dependent kinase 2 inhibitors: Synthesis, activity measurement, docking, and quantum mechanical scoring. J. Mol. Recognit., 31(9), e2720, 2018. (DOI)
- de la Torre B, Švec M, Hapala P, Redondo J, Krejčí O, Lo R, Manna D, Sarmah A, Nachtigallová D, Tuček J, Blonski P, Otyepka M, Zbořil R, Hobza P, Jelínek P: Non-covalent control of spin-state in metal-organic complex by positioning on N-doped graphene. Nat. Commun., 9, 2831 , 2018. (DOI)
- Nachtigallová D, Antalík A, Lo R, Sedlak R, Manna D, Tuček J, Ugolotti J, Veis L, Legeza Ö, Pittner J, Zbořil R, Hobza P: Isolated Molecule of Iron(II)Phtalocyanine Exhibits Quintet Ground‐State: A Nexus between Theory and Experiment. Chem. Eur. J., 24(51), 13413-13417, 2018. (DOI)
- Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Hořejší M, Eyrilmez SM, Řezáč J, Lepšík M, Řezáčová P, Hobza P, Majer P, Veverka V, Fanfrlik J: Ranking Power of the SQM/COSMO Scoring Function on Carbonic AnhydraseII-Inhibitor Complexes. ChemPhysChem, 19(7), 873-879, 2018. (DOI)
- Sarmah A, Hobza P: Sequential BN-doping induced tuning of electronic properties in zigzag-edged graphene nanoribbons: a computational approach. RSC Adv., 8, 10964-10974 , 2018. (DOI)
- Sarmah A, Hobza P: Understanding the non-covalent interaction mediated modulations on the electronic structure of quasi-zero-dimensional graphene nanoflakes. Phys. Chem. Chem. Phys., 20(27), 18718-18728, 2018. (DOI)
- Sedlak R, Eyrilmez SM, Hobza P, Nachtigallova D: The role of the sigma-holes in stability of non-bonded chalcogenide ... benzene interactions: the ground and excited states. Phys. Chem. Chem. Phys., 20(1), 299-306, 2018. (DOI)
- Sedlák R, Eyrilmez,Saltuk M. , Hobza P, Nachtigallová D: The role of the σ-holes in stability of non-bonded chalcogenide⋯benzene interactions: the ground and excited states. Phys. Chem. Chem. Phys., 20, 299-306, 2018. (DOI)
- Stasyuk OA, Sedlák R, Guerra CF, Hobza P: Comparison of the DFT-SAPT and Canonical EDA Schemes for the Energy Decomposition of Various Types of Noncovalent Interactions. J. Chem. Theory Comput., 14(7), 3440–3450, 2018. (DOI)
- Zierkiewicz W, Fanfrlík J, Michalczyk M, Michalska D, Hobza P: S⋯N chalcogen bonded complexes of carbon disulfide with diazines. Theoretical study. Chem. Phys., 500, 37-44, 2018. (DOI)
2017
- Ajani H, Pecina A, Eyrilmez SM, Fanfrlik J, Haldar S, Řezáč J, Hobza P, Lepšík M: Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein–Ligand Complexes in Cognate Docking. ACS Omega, 2(7), 4022–4029, 2017. (DOI)
- Eiyrilmez SM, Bernhardt E, Davalos J, Lepšík M, Hobza P, Assaf KI, Nau W H, Oliva JM, Fanfrlik J, Hnyk D: Binary twinned-icosahedral [B21H18]− interacts with cyclodextrins as a precedent for its complexation with other organic motifs. Phys. Chem. Chem. Phys., 19, 11748-11752, 2017. (DOI)
- Fanfrlik J, Pecina A, Řezáč J, Sedlak R, Hnyk D, Lepšík M, Hobza P: B−H···π: A Nonclassical Hydrogen Bond or Dispersion Contact? Phys. Chem. Chem. Phys., 19, 18194-18200, 2017. (DOI)
- Fanfrlik J, Švec P, Růžičková Z, Hnyk D, Růžička A, Hobza P: The Interplay between Various σ- and π-Hole Interactions of Trigonal Boron and Trigonal Pyramidal Arsenic Triiodides. Crystals , 7(7), 225, 2017. (DOI)
- Fanfrlik J, Zierkiewicz W, Švec P, Růžičková Z, Řezáč J, Michalczyk M, Růžička A, Michalska D, Hobza P: Pnictogen bonding in pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes. J. Mol. Model., 23, 328, 2017. (DOI)
- Hylsová M, Carbain B, Fanfrlík J, Musilová L, Haldar S, Köprülüoğlu C, Ajani H, Brahmkshatriya PS, Jorda R, Kryštof V, Hobza P, Echalier AP, Lepšík M: Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines. Eur. J. Med. Chem., 126, 1118–1128, 2017. (DOI)
- Karlický F, Otyepková E, Lo R, Pitoňák M, Jurečka P, Pykal M, Hobza P, Otyepka M: Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite. J. Chem. Theory Comput., 13(3), 1328–1340, 2017. (DOI)
- Sarmah A, Hobza P: Understanding the spin-dependent electronic properties of symmetrically far-edge doped zigzag graphene nanoribbon from a first principles study. RSC Adv., 7, 46604-46614, 2017. (DOI)
- Sigwalt D, Šekutor M, Cao L, Zavalij PY, Hostaš J, Ajani H, Hobza P, Mlinarić-Majerski K, Glaser R, Isaacs L: Unraveling the Structure–Affinity Relationship between Cucurbit[n]urils (n = 7, 8) and Cationic Diamondoids. J. Am. Chem. Soc., 139(8), 3249–3258, 2017. (DOI)
- Stasyuk OA, Jakubec D, Vondrášek J, Hobza P: Noncovalent interactions in specific recognition motifs of protein–DNA complexes. J. Chem. Theory Comput., 13(2), 877–885, 2017. (DOI)
2016
- Cousido-Siah A, Ruiz FX, Fanfrlík J, Giménez-Dejoz J, Mitschler A, Kamlar M, Veselý J, Ajani H, Parés X, Farrés J, Hobza P, Podjarny AD: IDD388 polyhalogenated derivatives as probes for an improved structure-based selectivity of AKR1B10 inhibitors. ACS Chem. Biol., 11(10), 2693–2705, 2016. (DOI)
- Fanfrlik J, Holub J, Růžičková Z, Řezáč J, Lane P, Wann D, Hnyk D, Růžička A, Hobza P: Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes. ChemPhysChem, 17(21), 3373–3376, 2016. (DOI)
- Fanfrlík J, Sedlak R, Pecina A, Rulíšek L, Dostál L, Moncol J, Růžička A, Hobza P: The non-planarity of the Benzene Molecule in the X-ray Structure of the Chelated Bismuth(III) Heteroboroxine Complex Is not Supported by Quantum Mechanical Calculations. Dalton T., 45(2), 462-465, 2016. (DOI)
- Hostaš J, Sigwalt D, Šekutor M, Ajani H, Dubecký M, Řezáč J, Zavalij PY, Cao L, Wohlschlager C, Mlinarić-Majerski K, Isaacs L, Glaser R, Hobza P: A Nexus between Theory and Experiment: Non-Empirical Quantum Mechanical Computational Methodology Applied to Cucurbit[n]uril⋅Guest Binding Interactions. Chem. Eur. J., 22(48), 17226–17238, 2016. (DOI)
- Kokoschka M, Galgonek J, Vondrášek J, Hobza P: Computational methods for the description of pharmacologically relevant platinum complexes - molecular structure and bond dissociation. Phys. Chem. Chem. Phys. , 18(5), 4051-4062, 2016. (DOI)
- Kolář MH, Hobza P: Computer Modeling of Halogen Bonds and Other σ-Hole Interactions. Chem. Rev., 116(9), 5155–5187, 2016. (DOI)
- Lo R, Švec P, Růžičková Z, Růžička A, Hobza P: On the nature of the stabilisation of the E⋯π pnicogen bond in the SbCl3⋯toluene complex. Chem. Commun., 52, 3500-3503, 2016. (DOI)
- Pecina A, Meier R, Fanfrlík J, Lepšík M, Řezáč J, Hobza P, Baldauf C: The SQM/COSMO Filter: Reliable Native Pose Identification Based on the Quantum-Mechanical Description of Protein–Ligand Interactions and Implicit COSMO Solvation. Chem. Commun., 52, 3312-3315, 2016. (DOI)
- Rai SL, Singh P, Kumar R, Tewari AK, Hostáš J, Gnanasekaran R, Hobza P: Experimental and Theoretical Study for the Assessment of the Conformational Stability of Polymethylene-Bridged Heteroaromatic Dimers: A Case of Unprecedented Folding. Cryst. Growth Des., 16(3), 1176–1180, 2016. (DOI)
- Řezáč J, Hobza P: Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications. Chem. Rev., 116(9), 5038–5071, 2016. (DOI)
- Sedlák R, Stasyuk OA, Guerra CF, Řezáč J, Růžička A, Hobza P: A new insight into the nature of bonding in the dimers of Lappert’s stannylene and its Ge analogs. A quantum mechanical study. J. Chem. Theory Comput., 12(4), 1696–1704, 2016. (DOI)
- Zierkiewicz W, Fanfrlík J, Hobza P, Michalska D, Zeegers-Huyskens T: Ab initio and DFT studies of the interaction between carbonyl and thiocarbonyl groups: the role of S···O chalcogen bonds. Theor. Chem. Acc., 135, 217-227, 2016. (DOI)
2015
- Cao L, Škalamera Đ, Zavalij PY, Hostaš J, Hobza P, Mlinarić-Majerski K, Glaser R, Isaacs L: Influence of hydrophobic residues on the binding of CB[7] toward diammonium ions of common ammonium⋯ammonium distance. Org. Biomol. Chem., 13(22), 6249-6254, 2015. (DOI)
- Fanfrlík J, Ruiz FX, Kadlčíková A, Řezáč J, Cousido-Siah A, Mitschler A, Haldar S, Lepšík M, Kolář MH, Majer P, Podjarny AD, Hobza P: The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition. ACS Chem. Biol., 10(7), 1637-1642, 2015. (DOI)
- Haldar S, Gnanasekaran R, Hobza P: A comparison of ab initio quantum-mechanical and experimental D 0 binding energies of eleven H-bonded and eleven dispersion-bound complexes. Phys. Chem. Chem. Phys., 17(40), 26645-26652, 2015. (DOI)
- Haldar S, Kührová P, Banáš P, Spiwok V, Šponer J, Hobza P, Otyepka M: Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics. J. Chem. Theory Comput., 11(8), 3866-3877, 2015. (DOI)
- Hostaš J, Jakubec D, Laskowski RA, Gnanasekaran R, Řezáč J, Vondrášek J, Hobza P: Representative Amino Acid Side-Chain Interactions in Protein–DNA Complexes: A Comparison of Highly Accurate Correlated Ab Initio Quantum Mechanical Calculations and Efficient Approaches for Applications to Large Systems. J. Chem. Theory Comput., 11(9), 4086-4092, 2015. (DOI)
- Lo R, Fanfrlík J, Lepšík M, Hobza P: The properties of substituted 3D-aromatic neutral carboranes: the potential for o-hole bonding. Phys. Chem. Chem. Phys., 17(32), 20814-20821, 2015. (DOI)
- Mazzoni F, Becucci M, Řezáč J, Nachtigallová D, Michels F, Hobza P, Müller-Dethlefs K: Structure and energetics of the anisole–Ar n (n = 1, 2, 3) complexes: high-resolution resonant two-photon and threshold ionization experiments, and quantum chemical calculations. Phys. Chem. Chem. Phys., 17(19), 12530-12537, 2015. (DOI)
- Pecina A, Lepšík M, Hnyk D, Hobza P, Fanfrlík J: Chalcogen and Pnicogen Bonds in Complexes of Neutral Icosahedral and Bicapped Square-Antiprismatic Heteroboranes. J. Phys. Chem. A., 119(8), 1388-1395, 2015. (DOI)
- Řezáč J, Dubecký M, Jurečka P, Hobza P: Extensions and applications of the A24 data set of accurate interaction energies. Phys. Chem. Chem. Phys., 17(29), 19268-19277, 2015. (DOI)
- Řezáč J, Huang Y, Hobza P, Beran GJO: Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods. J Chem. Theory Comput., 11(7), 3065-3079, 2015. (DOI)
- Řezáč J, Nachtigallová D, Mazzoni F, Pasquini M, Pietraperzia G, Becucci M, Müller-Dethlefs K, Hobza P: Binding Energies of the pi-Stacked Anisole Dimer: New Molecular Beam-Laser Spectroscopy Experiments and CCSD(T) Calculations. Chem. Eur. J., 21(18), 6740-6746, 2015. (DOI)
- Sedlak R, Fanfrlik J, Pecina A, Hnyk D, Hobza P, Lepšík M: Noncovalent Interactions of Heteroboranes. Boron, 20, 219-239, 2015. (DOI)
- Sedlák R, Kolář MH, Hobza P: Polar Flattening and the Strength of Halogen Bonding. J. Chem. Theory Comput., 11(10), 4727-4732, 2015. (DOI)
- Vorlová B, Nachtigallová D, Jirásková-Vaníčková J, Ajani H, Jansa P, Řezáč J, Fanfrlík J, Otyepka M, Hobza P, Konvalinka J, Lepšík M: Malonate-based inhibitors of mammalian serine racemase: Kinetic characterization and structure-based computational study. Eur. J. Med. Chem., 89, 189-197, 2015. (DOI)
2014
- Deepa P, Vijaya Pandiyan B, Kolandaivel P, Hobza P: Halogen bonds in crystal TTF derivatives: an ab initio quantum mechanical study. Phys. Chem. Chem. Phys., 16(5), 2038-2047, 2014. (DOI)
- Deepa P, Sedlák R, Hobza P: On the origin of the substantial stabilisation of the electron-donor 1,3-dithiole-2-thione-4-carboxyclic acid⋯I2 and DABCO⋯I2 complexes. Phys. Chem. Chem. Phys., 16(14), 6679-6686, 2014. (DOI)
- Demovičová L, Hobza P, Řezáč J: Evaluation of composite schemes for CCSDT(Q) calculations of interaction energies of noncovalent complexes. Phys. Chem. Chem. Phys., 16(36), 19115-19121, 2014. (DOI)
- Dubecký M, Derian R, Jurečka P, Mitas L, Hobza P, Otyepka M: Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy. Phys. Chem. Chem. Phys., 16(38), 20915-20923, 2014. (DOI)
- Fanfrlík J, Přáda A, Padělková Z, Pecina A, Macháček J, Lepšík M, Holub J, Růžička A, Hnyk D, Hobza P: The Dominant Role of Chalcogen Bonding in the Crystal Packing of 2D/3D Aromatics. Angew. Chem. Int. Ed. , 126(38), 10303-10306, 2014. (DOI)
- Kolář M, Hostaš J, Hobza P: The strength and directionality of a halogen bond are co-determined by the magnitude and size of the sigma-hole. Phys. Chem. Chem. Phys., 16(21), 9987-9996, 2014. (DOI)
- Kolář MH, Carloni P, Hobza P: Statistical analysis of $sigma$-holes: a novel complementary view on halogen bonding. Phys. Chem. Chem. Phys., 16(36), 19111-19114, 2014. (DOI)
- Lazar P, Granatier J, Klimeš J, Hobza P, Otyepka M: The nature of bonding and electronic properties of graphene and benzene with iridium adatoms. Phys. Chem. Chem. Phys., 16(38), 20818-20827, 2014. (DOI)
- Mader P, Pecina A, Cígler P, Lepšík M, Šícha V, Hobza P, Grüner B, Fanfrlík J, Brynda J, Řezáčová P: Carborane-Based Carbonic Anhydrase Inhibitors: Insight into CAII/CAIX Specificity from a High-Resolution Crystal Structure, Modeling, and Quantum Chemical Calculations. Biomed Res. Int., 2014, 1-9, 2014. (DOI)
- Řezáč J, Hobza P: Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer. J. Chem. Theory Comput., 10(8), 3066-3073, 2014. (DOI)
- Sedlák R, Deepa P, Hobza P: Why Is the L-Shaped Structure of X 2 ···X 2 (X = F, Cl, Br, I) Complexes More Stable Than Other Structures?. J. Phys. Chem. A, 118(21), 3846-3855, 2014. (DOI)
2013
- Dubecký M, Jurečka P, Derian R, Hobza P, Otyepka M, Mitas L: Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy. J. Chem. Theory Comput., 9(10), 4287-4292, 2013. (DOI)
- Fanfrlík J, Brahmkshatriya PS, Řezáč J, Jílková A, Horn M, Mareš M, Hobza P, Lepšík M: Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors. J. Phys. Chem. B, 117(48), 14973-14982, 2013. (DOI)
- Fanfrlík J, Kolář M, Kamlar M, Hurný D, Ruiz FX, Cousido-Siah A, Mitschler A, Řezáč J, Munusamy E, Lepšík M, Matějíček P, Veselý J, Podjarny A, Hobza P: Modulation of Aldose Reductase Inhibition by Halogen Bond Tuning. ACS Chem. Biol., 8(11), 2484-2492, 2013. (DOI)
- Granatier J, Dubecký M, Lazar P, Otyepka M, Hobza P: Spin-Crossing in an Organometallic Pt–Benzene Complex. J. Chem. Theory Comput., 9(3), 1461-1468, 2013. (DOI)
- Haldar S, Spiwok V, Hobza P: On the Association of the Base Pairs on the Silica Surface Based on Free Energy Biased Molecular Dynamics Simulation and Quantum Mechanical Calculations. J. Phys. Chem. C, 117(21), 11066-11075, 2013. (DOI)
- Hostaš J, Řezáč J, Hobza P: On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions. Chem. Phys. Lett., 568-569, 161-166, 2013. (DOI)
- Kolář M, Fanfrlík J, Lepšík M, Forti F, Luque FJ, Hobza P: Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches. J. Phys. Chem. B, 117(19), 5950-5962, 2013. (DOI)
- Kolář M, Hobza P, Bronowska AK: Plugging the explicit sigma-holes in molecular docking. Chem. Commun., 49(10), 981-983, 2013. (DOI)
- Lazar P, Zhang S, Šafářová K, Li Q, Froning JP, Granatier J, Hobza P, Zbořil R, Besenbacher F, Dong M, Otyepka M: Quantification of the Interaction Forces between Metals and Graphene by Quantum Chemical Calculations and Dynamic Force Measurements under Ambient Conditions. ACS Nano, 7(2), 1646-1651, 2013. (DOI)
- Lepšík M, Řezáč J, Kolář M, Pecina A, Hobza P, Fanfrlík J: The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design. ChemPlusChem, 78(9), 921-931, 2013. (DOI)
- Melicherčík M, Pitoňák M, Kellö V, Hobza P, Neogrády P: Off-Center Gaussian Functions, an Alternative Atomic Orbital Basis Set for Accurate Noncovalent Interaction Calculations of Large Systems. J. Chem. Theory Comput., 9(12), 5296-5304, 2013. (DOI)
- Pecina A, Lepšík M, Řezáč J, Brynda J, Mader P, Řezáčová P, Hobza P, Fanfrlík J: QM/MM Calculations Reveal the Different Nature of the Interaction of Two Carborane-Based Sulfamide Inhibitors of Human Carbonic Anhydrase II. J. Phys. Chem. B, 117(50), 16096-16104, 2013. (DOI)
- Řezáč J, Hobza P: Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit?. J. Chem. Theory Comput., 9(5), 2151-2155, 2013. (DOI)
- Řezáč J, Šimová L, Hobza P: CCSD[T] Describes Noncovalent Interactions Better than the CCSD(T), CCSD(TQ), and CCSDT Methods. J. Chem. Theory Comput., 9(1), 364-369, 2013. (DOI)
- Riley KE, Hobza P: On the Importance and Origin of Aromatic Interactions in Chemistry and Biodisciplines. Acc. Chem. Res., 46(4), 927-936, 2013. (DOI)
- Riley KE, Řezáč J, Hobza P: Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers. J. Mol. Model., 19(7), 2879-2883, 2013. (DOI)
- S. Brahmkshatriya P, Dobeš P, Fanfrlík J, Řezáč J, Paruch K, Bronowska A, Lepšík M, Hobza P: Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines. Curr. Comp. Aid. Drug Des., 9(1), 118-129, 2013. (DOI)
- Sedlak R, Janowski T, Pitoňák M, Řezáč J, Pulay P, Hobza P: Accuracy of Quantum Chemical Methods for Large Noncovalent Complexes. J. Chem. Theory Comput., 9(8), 3364-3374, 2013. (DOI)
- Sedlak R, Riley KE, Řezáč J, Pitoňák M, Hobza P: MP2.5 and MP2.X: Approaching CCSD(T) Quality Description of Noncovalent Interaction at the Cost of a Single CCSD Iteration. ChemPhysChem, 14(4), 698-707, 2013. (DOI)
- Šimová L, Řezáč J, Hobza P: Convergence of the Interaction Energies in Noncovalent Complexes in the Coupled-Cluster Methods Up to Full Configuration Interaction. J. Chem. Theory Comput., 9(8), 3420-3428, 2013. (DOI)
- Trnka J, Sedlak R, Kolář M, Hobza P: Differences in the Sublimation Energy of Benzene and Hexahalogenbenzenes Are Caused by Dispersion Energy. J. Phys. Chem. A, 117(20), 4331-4337, 2013. (DOI)
2012
- Georgakilas V, Otyepka M, Bourlinos AB, Chandra V, Kim N, Kemp KC, Hobza P, Zbořil R, Kim KS: Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications. Chem. Rev., 112(11), 6156-6214, 2012. (DOI)
- Granatier J, Lazar P, Prucek R, Šafářová K, Zbořil R, Otyepka M, Hobza P: Interaction of Graphene and Arenes with Noble Metals. J. Phys. Chem. C, 116(26), 14151-14162, 2012. (DOI)
- Granatier J, Pitoňák M, Hobza P: Accuracy of Several Wave Function and Density Functional Theory Methods for Description of Noncovalent Interaction of Saturated and Unsaturated Hydrocarbon Dimers. J. Chem. Theory Comput., 8(7), 2282-2292, 2012. (DOI)
- Haldar S, Kolář M, Sedlák R, Hobza P: Adsorption of Organic Electron Acceptors on Graphene-like Molecules: Quantum Chemical and Molecular Mechanical Study. J. Phys. Chem. C, 116(48), 25328-25336, 2012. (DOI)
- Hobza P: Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies. Acc. Chem. Res., 45(4), 663-672, 2012. (DOI)
- Kolář M, Hobza P: On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds. J. Chem. Theory Comput., 8(4), 1325-1333, 2012. (DOI)
- Kraus M, Pitoňák M, Hobza P, Urban M, Neogrády P: Highly correlated calculations using optimized virtual orbital space with controlled accuracy. Application to counterpoise corrected interaction energy calculations. Int. J. Quantum Chem., 112(4), 948-959, 2012. (DOI)
- Řezáč J, Hobza P: Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. J. Chem. Theory Comput., 8(1), 141-151, 2012. (DOI)
- Řezáč J, Riley KE, Hobza P: Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules. J. Chem. Theory Comput., 8(11), 4285-4292, 2012. (DOI)
- Řezáč J, Riley KE, Hobza P: Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes. J. Comput. Chem., 33(6), 691-694, 2012. (DOI)
- Riley KE, Platts JA, Řezáč J, Hobza P, Hill JG: Assessment of the Performance of MP2 and MP2 Variants for the Treatment of Noncovalent Interactions. J. Phys. Chem. A, 116(16), 4159-4169, 2012. (DOI)
- Riley KE, Řezáč J, Hobza P: The performance of MP2.5 and MP2.X methods for nonequilibrium geometries of molecular complexes. Phys. Chem. Chem. Phys., 14(38), 13187-13193, 2012. (DOI)
2011
- Černý J, Pitoňák M, Riley KE, Hobza P: Complete Basis Set Extrapolation and Hybrid Schemes for Geometry Gradients of Noncovalent Complexes. J. Chem. Theory Comput., 7(12), 3924-3934, 2011. (DOI)
- Dobeš P, Fanfrlík J, Řezáč J, Otyepka M, Hobza P: Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. J. Comput.-Aided Mol. Des., 25(3), 223-235, 2011. (DOI)
- Dobeš P, Řezáč J, Fanfrlík J, Otyepka M, Hobza P: Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails. J. Phys. Chem. B, 115(26), 8581-8589, 2011. (DOI)
- Granatier J, Lazar P, Otyepka M, Hobza P: The Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations. J. Chem. Theory Comput., 7(11), 3743-3755, 2011. (DOI)
- Kolář M, Fanfrlík J, Hobza P: Ligand Conformational and Solvation/Desolvation Free Energy in Protein−Ligand Complex Formation. J. Phys. Chem. B, 115(16), 4718-4724, 2011. (DOI)
- Kolář M, Kubař T, Hobza P: On the Role of London Dispersion Forces in Biomolecular Structure Determination. J. Phys. Chem. B, 115(24), 8038-8046, 2011. (DOI)
- Maity S, Patwari GN, Sedlak R, Hobza P: A pi-stacked phenylacetylene dimer. Phys. Chem. Chem. Phys., 13(37), 16706-16712, 2011. (DOI)
- Munusamy E, Sedlák R, Hobza P: On the Nature of the Stabilization of Benzene⋅⋅⋅Dihalogen and Benzene⋅⋅⋅Dinitrogen Complexes: CCSD(T)/CBS and DFT-SAPT Calculations. ChemPhysChem, 12(17), 3253-3261, 2011. (DOI)
- Pitoňák M, Aquilante F, Hobza P, Neogrády P, Noga J, Urban M: Parallelized implementation of the CCSD(T) method in MOLCAS using optimized virtual orbitals space and Cholesky decomposed two-electron integrals. Collect. Czech. Chem. Commun., 76(6), 713-742, 2011. (DOI)
- Přenosil O, Pitoňák M, Sedlák R, Kabeláč M, Hobza P: H-Bonding Cooperativity Effects in Amyloids: Quantum Mechanical and Molecular Mechanics Study. Z. Phys. Chem., 225(5), 553-574, 2011. (DOI)
- Řezáč J, Hobza P: A halogen-bonding correction for the semiempirical PM6 method. Chem. Phys. Lett., 506(4-6), 286-289, 2011. (DOI)
- Řezáč J, Riley KE, Hobza P: Extensions of the S66 Data Set: More Accurate Interaction Energies and Angular-Displaced Nonequilibrium Geometries. J. Chem. Theory Comput., 7(11), 3466-3470, 2011. (DOI)
- Riley KE, Hobza P: Strength and Character of Halogen Bonds in Protein–Ligand Complexes. Cryst. Growth Des., 11(10), 4272-4278, 2011. (DOI)
- Riley KE, Hobza P: Noncovalent interactions in biochemistry. WIREs Comput. Mol. Sci., 1(1), 3-17, 2011. (DOI)
- Riley KE, Řezáč J, Hobza P: MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets. Phys. Chem. Chem. Phys., 13(47), 21121-21125, 2011. (DOI)
- Řezáč J, Hobza P: Extrapolation and Scaling of the DFT-SAPT Interaction Energies toward the Basis Set Limit. J. Chem. Theory Comput., 7(3), 685-689, 2011. (DOI)
- Řezáč J, Riley KE, Hobza P: S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures. J. Chem. Theory Comput., 7(8), 2427-2438, 2011. (DOI)
- Spiwok V, Hobza P, Řezáč J: Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface. J. Phys. Chem. C, 115(40), 19455-19462, 2011. (DOI)
- Zelený T, Hobza P, Nachtigallová D, Ruckenbauer M, Lischka H: Photodynamics of the adenine model 4-aminopyrimidine embedded within double strand of DNA. Collect. Czech. Chem. Commun., 76(6), 631-643, 2011. (DOI)
- Zierkiewicz W, Wieczorek R, Hobza P, Michalska D: Halogen bonded complexes between volatile anaesthetics (chloroform, halothane, enflurane, isoflurane) and formaldehyde: a theoretical study. Phys. Chem. Chem. Phys., 13(11), 5105-5113, 2011. (DOI)
2010
- Berka K, Laskowski RA, Hobza P, Vondrášek J: Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins. J. Chem. Theory Comput., 6(7), 2191-2203, 2010. (DOI)
- Černý J, Hobza P: Energy barriers between H-bonded and stacked structures of 9-methyladenine⋯1-methylthymine and 9-methylguanine⋯1-methylcytosine complexes. Chem. Commun., 46(3), 383-385, 2010. (DOI)
- Crews BO, Abo-Riziq A, Pluháčková K, Thompson P, Hill G, Hobza P, de Vries MS: Guanine–aspartic acid interactions probed with IR–UV resonance spectroscopy. Phys. Chem. Chem. Phys., 12(14), 3597-3605, 2010. (DOI)
- Fanfrlík J, Bronowska AK, Řezáč J, Přenosil O, Konvalinka J, Hobza P: A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands. J. Phys. Chem. B, 114(39), 12666-12678, 2010. (DOI)
- Gráfová L, Pitoňák M, Řezáč J, Hobza P: Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set. J. Chem. Theory Comput., 6(8), 2365-2376, 2010. (DOI)
- Kolář M, Berka K, Jurečka P, Hobza P: On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes. ChemPhysChem, 11(11), 2399-2408, 2010. (DOI)
- Korth M, Pitoňák M, Řezáč J, Hobza P: A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. J. Chem. Theory Comput., 6(1), 344-352, 2010. (DOI)
- Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys. Chem. Chem. Phys., 12(14), 3522-3534, 2010. (DOI)
- Nachtigallová D, Zelený T, Ruckenbauer M, Müller T, Barbatti M, Hobza P, Lischka H: Does Stacking Restrain the Photodynamics of Individual Nucleobases? J. Am. Chem. Soc., 132(24), 8261-8263, 2010. (DOI)
- Pitoňák M, Neogrády P, Hobza P: Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study. Phys. Chem. Chem. Phys., 12(6), 1369-1378, 2010. (DOI)
- Pitoňák M, Řezáč J, Hobza P: Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions. Phys. Chem. Chem. Phys., 12(33), 9611-9614, 2010. (DOI)
- Riley KE, Pitoňák M, Černý J, Hobza P: On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X−H···pi): WFT and DFT Calculations. J. Chem. Theory Comput., 6(1), 66-80, 2010. (DOI)
- Riley KE, Pitoňák M, Jurečka P, Hobza P: Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories. Chem. Rev., 110(9), 5023-5063, 2010. (DOI)
- Svozil D, Hobza P, Šponer J: Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations? J. Phys. Chem. B, 114(2), 1191-1203, 2010. (DOI)
- Zgarbová M, Otyepka M, Šponer J, Hobza P, Jurečka P: Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys. Chem. Chem. Phys., 12(35), 10476-10493, 2010. (DOI)
- Zierkiewicz W, Michalska D, Hobza P: Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study. Phys. Chem. Chem. Phys., 12(12), 2888-2894, 2010. (DOI)
2009
- Berka K, Hobza P, Vondrášek J: Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin. ChemPhysChem, 10(3), 543-548, 2009. (DOI)
- Černý J, Vondrášek J, Hobza P: Loss of Dispersion Energy Changes the Stability and Folding/Unfolding Equilibrium of the Trp-Cage Protein. J. Phys. Chem. B, 113(16), 5657-5660, 2009. (DOI)
- Kabeláč M, Hobza P, Špirko V: The ab initio assigning of the vibrational probing modes of tryptophan: linear shifting of approximate anharmonic frequencies vs. multiplicative scaling of harmonic frequencies. Phys. Chem. Chem. Phys., 11(20), 3921-3926, 2009. (DOI)
- Kabeláč M, Hobza P, Špirko V: The structure and vibrational dynamics of the pyrrole dimer. Phys. Chem. Chem. Phys., 11(20), 3885-3891, 2009. (DOI)
- Maity S, Sedlák R, Hobza P, Patwari GN: Infrared–optical double resonance spectroscopic measurements and high level ab initio calculations on a binary complex between phenylacetylene and borane-trimethylamine. Understanding the role of C–H⋯pi interactions. Phys. Chem. Chem. Phys., 11(42), 9738-9743, 2009. (DOI)
- Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J: Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description. J. Chem. Theory Comput., 5(6), 1524-1544, 2009. (DOI)
- Pitoňák M, Janowski T, Neogrády P, Pulay P, Hobza P: Convergence of the CCSD(T) Correction Term for the Stacked Complex Methyl Adenine−Methyl Thymine: Comparison with Lower-Cost Alternatives. J. Chem. Theory Comput., 5(7), 1761-1766, 2009. (DOI)
- Ran J, Hobza P: On the Nature of Bonding in Lone Pair···pi-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations. J. Chem. Theory Comput., 5(4), 1180-1185, 2009. (DOI)
- Ran J, Hobza P: Nature of Bonding in Nine Planar Hydrogen-Bonded Adenine···Thymine Base Pairs. J. Phys. Chem. B, 113(9), 2933-2936, 2009. (DOI)
- Řezáč J, Fanfrlík J, Salahub D, Hobza P: Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes. J. Chem. Theory Comput., 5(7), 1749-1760, 2009. (DOI)
- Riley KE, Murray JS, Politzer P, Concha MC, Hobza P: Br···O Complexes as Probes of Factors Affecting Halogen Bonding: Interactions of Bromobenzenes and Bromopyrimidines with Acetone. J. Chem. Theory Comput., 5(1), 155-163, 2009. (DOI)
- Sedlák R, Hobza P, Patwari GN: Hydrogen-Bonded Complexes of Phenylacetylene with Water, Methanol, Ammonia, and Methylamine. The Origin of Methyl Group-Induced Hydrogen Bond Switching. J. Phys. Chem. A, 113(24), 6620-6625, 2009. (DOI)
- Šponer J, Zgarbová M, Jurečka P, Riley KE, Šponer JE, Hobza P: Reference Quantum Chemical Calculations on RNA Base Pairs Directly Involving the 2′-OH Group of Ribose. J. Chem. Theory Comput., 5(4), 1166-1179, 2009. (DOI)
- Valdes H, Pluháčková K, Hobza P: Phenylalanyl-Glycyl-Phenylalanine Tripeptide: A Model System for Aromatic−Aromatic Side Chain Interactions in Proteins. J. Chem. Theory Comput., 5(9), 2248-2256, 2009. (DOI)
- Zelený T, Hobza P, Kabeláč M: Microhydration of guanine⋯cytosine base pairs, a theoretical Study on the role of water in stability, structure and tautomeric equilibrium. Phys. Chem. Chem. Phys., 11(18), 3430-3435, 2009. (DOI)
2008
- Černý J, Kabeláč M, Hobza P: Double-Helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of Dispersion Energy. J. Am. Chem. Soc., 130(47), 16055-16059, 2008. (DOI)
- Pitoňák M, Neogrády P, Řezáč J, Jurečka P, Urban M, Hobza P: Benzene Dimer: High-Level Wave Function and Density Functional Theory Calculations. J. Chem. Theory Comput., 4(11), 1829-1834, 2008. (DOI)
- Pluháčková K, Grimme S, Hobza P: On the Importance of Electron Correlation Effects for the Intramolecular Stacking Geometry of a Bis-Thiophene Derivative. J. Phys. Chem. A, 112(48), 12469-12474, 2008. (DOI)
- Řezáč J, Jurečka P, Riley KE, Černý J, Valdes H, Pluháčková K, Berka K, Řezáč T, Pitoňák M, Vondrášek J, Hobza P: Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples. Collect. Czech. Chem. Commun., 73(10), 1261-1270, 2008. (DOI)
2007
- Bendová L, Jurečka P, Hobza P, Vondrášek J: Model of Peptide Bond−Aromatic Ring Interaction: Correlated Ab Initio Quantum Chemical Study. J. Phys. Chem. B, 111(33), 9975-9979, 2007. (DOI)
- Černý J, Jurečka P, Hobza P, Valdés H: Resolution of Identity Density Functional Theory Augmented with an Empirical Dispersion Term (RI-DFT-D): A Promising Tool for Studying Isolated Small Peptides. J. Phys. Chem. A, 111(6), 1146-1154, 2007. (DOI)
- Jurečka P, Černý J, Hobza P, Salahub DR: Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. J. Comput. Chem., 28(2), 555-569, 2007. (DOI)
- Kubař T, Jurečka P, Černý J, Řezáč J, Otyepka M, Valdés H, Hobza P: Density-Functional, Density-Functional Tight-Binding, and Wave Function Calculations on Biomolecular Systems. J. Phys. Chem. A, 111(26), 5642-5647, 2007. (DOI)
- Lee EC, Kim D, Jurečka P, Tarakeshwar P, Hobza P, Kim KS: Understanding of Assembly Phenomena by Aromatic−Aromatic Interactions: Benzene Dimer and the Substituted Systems. J. Phys. Chem. A, 111(18), 3446-3457, 2007. (DOI)
- Pluháčková K, Jurečka P, Hobza P: Stabilisation energy of C 6 H 6 ⋯C 6 X 6 (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels. Phys. Chem. Chem. Phys., 9(6), 755-760, 2007. (DOI)
- Sedlák R, Jurečka P, Hobza P: Density functional theory-symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry. J. Chem. Phys., 127(7), 075104, 2007. (DOI)
2006
- Dobeš P, Otyepka M, Strnad M, Hobza P: Interaction Energies for the Purine Inhibitor Roscovitine with Cyclin-Dependent Kinase 2: Correlated Ab Initio Quantum-Chemical, DFT and Empirical Calculations. Chem. Eur. J., 12(16), 4297-4304, 2006. (DOI)
- Otyepka M, Sklenovský P, Horinek D, Kubař T, Hobza P: How the Stabilization of INK4 Tumor Suppressor 3D Structure Evaluated by Quantum Chemical and Molecular Mechanics Calculations Corresponds Well with Experimental Results: Interplay of Association Enthalpy, Entropy, and Solvation Effects. J. Phys. Chem. B, 110(9), 4423-4429, 2006. (DOI)