Pavel Hobza

Pavel Hobza

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Pavel Hobza

Publications by authors named "Pavel Hobza"

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An Isolated Molecule of Iron(II) Phthalocyanin Exhibits Quintet Ground-State: A Nexus between Theory and Experiment.

Chemistry 2018 Sep 29;24(51):13413-13417. Epub 2018 Aug 29.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610, Prague 6, Czech Republic.

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http://dx.doi.org/10.1002/chem.201803380DOI Listing
September 2018

Comparison of the DFT-SAPT and Canonical EDA Schemes for the Energy Decomposition of Various Types of Noncovalent Interactions.

J Chem Theory Comput 2018 Jul 21;14(7):3440-3450. Epub 2018 Jun 21.

Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.8b00034DOI Listing
July 2018

Understanding the non-covalent interaction mediated modulations on the electronic structure of quasi-zero-dimensional graphene nanoflakes.

Phys Chem Chem Phys 2018 Jul;20(27):18718-18728

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c8cp02027bDOI Listing
July 2018

Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes.

Chemphyschem 2018 04 19;19(7):873-879. Epub 2018 Feb 19.

Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.

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http://dx.doi.org/10.1002/cphc.201701104DOI Listing
April 2018

The role of the σ-holes in stability of non-bonded chalcogenidebenzene interactions: the ground and excited states.

Phys Chem Chem Phys 2017 Dec;20(1):299-306

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c7cp05537dDOI Listing
December 2017

Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box.

Nat Commun 2017 10 16;8(1):938. Epub 2017 Oct 16.

Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 710069, Xi'an, China.

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http://dx.doi.org/10.1038/s41467-017-00915-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5643546PMC
October 2017

Pnictogen bonding in pyrazine•PnX (Pn = P, As, Sb and X = F, Cl, Br) complexes.

J Mol Model 2017 Oct 30;23(11):328. Epub 2017 Oct 30.

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic.

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http://dx.doi.org/10.1007/s00894-017-3502-xDOI Listing
October 2017

Non-covalent interactions in anisole-(CO) (n = 1, 2) complexes.

Phys Chem Chem Phys 2017 Aug;19(34):22749-22758

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c7cp03763eDOI Listing
August 2017

B-Hπ: a nonclassical hydrogen bond or dispersion contact?

Phys Chem Chem Phys 2017 Jul;19(28):18194-18200

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c7cp02762aDOI Listing
July 2017

Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein-Ligand Complexes in Cognate Docking.

ACS Omega 2017 Jul 27;2(7):4022-4029. Epub 2017 Jul 27.

Department of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nam. 2, 16610 Praha 6, Czech Republic.

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http://dx.doi.org/10.1021/acsomega.7b00503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044937PMC
July 2017

Binary twinned-icosahedral [BH] interacts with cyclodextrins as a precedent for its complexation with other organic motifs.

Phys Chem Chem Phys 2017 May;19(19):11748-11752

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic.

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http://xlink.rsc.org/?DOI=C7CP01074E
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http://dx.doi.org/10.1039/c7cp01074eDOI Listing
May 2017

Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite.

J Chem Theory Comput 2017 Mar 14;13(3):1328-1340. Epub 2017 Feb 14.

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. listopadu 12, 77 146 Olomouc, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.6b01130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5352977PMC
March 2017

Unraveling the Structure-Affinity Relationship between Cucurbit[n]urils (n = 7, 8) and Cationic Diamondoids.

J Am Chem Soc 2017 03 21;139(8):3249-3258. Epub 2017 Feb 21.

Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States.

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http://dx.doi.org/10.1021/jacs.7b00056DOI Listing
March 2017

Noncovalent Interactions in Specific Recognition Motifs of Protein-DNA Complexes.

J Chem Theory Comput 2017 Feb 6;13(2):877-885. Epub 2017 Jan 6.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.6b00775DOI Listing
February 2017

SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses.

J Chem Inf Model 2017 02 17;57(2):127-132. Epub 2017 Jan 17.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/acs.jcim.6b00513DOI Listing
February 2017

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 2017 Jan 11;126:1118-1128. Epub 2016 Dec 11.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2016.12.023DOI Listing
January 2017

Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes.

Chemphyschem 2016 Nov 22;17(21):3373-3376. Epub 2016 Sep 22.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic v.v.i., Flemingovo nám. 2, 16610, Prague 6, Czech Republic.

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http://dx.doi.org/10.1002/cphc.201600848DOI Listing
November 2016

IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors.

ACS Chem Biol 2016 10 5;11(10):2693-2705. Epub 2016 Aug 5.

Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS , 1 rue Laurent Fries 67404 CEDEX Illkirch, France.

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http://dx.doi.org/10.1021/acschembio.6b00382DOI Listing
October 2016

Computer Modeling of Halogen Bonds and Other σ-Hole Interactions.

Chem Rev 2016 05 3;116(9):5155-87. Epub 2016 Feb 3.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 16610 Prague, Czech Republic.

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http://dx.doi.org/10.1021/acs.chemrev.5b00560DOI Listing
May 2016

Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications.

Chem Rev 2016 05 4;116(9):5038-71. Epub 2016 Mar 4.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/acs.chemrev.5b00526DOI Listing
May 2016

Introduction: Noncovalent Interactions.

Chem Rev 2016 05;116(9):4911-2

Academy of Sciences of the Czech Republic, Prague.

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http://dx.doi.org/10.1021/acs.chemrev.6b00247DOI Listing
May 2016

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 2016 Apr 17;12(4):1696-704. Epub 2016 Mar 17.

Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.6b00065DOI Listing
April 2016

Computational methods for the description of pharmacologically relevant platinum complexes--molecular structure and bond dissociation.

Phys Chem Chem Phys 2016 Feb;18(5):4051-62

Gilead Sciences & IOCB Research Center, Department of Computational Chemistry, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic. and Department of Physical Chemistry, Palacky University, 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1039/c5cp03391hDOI Listing
February 2016

The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation.

Chem Commun (Camb) 2016 Feb;52(16):3312-5

Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, D-14195 Berlin, Germany.

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http://dx.doi.org/10.1039/c5cc09499bDOI Listing
February 2016

On the nature of the stabilisation of the E···π pnicogen bond in the SbCl3···toluene complex.

Chem Commun (Camb) 2016 Feb 3;52(17):3500-3. Epub 2016 Feb 3.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c5cc10363kDOI Listing
February 2016

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 Trans 2016 Jan;45(2):462-5

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic. and Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1039/c5dt04381fDOI Listing
January 2016

From Dibismuthenes to Three- and Two-Coordinated Bismuthinidenes by Fine Ligand Tuning: Evidence for Aromatic BiC3N Rings through a Combined Experimental and Theoretical Study.

Chemistry 2015 Nov 5;21(47):16917-28. Epub 2015 Oct 5.

Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, Pardubice 532 10 (Czech Republic).

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http://dx.doi.org/10.1002/chem.201502724DOI Listing
November 2015

A comparison of ab initio quantum-mechanical and experimental D0 binding energies of eleven H-bonded and eleven dispersion-bound complexes.

Phys Chem Chem Phys 2015 Oct;17(40):26645-52

Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovonám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c5cp04427hDOI Listing
October 2015

Polar flattening and the strength of halogen bonding.

J Chem Theory Comput 2015 Oct 23;11(10):4727-32. Epub 2015 Sep 23.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.5b00687DOI Listing
October 2015

Characteristics of a σ-Hole and the Nature of a Halogen Bond.

Top Curr Chem 2015 ;359:1-25

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic.

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http://dx.doi.org/10.1007/128_2014_606DOI Listing
September 2015

Correction: The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole.

Phys Chem Chem Phys 2015 Sep 17;17(35):23279-80. Epub 2015 Aug 17.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c5cp90146dDOI Listing
September 2015

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 2015 Sep 6;11(9):4086-92. Epub 2015 Aug 6.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.5b00398DOI Listing
September 2015

The properties of substituted 3D-aromatic neutral carboranes: the potential for σ-hole bonding.

Phys Chem Chem Phys 2015 Aug 27;17(32):20814-21. Epub 2015 Jul 27.

Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c5cp03617hDOI Listing
August 2015

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.

J Chem Theory Comput 2015 Aug;11(8):3866-77

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tř. 17. Listopadu 12, 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1021/acs.jctc.5b00010DOI Listing
August 2015

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 18;2014:389869. Epub 2014 Sep 18.

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 140 00 Prague 4, Czech Republic ; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

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http://downloads.hindawi.com/journals/bmri/2014/389869.pdf
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http://www.hindawi.com/journals/bmri/2014/389869/
Publisher Site
http://dx.doi.org/10.1155/2014/389869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189773PMC
July 2015

The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition.

ACS Chem Biol 2015 Jul 6;10(7):1637-42. Epub 2015 May 6.

†Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/acschembio.5b00151DOI Listing
July 2015

Extensions and applications of the A24 data set of accurate interaction energies.

Phys Chem Chem Phys 2015 Jul;17(29):19268-77

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1039/c5cp03151fDOI Listing
July 2015

Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods.

J Chem Theory Comput 2015 Jul;11(7):3065-79

Department of Chemistry, University of California , Riverside, California 92521 United States.

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http://dx.doi.org/10.1021/acs.jctc.5b00281DOI Listing
July 2015

Influence of hydrophobic residues on the binding of CB[7] toward diammonium ions of common ammonium···ammonium distance.

Org Biomol Chem 2015 Jun;13(22):6249-54

Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1039/c5ob00784dDOI Listing
June 2015

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 2015 May;17(19):12530-7

Dipartimento di Chimica 'Ugo Schiff' Università di Firenze, via della Lastruccia 3 and LENS, via N. Carrara 1, 50019 Sesto Fiorentino (FI), Italy.

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http://dx.doi.org/10.1039/c5cp01166cDOI Listing
May 2015

Binding energies of the π-stacked anisole dimer: new molecular beam-laser spectroscopy experiments and CCSD(T) calculations.

Chemistry 2015 Apr 5;21(18):6740-6. Epub 2015 Mar 5.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic).

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http://dx.doi.org/10.1002/chem.201406134DOI Listing
April 2015

Chalcogen and pnicogen bonds in complexes of neutral icosahedral and bicapped square-antiprismatic heteroboranes.

J Phys Chem A 2015 Feb 12;119(8):1388-95. Epub 2015 Feb 12.

Gilead Sciences and IOCB Research Center and Institute of Organic Chemistry and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, v.v.i. , Flemingovo nám. 2, 16610 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp511101nDOI Listing
February 2015

Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.

Eur J Med Chem 2015 Jan 16;89:189-97. Epub 2014 Oct 16.

Institute of Organic Chemistry and Biochemistry, Gilead Sciences and IOCB Research Centre, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2014.10.043DOI Listing
January 2015

The nature of bonding and electronic properties of graphene and benzene with iridium adatoms.

Phys Chem Chem Phys 2014 Oct 28;16(38):20818-27. Epub 2014 Aug 28.

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1039/c4cp02608jDOI Listing
October 2014

Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy.

Phys Chem Chem Phys 2014 Oct 29;16(38):20915-23. Epub 2014 Aug 29.

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1039/c4cp02093fDOI Listing
October 2014

The dominant role of chalcogen bonding in the crystal packing of 2D/3D aromatics.

Angew Chem Int Ed Engl 2014 Sep 27;53(38):10139-42. Epub 2014 Jul 27.

Gilead Sciences Research Center and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, 16610 Prague 6 (Czech Republic).

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http://dx.doi.org/10.1002/anie.201405901DOI Listing
September 2014

Evaluation of composite schemes for CCSDT(Q) calculations of interaction energies of noncovalent complexes.

Phys Chem Chem Phys 2014 Sep;16(36):19115-21

Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic.

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http://dx.doi.org/10.1039/c4cp02617aDOI Listing
September 2014

Statistical analysis of σ-holes: a novel complementary view on halogen bonding.

Phys Chem Chem Phys 2014 Sep;16(36):19111-4

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c4cp02621gDOI Listing
September 2014

Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer.

J Chem Theory Comput 2014 Aug 25;10(8):3066-73. Epub 2014 Jun 25.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/ct500047xDOI Listing
August 2014

The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole.

Phys Chem Chem Phys 2014 Jun 30;16(21):9987-96. Epub 2014 Jan 30.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c3cp55188aDOI Listing
June 2014

Why Is the L-Shaped Structure of X···X (X = F, Cl, Br, I) Complexes More Stable Than Other Structures?

J Phys Chem A 2014 May 14;118(21):3846-3855. Epub 2014 May 14.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp502648eDOI Listing
May 2014

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 2014 Apr 3;16(14):6679-86. Epub 2014 Mar 3.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c4cp00055bDOI Listing
April 2014

Erratum to "S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures".

J Chem Theory Comput 2014 Mar;10(3):1359-60

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ct5000692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954041PMC
March 2014

Halogen bonds in crystal TTF derivatives: an ab initio quantum mechanical study.

Phys Chem Chem Phys 2014 Feb;16(5):2038-47

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c3cp53976hDOI Listing
February 2014

Quantum mechanics-based scoring rationalizes the irreversible inactivation of parasitic Schistosoma mansoni cysteine peptidase by vinyl sulfone inhibitors.

J Phys Chem B 2013 Dec 21;117(48):14973-82. Epub 2013 Nov 21.

Institute of Organic Chemistry and Biochemistry, v.v.i., and Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic , Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp409604nDOI Listing
December 2013

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 2013 Dec 11;117(50):16096-104. Epub 2013 Dec 11.

Institute of Organic Chemistry and Biochemistry (IOCB), Academy of Sciences of the Czech Republic , v.v.i., Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 166 10, Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp410216mDOI Listing
December 2013

Off-Center Gaussian Functions, an Alternative Atomic Orbital Basis Set for Accurate Noncovalent Interaction Calculations of Large Systems.

J Chem Theory Comput 2013 Dec 19;9(12):5296-304. Epub 2013 Nov 19.

Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University , Mlynská Dolina, 842 15 Bratislava, Slovakia.

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http://dx.doi.org/10.1021/ct400692bDOI Listing
December 2013

Modulation of aldose reductase inhibition by halogen bond tuning.

ACS Chem Biol 2013 Nov 17;8(11):2484-92. Epub 2013 Sep 17.

Institute of Organic Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/cb400526nDOI Listing
November 2013

The relative roles of electrostatics and dispersion in the stabilization of halogen bonds.

Phys Chem Chem Phys 2013 Nov;15(41):17742-51

Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, Box 22, New Orleans, LA 70125, USA.

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http://dx.doi.org/10.1039/c3cp52768aDOI Listing
November 2013

Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy.

J Chem Theory Comput 2013 Oct 6;9(10):4287-92. Epub 2013 Sep 6.

Department of Physics and CHiPS, North Carolina State University , Raleigh, North Carolina 27695, United States.

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http://dx.doi.org/10.1021/ct4006739DOI Listing
October 2013

Convergence of the Interaction Energies in Noncovalent Complexes in the Coupled-Cluster Methods Up to Full Configuration Interaction.

J Chem Theory Comput 2013 Aug 18;9(8):3420-8. Epub 2013 Jul 18.

Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University , 771 46 Olomouc, Czech Republic.

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http://dx.doi.org/10.1021/ct4002762DOI Listing
August 2013

The accuracy of quantum chemical methods for large noncovalent complexes.

J Chem Theory Comput 2013 Aug;9(8):3364-3374

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic ; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Albertov 6, 128 43 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ct400036bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789125PMC
August 2013

Competition between halogen, dihalogen and hydrogen bonds in bromo- and iodomethanol dimers.

J Mol Model 2013 Jul 8;19(7):2879-83. Epub 2013 Jan 8.

Department of Chemistry, Xavier University of Louisiana, New Orleans, LA 17025, USA.

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http://link.springer.com/10.1007/s00894-012-1727-2
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July 2013

Assessing the accuracy and performance of implicit solvent models for drug molecules: conformational ensemble approaches.

J Phys Chem B 2013 May 6;117(19):5950-62. Epub 2013 May 6.

Institute of Organic Chemistry and Biochemistry and Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, v.v.i., 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp402117cDOI Listing
May 2013

Differences in the sublimation energy of benzene and hexahalogenbenzenes are caused by dispersion energy.

J Phys Chem A 2013 May 10;117(20):4331-7. Epub 2013 May 10.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam 2, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/jp401961gDOI Listing
May 2013

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 2013 May 4;9(5):2151-5. Epub 2013 Apr 4.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ct400057wDOI Listing
May 2013

On the importance and origin of aromatic interactions in chemistry and biodisciplines.

Acc Chem Res 2013 Apr 8;46(4):927-36. Epub 2012 Aug 8.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.

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http://pubs.acs.org/doi/10.1021/ar300083h
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April 2013

On the nature of unusual intensity changes in the infrared spectra of the enflurane···acetone complexes.

Phys Chem Chem Phys 2013 Apr 15;15(16):6001-7. Epub 2013 Mar 15.

Faculty of Chemistry, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.

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http://dx.doi.org/10.1039/c3cp50385bDOI Listing
April 2013

Quantum mechanical scoring: structural and energetic insights into cyclin-dependent kinase 2 inhibition by pyrazolo[1,5-a]pyrimidines.

Curr Comput Aided Drug Des 2013 Mar;9(1):118-29

Institute of Organic Chemistry and Biochemistry, v.v.i. and Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, Czech Republic.

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March 2013

MP2.5 and MP2.X: approaching CCSD(T) quality description of noncovalent interaction at the cost of a single CCSD iteration.

Chemphyschem 2013 Mar 11;14(4):698-707. Epub 2013 Jan 11.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1002/cphc.201200850DOI Listing
March 2013

Spin-Crossing in an Organometallic Pt-Benzene Complex.

J Chem Theory Comput 2013 Mar 28;9(3):1461-8. Epub 2013 Feb 28.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/ct400016cDOI Listing
March 2013

Plugging the explicit σ-holes in molecular docking.

Chem Commun (Camb) 2013 Feb 21;49(10):981-3. Epub 2012 Dec 21.

Institute of Organic Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic.

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http://dx.doi.org/10.1039/c2cc37584bDOI Listing
February 2013

Quantification of the interaction forces between metals and graphene by quantum chemical calculations and dynamic force measurements under ambient conditions.

ACS Nano 2013 Feb 30;7(2):1646-51. Epub 2013 Jan 30.

Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 77146 Olomouc, Czech Republic.

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http://pubs.acs.org/doi/10.1021/nn305608a
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February 2013

Basis Set Dependence of Interaction Energies Computed Using Composite Post-MP2 Methods.

J Chem Theory Comput 2013 Jan 27;9(1):330-7. Epub 2012 Nov 27.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems , 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ct300842dDOI Listing
January 2013

CCSD[T] Describes Noncovalent Interactions Better than the CCSD(T), CCSD(TQ), and CCSDT Methods.

J Chem Theory Comput 2013 Jan 16;9(1):364-9. Epub 2012 Nov 16.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ct3008777DOI Listing
January 2013

Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications.

Chem Rev 2012 Nov 25;112(11):6156-214. Epub 2012 Sep 25.

Institute of Materials Science, NCSR "Demokritos", Athens, Greece.

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http://dx.doi.org/10.1021/cr3000412DOI Listing
November 2012

Benchmark Calculations of Noncovalent Interactions of Halogenated Molecules.

J Chem Theory Comput 2012 Nov 28;8(11):4285-92. Epub 2012 Sep 28.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ct300647kDOI Listing
November 2012

The performance of MP2.5 and MP2.X methods for nonequilibrium geometries of molecular complexes.

Phys Chem Chem Phys 2012 Oct;14(38):13187-93

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic.

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http://dx.doi.org/10.1039/c2cp41874fDOI Listing
October 2012

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 2012 Jul 4;8(7):2282-92. Epub 2012 Jun 4.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v. v. i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic.

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http://dx.doi.org/10.1021/ct300215pDOI Listing
July 2012

Calculations on noncovalent interactions and databases of benchmark interaction energies.

Authors:
Pavel Hobza

Acc Chem Res 2012 Apr 6;45(4):663-72. Epub 2012 Jan 6.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ar200255pDOI Listing
April 2012

Assessment of the performance of MP2 and MP2 variants for the treatment of noncovalent interactions.

J Phys Chem A 2012 Apr 18;116(16):4159-69. Epub 2012 Apr 18.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic.

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http://dx.doi.org/10.1021/jp211997bDOI Listing
April 2012

On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds.

J Chem Theory Comput 2012 Apr 20;8(4):1325-33. Epub 2012 Mar 20.

Institute of Organic Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague 6, The Czech Republic.

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http://dx.doi.org/10.1021/ct2008389DOI Listing
April 2012

Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes.

J Comput Chem 2012 Mar 16;33(6):691-4. Epub 2011 Dec 16.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1002/jcc.22899DOI Listing
March 2012

Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods.

J Chem Theory Comput 2012 Jan 22;8(1):141-51. Epub 2011 Dec 22.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1021/ct200751eDOI Listing
January 2012

On the nature of the stabilization of benzene···dihalogen and benzene···dinitrogen complexes: CCSD(T)/CBS and DFT-SAPT calculations.

Chemphyschem 2011 Dec 13;12(17):3253-61. Epub 2011 Oct 13.

Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea.

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http://dx.doi.org/10.1002/cphc.201100455DOI Listing
December 2011

MP2.X: a generalized MP2.5 method that produces improved binding energies with smaller basis sets.

Phys Chem Chem Phys 2011 Dec 24;13(47):21121-5. Epub 2011 Oct 24.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic.

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http://dx.doi.org/10.1039/c1cp22525aDOI Listing
December 2011

Complete Basis Set Extrapolation and Hybrid Schemes for Geometry Gradients of Noncovalent Complexes.

J Chem Theory Comput 2011 Dec 28;7(12):3924-34. Epub 2011 Oct 28.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v. v. i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic.

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http://dx.doi.org/10.1021/ct200484eDOI Listing
December 2011

A π-stacked phenylacetylene dimer.

Phys Chem Chem Phys 2011 Oct 19;13(37):16706-12. Epub 2011 Aug 19.

Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India.

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http://xlink.rsc.org/?DOI=c1cp20677j
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October 2011

Autobiography of Pavel Hobza.

Authors:
Pavel Hobza

J Phys Chem A 2011 Oct;115(41):11115-8

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic.

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http://dx.doi.org/10.1021/jp208265uDOI Listing
October 2011

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 2011 Jul 16;115(26):8581-9. Epub 2011 Jun 16.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.

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http://dx.doi.org/10.1021/jp202149zDOI Listing
July 2011

Isolated gramicidin peptides probed by IR spectroscopy.

Chemphyschem 2011 Jul 8;12(10):1816-21. Epub 2011 Jun 8.

FOM Institute for Plasma Physics Rijnhuizen, Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands.

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http://dx.doi.org/10.1002/cphc.201100212DOI Listing
July 2011

Nonadiabatic dynamics of uracil: population split among different decay mechanisms.

J Phys Chem A 2011 Jun 6;115(21):5247-55. Epub 2011 May 6.

Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic.

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http://dx.doi.org/10.1021/jp201327wDOI Listing
June 2011

On the role of London dispersion forces in biomolecular structure determination.

J Phys Chem B 2011 Jun 27;115(24):8038-46. Epub 2011 May 27.

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

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http://dx.doi.org/10.1021/jp202878dDOI Listing
June 2011