2013

Jaklová Dytrtová J., Fanfrlík J., Norková R., Jakl M., Hobza P.:
Theoretical insight into the stabilization of triazole fungicides via their interactions with dications .
International Journal of Mass Spectrometry in press, 2013.

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 .
Journal of Physical Chemistry B 117: 16096-16104, 2013.

Meliá C., Ferrer S., Řezáč J., Parisel O., Reinaud O., Moliner V., De La Lande A.:
Investigation of the hydroxylation mechanism of noncoupled copper oxygenases by Ab initio molecular dynamics simulations .
Chemistry - A European Journal 19: 17328-17337, 2013.

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 .
Journal of Chemical Theory and Computation 9: 5296-5304, 2013.

Fanfrlík J., Brahmkshatriya P.S., 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 .
Journal of Physical Chemistry B 117: 14973-14982, 2013.

Fanfrlík J., Kolář M., Kamlar M., Hurný D., Ruiz F.X., 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 Chemical Biology 8: 2484-2492, 2013.

Patel C., Dršata T., Lankaš F., Dumont E.:
Structure dynamics and interactions of a C4′-oxidized abasic site in DNA: A concomitant strand scission reverses affinities .
Biochemistry 52: 8115-8125, 2013.

Riley K.E., Hobza P.:
The relative roles of electrostatics and dispersion in the stabilization of halogen bonds .
Physical Chemistry Chemical Physics 15: 17742-17751, 2013.

Riley K.E., Murray J.S., Fanfrlík J., Řezáč J., Solá R.J., Concha M.C., Ramos F.M., Politzer P.:
Halogen bond tunability II: The varying roles of electrostatic and dispersion contributions to attraction in halogen bonds .
Journal of Molecular Modeling 19: 4651-4659, 2013.

Dubecký M., Jurečka P., Derian R., Hobza P., Otyepka M., Mitas L.:
Quantum Monte Carlo methods describe noncovalent interactions with subchemical accuracy .
Journal of Chemical Theory and Computation 9: 4287-4292, 2013.

Dršata T., Kara M., Zacharias M., Lankaš F.:
Effect of 8-oxoguanine on DNA structure and deformability .
Journal of Physical Chemistry B 117: 11617-11622, 2013.

Klemsa J., Řezáč J.:
Parallel low-memory quasi-Newton optimization algorithm for molecular structure .
Chemical Physics Letters 584: 10-13, 2013.

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: 921-931, 2013.

Sedlák R., Janowski T., Pitoňák M., Řezáč J., Pulay P., Hobza P.:
Accuracy of quantum chemical methods for large noncovalent complexes .
Journal of Chemical Theory and Computation 9: 3364-3374, 2013.

Šímová L., Řezáč J., Hobza P.:
Convergence of the interaction energies in noncovalent complexes in the coupled-cluster methods up to full configuration interaction .
Journal of Chemical Theory and Computation 9: 3420-3428, 2013.

Kokoschka M., Henry J.B., Bandarenka A.S.:
Multiparametric characterization of nonelectroactive self-assembled monolayers during their formation .
Langmuir 29: 9909-9917, 2013.

Nachtigallová D., Aquino A.J.A., Horn S., Lischka H.:
The effect of dimerization on the excited state behavior of methylated xanthine derivatives: A computational study .
Photochemical and Photobiological Sciences 12: 1496-1508, 2013.

Dršata T., Lankaš F.:
Theoretical models of DNA flexibility .
Wiley Interdisciplinary Reviews: Computational Molecular Science 3: 355-363, 2013.

Riley K.E., Řezáč J., Hobza P.:
Competition between halogen dihalogen and hydrogen bonds in bromo- and iodomethanol dimers .
Journal of Molecular Modeling 19: 2879-2883, 2013.

Matějíček P., Uchman M., Lepšík M., Srnec M., Zedník J., Kozlík P., Kalíková K.:
Preparation and separation of telechelic carborane-containing poly(ethylene glycol)s .
ChemPlusChem 78: 528-535, 2013.

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 .
Journal of Physical Chemistry C 117: 11066-11075, 2013.

Trnka J., Sedlák R., Kolář M., Hobza P.:
Differences in the sublimation energy of benzene and hexahalogenbenzenes are caused by dispersion energy .
Journal of Physical Chemistry A 117: 4331-4337, 2013.

Kolář M., Fanfrlík J., Lepšík M., Forti F., Luque F.J., Hobza P.:
Assessing the accuracy and performance of implicit solvent models for drug molecules: Conformational ensemble approaches .
Journal of Physical Chemistry B 117: 5950-5962, 2013.

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? .
Journal of Chemical Theory and Computation 9: 2151-2155, 2013.

Augustovičová L., Špirko V., Kraemer W.P., Soldán P.:
Radiative association of He+ 2 He 2 + revisited .
Astronomy and Astrophysics in press, 2013.

Brahmkshatriya P.S., 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[15-a]pyrimidines .
Current Computer-Aided Drug Design 9: 118-129, 2013.

Hostaš J., Řezáč J., Hobza P.:
On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions .
Chemical Physics Letters 568-569: 161-166, 2013.

Zierkiewicz W., Zaleśny R., Hobza P.:
On the nature of unusual intensity changes in the infrared spectra of the enflurane⋯acetone complexes .
Physical Chemistry Chemical Physics 15: 6001-6007, 2013.

Riley K.E., Hobza P.:
On the importance and origin of aromatic interactions in chemistry and biodisciplines .
Accounts of Chemical Research 46: 927-936, 2013.

Žáková L., Kletvíková E., Veverka V., Lepšík M., Watson C.J., Turkenburg J.P., Jiráček J., Brzozowski A.M.:
Structural integrity of the B24 site in human insulin is important for hormone functionality .
Journal of Biological Chemistry 288: 10230-10240, 2013.

Sedlák R., Riley K.E., 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: 698-707, 2013.

Granatier J., Dubecký M., Lazar P., Otyepka M., Hobza P.:
Spin-crossing in an organometallic Pt-benzene complex .
Journal of Chemical Theory and Computation 9: 1461-1468, 2013.

Lazar P., Zhang S., Šafářová K., Li Q., Froning J.P., 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: 1646-1651, 2013.

Kolář M., Hobza P., Bronowska A.K.:
Plugging the explicit σ-holes in molecular docking .
Chemical Communications 49: 981-983, 2013.

Špirko V., Sauer S.P.A., Szalewicz K.:
Relation between properties of long-range diatomic bound states .
Physical Review A - Atomic Molecular and Optical Physics in press, 2013.

Sauer S.P.A., Špirko V.:
Effective potential energy curves of the ground electronic state of CH + .
Journal of Chemical Physics in press, 2013.

Dršata T., Pérez A., Orozco M., Morozov A.V., Šponer J., Lankaš F.:
Structure stiffness and substates of the dickerson-drew dodecamer .
Journal of Chemical Theory and Computation 9: 707-721, 2013.

Platts J.A., Hill J.G., Riley K.E., Řezáč J., Hobza P.:
Basis set dependence of interaction energies computed using composite post-MP2 methods .
Journal of Chemical Theory and Computation 9: 330-337, 2013.

Řezáč J., Šímová L., Hobza P.:
CCSD[T] describes noncovalent interactions better than the CCSD(T) CCSD(TQ) and CCSDT methods .
Journal of Chemical Theory and Computation 9: 364-369, 2013.

Kalachová L., Pohl R., Bednárová L., Fanfrlík J., Hocek M.:
Synthesis of nucleosides and dNTPs bearing oligopyridine ligands linked through an octadiyne tether their incorporation into DNA and complexation with transition metal cations .
Organic and Biomolecular Chemistry 11: 78-89, 2013.