prof. Ing. Pavel Hobza, DrSc., FRSC

Tel: 58 563 4760, E-mail: pavel.hobza@upol.cz, Room: 3.006

Research interests Education Employment International experience

Publications

2020

  1. 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

  1. 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)
  2. 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)
  3. Hobza P: In My Element: Hydrogen Chem. Eur. J., 25(6), 1367-1368, 2019. (DOI)
  4. 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)
  5. 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)
  6. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. Kolář MH, Hobza P: Computer Modeling of Halogen Bonds and Other σ-Hole Interactions. Chem. Rev., 116(9), 5155–5187, 2016. (DOI)
  7. 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)
  8. 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)
  9. 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)
  10. Řezáč J, Hobza P: Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications. Chem. Rev., 116(9), 5038–5071, 2016. (DOI)
  11. 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)
  12. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. Sedlak R, Fanfrlik J, Pecina A, Hnyk D, Hobza P, Lepšík M: Noncovalent Interactions of Heteroboranes. Boron, 20, 219-239, 2015. (DOI)
  13. Sedlák R, Kolář MH, Hobza P: Polar Flattening and the Strength of Halogen Bonding. J. Chem. Theory Comput., 11(10), 4727-4732, 2015. (DOI)
  14. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. Kolář M, Hobza P, Bronowska AK: Plugging the explicit sigma-holes in molecular docking. Chem. Commun., 49(10), 981-983, 2013. (DOI)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. 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)
  16. 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)
  17. 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)
  18. 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)
  19. 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)
  20. 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)
  21. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. Hobza P: Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies. Acc. Chem. Res., 45(4), 663-672, 2012. (DOI)
  6. 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)
  7. 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)
  8. 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)
  9. Řezáč J, Riley KE, Hobza P: Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules. J. Chem. Theory Comput., 8(11), 4285-4292, 2012. (DOI)
  10. 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)
  11. 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)
  12. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. Maity S, Patwari GN, Sedlak R, Hobza P: A pi-stacked phenylacetylene dimer. Phys. Chem. Chem. Phys., 13(37), 16706-16712, 2011. (DOI)
  8. 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)
  9. 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)
  10. 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)
  11. Řezáč J, Hobza P: A halogen-bonding correction for the semiempirical PM6 method. Chem. Phys. Lett., 506(4-6), 286-289, 2011. (DOI)
  12. 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)
  13. Riley KE, Hobza P: Strength and Character of Halogen Bonds in Protein–Ligand Complexes. Cryst. Growth Des., 11(10), 4272-4278, 2011. (DOI)
  14. Riley KE, Hobza P: Noncovalent interactions in biochemistry. WIREs Comput. Mol. Sci., 1(1), 3-17, 2011. (DOI)
  15. 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)
  16. 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)
  17. 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)
  18. 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)
  19. 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)
  20. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. 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)
  16. 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

  1. Berka K, Hobza P, Vondrášek J: Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin. ChemPhysChem, 10(3), 543-548, 2009. (DOI)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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

  1. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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

  1. 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)
  2. 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)