List of Publications for Pavel Hobza - The Journal of Physical

SPECIAL ISSUE PREFACE pubs.acs.org/JPCA

List of Publications for Pavel Hobza 398. Zierkiewicz, W.; Wieczorek, R.; Hobza, P.; Michalska, D., Halogen bonded complexes between volatile anesthetics (chloroform, halothane, enflurane, isoflurane) and formaldehyde: A theoretical study. Physical Chemistry Chemical Physics 2011, 13, (11), 5105
5113. 397. Zeleny, T.; Hobza, P.; Nachtigallova, D.; Ruckenbauer, M.; Lischka, H., Photodynamics of the adenine model 4-aminopyrimidine embedded within double strand of DNA. Collection of Czechoslovak Chemical Communications 2011, 76, (6), 631
643. 396. Svadlenak, N.; Ligare, M.; Gulian, L. E.; Callahan, M. P.; Gengeliczki, Z.; Nachtigallova, D.; Hobza, P.; de Vries, M. S., Spectroscopy of isolated prebiotic nucleobases. Abstracts of Papers of the American Chemical Society 2011, 241. 395. Riley, K. E.; Pitonak, M.; Cerny, J.; Hobza, P., On the structure and geometry of biomolecular binding motifs (hydrogen-bonding, stacking, X
H 3 3 3 π): WFT and DFT calculations (vol 6, p 66, 2010). Journal of Chemical Theory and Computation 2011, 7, (3), 807
807. 394. Rezac, J.; Hobza, P., Extrapolation and scaling of the DFT
SAPT interaction energies toward the basis set limit. Journal of Chemical Theory and Computation 2011, 7, (3), 685
689. 393. Rezac, J.; Hobza, P., A halogen-bonding correction for the semiempirical PM6 method. Chemical Physics Letters 2011, 506, (4
6), 286
289. 392. Prenosil, O.; Pitonak, M.; Sedlak, R.; Kabelac, M.; Hobza, P., H-bonding cooperativity effects in amyloids: Quantum mechanical and molecular mechanics study. Zeitschrift Fur Physikalische Chemie—International Journal of Research in Physical Chemistry and Chemical Physics 2011, 225, (5), 553
574. 391. Pitonak, M.; Aquilante, F.; Hobza, P.; Neogrady, 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. Collection of Czechoslovak Chemical Communications 2011, 76, (6), 713
742. 390. Pecina, A.; Prenosil, O.; Fanfrlik, J.; Rezac, J.; Granatier, J.; Hobza, P.; Lepsik, M., On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes. Collection of Czechoslovak Chemical Communications 2011, 76, (5), 457
479. 389. Nachtigallova, D.; Aquino, A. J. A.; Szymczak, J. J.; Barbatti, M.; Hobza, P.; Lischka, H., Nonadiabatic dynamics of uracil: Population split among different decay mechanisms. Journal of Physical Chemistry A 2011, 115, (21), 5247
5255. 388. Kolar, M.; Kubar, T.; Hobza, P., On the role of London dispersion forces in biomolecular structure determination. Journal of Physical Chemistry B 2011, 115, (24), 8038
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387. Kolar, M.; Fanfrlik, J.; Hobza, P., Ligand conformational and solvation/desolvation free energy in protein
ligand complex formation. Journal of Physical Chemistry B 2011, 115, (16), 4718
4724. 386. Dobes, P.; Rezac, J.; Fanfrlik, 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. Journal of Physical Chemistry B 2011, 115, (26), 8581
8589. 385. Dobes, P.; Fanfrlik, J.; Rezac, J.; Otyepka, M.; Hobza, P., Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors. Journal of Computer-Aided Molecular Design 2011, 25, (3), 223
235. 384. Aquino, A. J. A.; Nachtigallova, D.; Hobza, P.; Truhlar, D. G.; Hattig, C.; Lischka, H., The charge-transfer states in a stacked nucleobase dimer complex: A benchmark study. Journal of Computational Chemistry 2011, 32, (7), 1217
1227. 383. Zierkiewicz, W.; Michalska, D.; Hobza, P., Adenine ribbon stabilized by Watson
Crick and Hoogsteen hydrogen bonds: WFT and DFT study. Physical Chemistry Chemical Physics 2010, 12, (12), 2888
2894. 382. Zgarbova, M.; Otyepka, M.; Sponer, J.; Hobza, P.; Jurecka, P., Large-scale compensation of errors in pairwiseadditive empirical force fields: Comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Physical Chemistry Chemical Physics 2010, 12, (35), 10476
10493. 381. Svozil, D.; Hobza, P.; Sponer, 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? Journal of Physical Chemistry B 2010, 114, (2), 1191
1203. 380. Svozil, D.; Hobza, P.; Sponer, 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? (vol 114, p 1191, 2010). Journal of Physical Chemistry B 2010, 114, (7), 2547
2547. 379. Sedlak, R.; Fanfrlik, J.; Hnyk, D.; Hobza, P.; Lepsik, M., Interactions of boranes and carboranes with aromatic systems: CCSD(T) complete basis set calculations and DFT-SAPT analysis of energy components. Journal of Physical Chemistry A 2010, 114, (42), 11304
11311. 378. Riley, K. E.; Pitonak, M.; Jurecka, P.; Hobza, P., Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave Special Issue: Pavel Hobza Festschrift Published: October 13, 2011 dx.doi.org/10.1021/jp208270u | J. Phys. Chem. A 2011, 115, 11121–11135

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function and density functional theories. Chemical Reviews 2010, 110, (9), 5023
5063. Riley, K. E.; Pitonak, M.; Cerny, J.; Hobza, P., On the structure and geometry of biomolecular binding motifs (hydrogen-bonding, stacking, X
H 3 3 3 π): WFT and DFT calculations. Journal of Chemical Theory and Computation 2010, 6, (1), 66
80. Rezac, J.; Hobza, P.; Harris, S. A., Stretched DNA investigated using molecular-dynamics and quantummechanical calculations. Biophysical Journal 2010, 98, (1), 101
110. Pitonak, M.; Rezac, J.; Hobza, P., Spin-component scaled coupled-clusters singles and doubles optimized toward calculation of noncovalent interactions. Physical Chemistry Chemical Physics 2010, 12, (33), 9611
9614. Pitonak, M.; Neogrady, P.; Hobza, P., Three- and fourbody nonadditivities in nucleic acid tetramers: A CCSD(T) study. Physical Chemistry Chemical Physics 2010, 12, (6), 1369
1378. Nachtigallova, D.; Zeleny, T.; Ruckenbauer, M.; Muller, T.; Barbatti, M.; Hobza, P.; Lischka, H., Does stacking restrain the photodynamics of individual nucleobases? Journal of the American Chemical Society 2010, 132, (24), 8261
8263. Nachtigallova, D.; Lischka, H.; Szymczak, J. J.; Barbatti, M.; Hobza, P.; Gengeliczki, Z.; Pino, G.; Callahan, M. P.; de Vries, M. S., The effect of C5 substitution on the photochemistry of uracil. Physical Chemistry Chemical Physics 2010, 12, (19), 4924
4933. Nachtigallova, D.; Barbatti, M.; Szymczak, J. J.; Hobza, P.; Lischka, H., The photodynamics of 2,4-diaminopyrimidine in comparison with 4-aminopyrimidine: The effect of amino-substitution. Chemical Physics Letters 2010, 497, (1
3), 129
134. Morgado, C. A.; Jurecka, P.; Svozil, D.; Hobza, P.; Sponer, J., Reference MP2/CBS and CCSD(T) quantumchemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Physical Chemistry Chemical Physics 2010, 12, (14), 3522
3534. Korth, M.; Pitonak, M.; Rezac, J.; Hobza, P., A transferable H-bonding correction for semiempirical quantumchemical methods. Journal of Chemical Theory and Computation 2010, 6, (1), 344
352. Kolar, M.; Kubar, T.; Hobza, P., Sequence-dependent configurational entropy change of DNA upon intercalation. Journal of Physical Chemistry B 2010, 114, (42), 13446
13454. Kolar, M.; Berka, K.; Jurecka, P.; Hobza, P., On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes. ChemPhysChem 2010, 11, (11), 2399
2408. Grafova, L.; Pitonak, M.; Rezac, J.; Hobza, P., Comparative study of selected wave function and density functional methods for noncovalent interaction energy calculations using the extended S22 data set. Journal of Chemical Theory and Computation 2010, 6, (8), 2365
2376. Gloaguen, E.; Valdes, H.; Pagliarulo, F.; Pollet, R.; Tardivel, B.; Hobza, P.; Piuzzi, F.; Mons, M., Experimental and theoretical investigation of the aromatic


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aromatic interaction in isolated capped dipeptides. Journal of Physical Chemistry A 2010, 114, (9), 2973
2982. Gengeliczki, Z.; Callahan, M. P.; Svadlenak, N.; Pongor, C. I.; Sztaray, B.; Meerts, L.; Nachtigallova, D.; Hobza, P.; Barbatti, M.; Lischka, H.; de Vries, M. S., Effect of substituents on the excited-state dynamics of the modified DNA bases 2,4-diaminopyrimidine and 2,6-diaminopurine. Physical Chemistry Chemical Physics 2010, 12, (20), 5375
5388. Fanfrlik, J.; Bronowska, A. K.; Rezac, J.; Prenosil, 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. Journal of Physical Chemistry B 2010, 114, (39), 12666
12678. Crews, B. O.; Abo-Riziq, A.; Pluhackova, K.; Thompson, P.; Hill, G.; Hobza, P.; de Vries, M. S., Guanine
aspartic acid interactions probed with IR-UV resonance spectroscopy. Physical Chemistry Chemical Physics 2010, 12, (14), 3597
3605. Cerny, J.; Hobza, P., Energy barriers between H-bonded and stacked structures of 9-methyladenine 3 3 3 1-methylthymine and 9-methylguanine 3 3 3 1-methylcytosine complexes. Chemical Communications 2010, 46, (3), 383
385. Berka, K.; Laskowski, R. A.; Hobza, P.; Vondrasek, J., Energy matrix of structurally important side-chain/sidechain interactions in proteins. Journal of Chemical Theory and Computation 2010, 6, (7), 2191
2203. Barbatti, M.; Aquino, A. J. A.; Szymczak, J. J.; Nachtigallova, D.; Hobza, P.; Lischka, H., Relaxation mechanisms of UVphotoexcited DNA and RNA nucleobases. Proceedings of the National Academy of Sciences of the United States of America 2010, 107, (50), 21453
21458. Zendlova, L.; Reha, D.; Hocek, M.; Hobza, P., Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues. Chemistry—A European Journal 2009, 15, (31), 7601
7610. Zeleny, T.; Hobza, P.; Kabelac, M., Microhydration of guanine 3 3 3 cytosine base pairs, A theoretical study on the role of water in stability, structure and tautomeric equilibrium. Physical Chemistry Chemical Physics 2009, 11, (18), 3430
3435. Valdes, H.; Pluhackova, K.; Hobza, P., Phenylalanyl
glycyl
phenylalanine tripeptide: A model system for aromatic
aromatic side chain interactions in proteins. Journal of Chemical Theory and Computation 2009, 5, (9), 2248
2256. Sponer, J.; Zgarbova, M.; Jurecka, P.; Riley, K. E.; Sponer, J. E.; Hobza, P., Reference quantum chemical calculations on RNA base pairs directly involving the 20 -OH group of ribose. Journal of Chemical Theory and Computation 2009, 5, (4), 1166
1179. Sedlak, R.; Hobza, P.; Patwari, G. N., Hydrogen-bonded complexes of phenylacetylene with water, methanol, ammonia, and methylamine. The origin of methyl group-induced hydrogen bond switching. Journal of Physical Chemistry A 2009, 113, (24), 6620
6625. Riley, K. E.; Murray, J. S.; Politzer, P.; Concha, M. C.; Hobza, P., Br 3 3 3 O complexes as probes of factors affecting halogen bonding: Interactions of bromobenzenes and bromopyrimidines with acetone. Journal of Chemical Theory and Computation 2009, 5, (1), 155
163. dx.doi.org/10.1021/jp208270u |J. Phys. Chem. A 2011, 115, 11121–11135

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352. Rezacova, P.; Pokorna, J.; Brynda, J.; Kozisek, M.; Cigler, P.; Lepsik, M.; Fanfrlik, J.; Rezac, J.; Saskova, K. G.; Sieglova, I.; Plesek, J.; Sicha, V.; Gruner, B.; Oberwinkler, H.; Sedlacek, J.; Krausslich, H. G.; Hobza, P.; Kral, V.; Konvalinka, J., Design of HIV protease inhibitors based on inorganic polyhedral metallacarboranes. Journal of Medicinal Chemistry 2009, 52, (22), 7132
7141. 351. Rezac, J.; Fanfrlik, 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. Journal of Chemical Theory and Computation 2009, 5, (7), 1749
1760. 350. Ran, J.; Hobza, P., Nature of bonding in nine planar hydrogen-bonded adenine 3 3 3 thymine base pairs. Journal of Physical Chemistry B 2009, 113, (9), 2933
2936. 349. Ran, J.; Hobza, P., On the nature of bonding in lone pair 3 3 3 π-electron complexes: CCSD(T)/complete basis set limit calculations. Journal of Chemical Theory and Computation 2009, 5, (4), 1180
1185. 348. Pitonak, M.; Neogrady, P.; Cerny, J.; Grimme, S.; Hobza, P., Scaled MP3 Non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data. ChemPhysChem 2009, 10, (1), 282
289. 347. Pitonak, M.; Janowski, T.; Neogrady, 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. Journal of Chemical Theory and Computation 2009, 5, (7), 1761
1766. 346. Morgado, C. A.; Jurecka, P.; Svozil, D.; Hobza, P.; Sponer, J., Balance of attraction and repulsion in nucleicacid base stacking: CCSD(T)/complete-basis-set-limit calculations on uracil dimer and a comparison with the force-field description. Journal of Chemical Theory and Computation 2009, 5, (6), 1524
1544. 345. Matejicek, P.; Zednik, J.; Uselova, K.; Plestil, J.; Fanfrlik, J.; Nykanen, A.; Ruokolainen, J.; Hobza, P.; Prochazka, K., Stimuli-responsive nanoparticles based on interaction of metallacarborane with poly(ethylene oxide). Macromolecules 2009, 42, (13), 4829
4837. 344. Maity, S.; Sedlak, R.; Hobza, P.; Patwari, G. N., 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 3 3 3 π interactions. Physical Chemistry Chemical Physics 2009, 11, (42), 9738
9743. 343. Konvalinka, J.; Illnerova, H.; Hobza, P.; Horejsi, V.; Holy, A.; Jungwirth, P.; Paces, V.; Martasek, P.; Zlatuska, J., Czech bibliometric system fosters mediocre research. Nature 2009, 460, (7259), 1079
1079. 342. Kabelac, M.; Hobza, P.; Spirko, V., The ab initio assigning of the vibrational probing modes of tryptophan: Linear shifting of approximate anharmonic frequencies vs multiplicative scaling of harmonic frequencies. Physical Chemistry Chemical Physics 2009, 11, (20), 3921
3926. 341. Kabelac, M.; Hobza, P.; Spirko, V., The structure and vibrational dynamics of the pyrrole dimer. Physical Chemistry Chemical Physics 2009, 11, (20), 3885
3891. 340. Cerny, J.; Vondrasek, J.; Hobza, P., Loss of dispersion energy changes the stability and folding/unfolding

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equilibrium of the Trp-cage protein. Journal of Physical Chemistry B 2009, 113, (16), 5657
5660. Berka, K.; Laskowski, R.; Riley, K. E.; Hobza, P.; Vondrasek, J., Representative amino acid side chain interactions in proteins. A comparison of highly accurate correlated ab initio quantum chemical and empirical potential procedures. Journal of Chemical Theory and Computation 2009, 5, (4), 982
992. Berka, K.; Hobza, P.; Vondrasek, J., Analysis of energy stabilization inside the hydrophobic core of rubredoxin. ChemPhysChem 2009, 10, (3), 543
548. Zierkiewicz, W.; Komorowski, L.; Michalska, D.; Cerny, J.; Hobza, P., The amino group in adenine: MP2 and CCSD(T) complete basis set limit calculations of the planarization barrier and DFT/B3LYP study of the anharmonic frequencies of adenine. Journal of Physical Chemistry B 2008, 112, (51), 16734
16740. Wang, W. Z.; Hobza, P., Application of Berlin’s theorem to bond-length changes in isolated molecules and red- and blue-shifting H-bonded clusters. Collection of Czechoslovak Chemical Communications 2008, 73, (6
7), 862
872. Wang, W. Z.; Hobza, P., Origin of the X
Hal (Hal = Cl, Br) bond-length change in the halogen-bonded complexes. Journal of Physical Chemistry A 2008, 112, (17), 4114
4119. Wang, W. Z.; Hobza, P., Theoretical study on the complexes of benzene with isoelectronic nitrogen-containing heterocycles. ChemPhysChem 2008, 9, (7), 1003
1009. Valdes, H.; Spiwok, V.; Rezac, J.; Reha, D.; Abo-Riziq, A. G.; de Vries, M. S.; Hobza, P., Potential-energy and freeenergy surfaces of glycyl
phenylalanyl
alanine (GFA) tripeptide: experiment and theory. Chemistry—A European Journal 2008, 14, (16), 4886
4898. Valdes, H.; Pluhackova, K.; Pitonak, M.; Rezac, J.; Hobza, P., Benchmark database on isolated small peptides containing an aromatic side chain: Comparison between wave function and density functional theory methods and empirical force field. Physical Chemistry Chemical Physics 2008, 10, (19), 2747
2757. Valdes, H.; Klusak, V.; Pitonak, M.; Exner, O.; Stary, I.; Hobza, P.; Rulisek, L., Evaluation of the intramolecular basis set superposition error in the calculations of larger molecules: [n]Helicenes and Phe
Gly
Phe tripeptide. Journal of Computational Chemistry 2008, 29, (6), 861
870. Vacha, R.; Cwiklik, L.; Rezac, J.; Hobza, P.; Jungwirth, P.; Valsaraj, K.; Bahr, S.; Kempter, V., Adsorption of aromatic hydrocarbons and ozone at environmental aqueous surfaces. Journal of Physical Chemistry A 2008, 112, (22), 4942
4950. Sponer, J.; Riley, K. E.; Hobza, P., Nature and magnitude of aromatic stacking of nucleic acid bases. Physical Chemistry Chemical Physics 2008, 10, (19), 2595
2610. Riley, K. E.; Hobza, P., A DFT-D investigation of the mechanisms for activation of the wild-type and S810L mutated mineralocorticoid receptor by steroid hormones. Journal of Physical Chemistry B 2008, 112, (10), 3157
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327. Riley, K. E.; Hobza, P., Investigations into the nature of halogen bonding including symmetry adapted perturbation theory analyses. Journal of Chemical Theory and Computation 2008, 4, (2), 232
242. 326. Rezac, J.; Jurecka, P.; Riley, K. E.; Cerny, J.; Valdes, H.; Pluhackova, K.; Berka, K.; Rezac, T.; Pitonak, M.; Vondrasek, 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. Collection of Czechoslovak Chemical Communications 2008, 73, (10), 1261
1270. 325. Rezac, J.; Hobza, P., Benzene dimer: Dynamic structure and thermodynamics derived from on-the-fly ab initio DFT-D molecular dynamic simulations. Journal of Chemical Theory and Computation 2008, 4, (11), 1835
1840. 324. Rezac, J.; Hobza, P., Correlation between the thermodynamic stability of DNA duplexes and the interaction and solvation energies of DNA building blocks. Collection of Czechoslovak Chemical Communications 2008, 73, (2), 161
174. 323. Rezac, J.; Berka, K.; Horinek, D.; Hobza, P.; Vondrasek, J., The stabilization energy of the Glu
Lys salt bridge in the protein/water environment: Correlated quantum chemical ab initio, DFT and empirical potential studies. Collection of Czechoslovak Chemical Communications 2008, 73, (6
7), 921
936. 322. Pluhackova, K.; Grimme, S.; Hobza, P., On the importance of electron correlation effects for the intramolecular stacking geometry of a bis-thiophene derivative. Journal of Physical Chemistry A 2008, 112, (48), 12469
12474. 321. Pitonak, M.; Riley, K. E.; Neogrady, P.; Hobza, P., Highly accurate CCSD(T) and DFT-SAPT stabilization energies of H-bonded and stacked structures of the uracil dimer. ChemPhysChem 2008, 9, (11), 1636
1644. 320. Pitonak, M.; Neogrady, P.; Rezac, J.; Jurecka, P.; Urban, M.; Hobza, P., Benzene dimer: High-level wave function and density functional theory calculations. Journal of Chemical Theory and Computation 2008, 4, (11), 1829
1834. 319. Nachtigallova, D.; Hobza, P.; Spirko, V., Assigning the NH stretches of the guanine tautomers using adiabatic separation: CCSD(T) benchmark calculations. Journal of Physical Chemistry A 2008, 112, (9), 1854
1856. 318. Nachtigallova, D.; Hobza, P.; Ritze, H. H., Electronic splitting in the excited states of DNA base homodimers and -trimers: An evaluation of short-range and coulombic interactions. Physical Chemistry Chemical Physics 2008, 10, (37), 5689
5697. 317. Murray, J. S.; Concha, M. C.; Lane, P.; Hobza, P.; Politzer, P., Blue shifts vs red shifts in σ-hole bonding. Journal of Molecular Modeling 2008, 14, (8), 699
704. 316. Hobza, P., Non-covalent interactions with participation of hydrogen: Hydrogen bond, blue-shifting hydrogen bond and dihydrogen bond. Chemicke Listy 2008, 102, (10), 884
888. 315. Hobza, P., Stacking interactions. Physical Chemistry Chemical Physics 2008, 10, (19), 2581
2583. 314. Fanfrlik, J.; Brynda, J.; Rezac, J.; Hobza, P.; Lepsik, M., Interpretation of protein/ligand crystal structure using QM/MM calculations: Case of HIV-1 protease/metallacarborane complex. Journal of Physical Chemistry B 2008, 112, (47), 15094
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313. Cerny, J.; Tong, X.; Hobza, P.; Muller-Dethlefs, K., Competition between stacking and hydrogen bonding: Theoretical study of the phenol 3 3 3 Ar cation and neutral complex and comparison to experiment. Physical Chemistry Chemical Physics 2008, 10, (19), 2780
2784. 312. Cerny, J.; Tong, X.; Hobza, P.; Muller-Dethlefs, K., State of the art theoretical study and comparison to experiment for the phenol 3 3 3 argon complex. Journal of Chemical Physics 2008, 128, (11). 311. Cerny, J.; Kabelac, M.; Hobza, P., Double-helical f ladder structural transition in the B-DNA is induced by a loss of dispersion energy. Journal of the American Chemical Society 2008, 130, (47), 16055
16059. 310. Callahan, M. P.; Gengeliczki, Z.; Svadlenak, N.; Valdes, H.; Hobza, P.; de Vries, M. S., Nonstandard base pairing and stacked structures in methyl xanthine clusters. Physical Chemistry Chemical Physics 2008, 10, (19), 2819
2826. 309. Biedermannova, L.; Riley, K. E.; Berka, K.; Hobza, P.; Vondrasek, J., Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane. Physical Chemistry Chemical Physics 2008, 10, (42), 6350
6359. 308. Bendova-Biedermannova, L.; Hobza, P.; Vondrasek, J., Identifying stabilizing key residues in proteins using interresidue interaction energy matrix. Proteins: Structure, Function, and Bioinformatics 2008, 72, (1), 402
413. 307. Zendlova, L.; Hobza, P.; Kabelac, M., Stability of nucleic acid base pairs in organic solvents: Molecular dynamics, molecular dynamics/quenching, and correlated ab initio study. Journal of Physical Chemistry B 2007, 111, (10), 2591
2609. 306. Wang, W. Z.; Pitonak, M.; Hobza, P., C
H stretching vibrational shift of benzene dimer: Consistency of experiment and calculation. ChemPhysChem 2007, 8, (14), 2107
2111. 305. Vrabel, M.; Hocek, M.; Havran, L.; Fojta, M.; Votruba, I.; Klepetarova, B.; Pohl, R.; Rulisek, L.; Zendlova, L.; Hobza, P.; Shih, I. H.; Mabery, E.; Mackman, R., Purines bearing phenanthroline or bipyridine ligands and their Ru
II complexes in position 8 as model compounds for electrochemical DNA labeling - Synthesis, crystal structure, electrochemistry, quantum chemical calculations, cytostatic and antiviral activity. European Journal of Inorganic Chemistry 2007, (12), 1752
1769. 304. Vondrasek, J.; Kubar, T.; Jenney, F. E.; Adams, M. W. W.; Kozisek, M.; Cerny, J.; Sklenar, V.; Hobza, P., Dispersion interactions govern the strong thermal stability of a protein. Chemistry—A European Journal 2007, 13, (32), 9022
9027. 303. Szatylowicz, H.; Krygowski, T. M.; Hobza, P., How the shape of the NH2 group depends on the substituent effect and H-bond formation in derivatives of aniline. Journal of Physical Chemistry A 2007, 111, (1), 170
175. 302. Sedlak, R.; Jurecka, P.; Hobza, P., Density functional theory
Symmetry adapted perturbation treatment energy decomposition of nucleic acid base pairs taken from DNA crystal geometry. Journal of Chemical Physics 2007, 127, (7). 301. Ritze, H. H.; Hobza, P.; Nachtigallova, D., Electronic coupling in the excited electronic state of stacked DNA base homodimers. Physical Chemistry Chemical Physics 2007, 9, (14), 1672
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300. Riley, K. E.; Vondrasek, J.; Hobza, P., Performance of the DFT-D method, paired with the PCM implicit solvation model, for the computation of interaction energies of solvated complexes of biological interest. Physical Chemistry Chemical Physics 2007, 9, (41), 5555
5560. 299. Riley, K. E.; Hobza, P., Assessment of the MP2 method, along with several basis sets, for the computation of interaction energies of biologically relevant hydrogen bonded and dispersion bound complexes. Journal of Physical Chemistry A 2007, 111, (33), 8257
8263. 298. Rezac, J.; Hobza, P., On the nature of DNA-duplex stability. Chemistry—A European Journal 2007, 13, (10), 2983
2989. 297. Rejnek, J.; Hobza, P., Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: Complete basis set calculations at the MP2 and CCSD(T) levels. Journal of Physical Chemistry B 2007, 111, (3), 641
645. 296. Pluhackova, K.; Jurecka, P.; Hobza, P., Stabilization energy of C6H6 3 3 3 C6X6 (X = F, Cl, Br, I, CN) complexes: Complete basis set limit calculations at MP2 and CCSD(T) levels. Physical Chemistry Chemical Physics 2007, 9, (6), 755
760. 295. Pluhackova, K.; Hobza, P., On the nature of the surprisingly small (red) shift in the halothane 3 3 3 acetone complex. ChemPhysChem 2007, 8, (9), 1352
1356. 294. Parreira, R. L. T.; Galembeck, S. E.; Hobza, P., On the origin of red and blue shifts of X
H and C
H stretching vibrations in formic acid (formate ion) and proton donor complexes. ChemPhysChem 2007, 8, (1), 87
92. 293. Muchova, E.; Slavicek, P.; Sobolewski, A. L.; Hobza, P., Glycine in an electronically excited state: Ab initio electronic structure and dynamical calculations. Journal of Physical Chemistry A 2007, 111, (24), 5259
5269. 292. Lee, E. C.; Kim, D.; Jurecka, P.; Tarakeshwar, P.; Hobza, P.; Kim, K. S., Understanding of assembly phenomena by aromatic
aromatic interactions: Benzene dimer and the substituted systems. Journal of Physical Chemistry A 2007, 111, (18), 3446
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2815. Wojciechowski, P. M.; Zierkiewicz, W.; Michalska, D.; Hobza, P., Electronic structures, vibrational spectra, and revised assignment of aniline and its radical cation: Theoretical study. Journal of Chemical Physics 2003, 118, (24), 10900
10911. Sychrovsky, V.; Schneider, B.; Hobza, P.; Zidek, L.; Sklenar, V., The effect of water on NMR spin
spin couplings in DNA: Improvement of calculated values by application of two solvent models. Physical Chemistry Chemical Physics 2003, 5, (4), 734
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Drug complexes. Minor groove binding between 40 ,6-diamidino-2-phenylindole and DNA duplexes in solution. Journal of the American Chemical Society 2003, 125, (7), 1759
1769. Slavicek, P.; Kalus, R.; Paska, P.; Odvarkova, I.; Hobza, P.; Malijevsky, A., State-of-the-art correlated ab initio potential energy curves for heavy rare gas dimers: Ar2, dx.doi.org/10.1021/jp208270u |J. Phys. Chem. A 2011, 115, 11121–11135

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3376. Lankas, F.; Cheatham, T. E.; Spackova, N.; Hobza, P.; Langowski, J.; Sponer, J., Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts. Biophysical Journal 2002, 82, (5), 2592
2609. Jurecka, P.; Hobza, P., On the convergence of the (ΔECCSD(T)
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2), 89
94. Chocholousova, J.; Vacek, J.; Huisken, F.; Werhahn, O.; Hobza, P., Stacked structure of the glycine dimer is more stable than the cyclic planar geometry with two O
H 3 3 3 O hydrogen bonds: Concerted action of empirical, high-level nonempirical ab initio, and experimental studies. Journal of Physical Chemistry A 2002, 106, (47), 11540
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709. 183. Kratochvil, M.; Sponer, J.; Hobza, P., Global minimum of the adenine 3 3 3 thymine base pair corresponds neither to Watson
Crick nor to Hoogsteen structures. Molecular dynamic/quenching/AMBER and ab initio beyond Hartree
Fock studies. Journal of the American Chemical Society 2000, 122, (14), 3495
3499. 182. Kratochvil, M.; Engkvist, O.; Vacek, J.; Jungwirth, P.; Hobza, P., Methylated uracil dimers: Potential energy and free energy surfaces. Physical Chemistry Chemical Physics 2000, 2, (10), 2419
2424. 181. Kabelac, M.; Ryjacek, F.; Hobza, P., Already two water molecules change planar H-bonded structures of the adenine 3 3 3 thymine base pair to the stacked ones: A molecular dynamics simulations study. Physical Chemistry Chemical Physics 2000, 2, (21), 4906
4909. 180. Kabelac, M.; Kratochvil, M.; Sponer, J.; Hobza, P., Structure, energetics, vibrational frequencies and charge transfer of base pairs, nucleoside pairs, nucleotide pairs and B-DNA pairs of trinucleotides: Ab initio HF/MINI1 and empirical force field study. Journal of Biomolecular Structure and Dynamics 2000, 17, (6), 1077
1086. 179. Hobza, P.; Sponer, J.; Cubero, E.; Orozco, M.; Luque, F. J., C
H 3 3 3 O contacts in the adenine 3 3 3 uracil Watson
Crick and uracil 3 3 3 uracil nucleic acid base pairs: Nonempirical ab initio study with inclusion of electron correlation effects. Journal of Physical Chemistry B 2000, 104, (26), 6286
6292. 178. Hobza, P.; Havlas, Z., Blue-shifting hydrogen bonds. Chemical Reviews 2000, 100, (11), 4253
4264. 177. Brutschy, B.; Hobza, P., van der Waals molecules III: Introduction. Chemical Reviews 2000, 100, (11), 3861
3862. 176. Bludsky, O.; Chocholousova, J.; Vacek, J.; Huisken, F.; Hobza, P., Anharmonic treatment of the lowest-energy conformers of glycine: A theoretical study. Journal of Chemical Physics 2000, 113, (11), 4629
4635. 175. Sponer, J.; Sabat, M.; Burda, J. V.; Leszczynski, J.; Hobza, P.; Lippert, B., Metal ions in non-cDNA base pairs: An ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine
adenine base pair. Journal of Biological Inorganic Chemistry 1999, 4, (5), 537
545. 174. Sponer, J.; Sabat, M.; Burda, J. V.; Leszczynski, J.; Hobza, P., Interaction of the adenine
thymine Watson
Crick and adenine
adenine reverse-Hoogsteen DNA base pairs with hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) metal cations: Absence of the base pair stabilization by metal-induced polarization effects. Journal of Physical Chemistry B 1999, 103, (13), 2528
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582. Shishkin, O. V.; Sponer, J.; Hobza, P., Intramolecular flexibility of DNA bases in adenine
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21. Ryjacek, F.; Kratochvil, M.; Hobza, P., Adenine 3 3 3 2,4difluorotoluene (modified base) pair: Potential and freeenergy surfaces - Nonempirical and empirical potential studies. Chemical Physics Letters 1999, 313, (1
2), 393
398. Hobza, P.; Sponer, J., Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations. Chemical Reviews 1999, 99, (11), 3247
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186. Hobza, P.; Havlas, Z., The fluoroform 3 3 3 ethylene oxide complex exhibits a C
H 3 3 3 O antihydrogen bond. Chemical Physics Letters 1999, 303, (3
4), 447
452. Hobza, P.; Bludsky, O.; Suhai, S., Reliable theoretical treatment of molecular clusters: Counterpoise-corrected potential energy surface and anharmonic vibrational frequencies of the water dimer. Physical Chemistry Chemical Physics 1999, 1, (13), 3073
3078. Engkvist, O.; Hobza, P.; Selzle, H. L.; Schlag, E. W., Benzene trimer and benzene tetramer: Structures and properties determined by the nonempirical model (NEMO) potential calibrated from the CCSD(T) benzene dimer energies. Journal of Chemical Physics 1999, 110, (12), 5758
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2), 248
248. Vacek, J.; Hobza, P.; Jortner, J., Nuclear dynamics of benzene 3 3 3 (Ar)n clusters. Journal of Physical Chemistry A 1998, 102, (43), 8268
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143. Sponer, J.; Burda, J. V.; Sabat, M.; Leszczynski, J.; Hobza, P., Interaction between the guanine
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3), 417
428. Hobza, P.; Sponer, J., Significant structural deformation of nucleic acid bases in stacked base pairs: An ab initio study beyond Hartree
Fock. Chemical Physics Letters 1998, 288, (1), 7
14. Hobza, P.; Spirko, V.; Selzle, H. L.; Schlag, E. W., Antihydrogen bond in the benzene dimer and other carbon proton donor complexes. Journal of Physical Chemistry A 1998, 102, (15), 2501
2504. Hobza, P.; Havlas, Z., Counterpoise-corrected potential energy surfaces of simple H-bonded systems. Theoretical Chemistry Accounts 1998, 99, (6), 372
377. Hobza, P.; Havlas, Z., Counterpoise-corrected potential energy surfaces of simple hydrogen-bonded systems. Collection of Czechoslovak Chemical Communications 1998, 63, (9), 1343
1354. Hobza, P.; Burda, J. V.; Zahradnik, R., Isoelectronic dimers [(XH3)2, (YH2)2, (ZH)2, and (Rg)2] in the groups of the periodic system: Ab initio quantum chemical calculations. Polish Journal of Chemistry 1998, 72, (7), 1497
1504. Burda, J. V.; Hobza, P.; Zahradnik, R., (HX)2 species (X = F through At) in the groups of the periodic system: MP2 and CCSD(T) ab initio quantum chemical calculations. Chemical Physics Letters 1998, 288, (1), 20
24. Sponer, J.; Leszczynski, J.; Hobza, P., Thioguanine and thiouracil: Hydrogen-bonding and stacking properties. Journal of Physical Chemistry A 1997, 101, (49), 9489
9495. Sponer, J.; Hobza, P., MP2 and CCSD(T) study on hydrogen bonding, aromatic stacking and nonaromatic stacking. Chemical Physics Letters 1997, 267, (3
4), 263
270. Sponer, J.; Gabb, H. A.; Leszczynski, J.; Hobza, P., Base
base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: A quantum-chemical study. Biophysical Journal 1997, 73, (1), 76
87. Sponer, J.; Burda, J. V.; Mejzlik, P.; Leszczynski, J.; Hobza, P., Hydrogen-bonded trimers of DNA bases and their interaction with metal cations: Ab initio quantum-chemical and empirical potential study. Journal of Biomolecular Structure and Dynamics 1997, 14, (5), 613
628. Spirko, V.; Sponer, J.; Hobza, P., Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs. Journal of Chemical Physics 1997, 106, (4), 1472
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molecule reactions HX+HX•+ (X = F, Cl, Br, I, At). Journal of Physical Chemistry A 1997, 101, (6), 1134
1139. Vacek, J.; Hobza, P., On the thermodynamic characteristics of the benzene 3 3 3 Ar2 complex: An application of the ab initio intermolecular potential. International Journal of Quantum Chemistry 1996, 57, (4), 551
557. Sponer, J.; Leszczynski, J.; Vetterl, V.; Hobza, P., Base stacking and hydrogen bonding in protonated cytosine dimer: The role of molecular ion
dipole and induction interactions. Journal of Biomolecular Structure and Dynamics 1996, 13, (4), 695
706. Sponer, J.; Leszczynski, J.; Hobza, P., Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations. Journal of Computational Chemistry 1996, 17, (7), 841
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base stacking: Nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. Journal of Physical Chemistry 1996, 100, (13), 5590
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970. Sponer, J.; Hobza, P., Nonempirical ab initio calculations on DNA base pairs. Chemical Physics 1996, 204, (2
3), 365
372. Sponer, J.; Florian, J.; Hobza, P.; Leszczynski, J., Nonplanar DNA base pairs. Journal of Biomolecular Structure and Dynamics 1996, 13, (5), 827
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12217. Hobza, P.; Sponer, J., MP2 and CCSD(T) calculations on H-bonded and stacked formamide 3 3 3 formamide and formamidine 3 3 3 formamidine dimers. Journal of Molecular Structure: THEOCHEM 1996, 388, 115
120. Hobza, P.; Sponer, J., Thermodynamic characteristics for the formation of H-bonded DNA base pairs. Chemical Physics Letters 1996, 261, (3), 379
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130. Hobza, P.; Selzle, H. L.; Schlag, E. W., Potential energy surface for the benzene dimer. Results of ab initio CCSD(T) calculations show two nearly isoenergetic structures: T-shaped and parallel-displaced. Journal of Physical Chemistry 1996, 100, (48), 18790
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2), 31
35. 128 Hobza, P.; Bludsky, O.; Selzle, H. L.; Schlag, E. W., Ab initio calculations on the structure, vibrational frequencies, and valence excitation energies of the benzene 3 3 3 Ar and benzene 3 3 3 Ar2 cluster. Chemical Physics Letters 1996, 250, (3
4), 402
408. 127. Burda, J. V.; Zahradnik, R.; Hobza, P.; Urban, M., Dimers of rare gas atoms: CCSD(T), CCSDT and FCI calculations on the (He)2 dimer, CCSD(T) and CCSDT calculations on the (Ne)2 dimer, and CCSD(T) allelectron and pseudopotential calculations on the dimers from (Ne)2 through (Xe)2. Molecular Physics 1996, 89, (2), 425
432. 126. Burda, J. V.; Sponer, J.; Hobza, P., Ab Initio study of the interaction of guanine and adenine with various mono- and bivalent metal cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+). Journal of Physical Chemistry 1996, 100, (17), 7250
7255. 125. Bludsky, O.; Sponer, J.; Leszczynski, J.; Spirko, V.; Hobza, P., Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are nonplanar: Results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion. Journal of Chemical Physics 1996, 105, (24), 11042
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8 argon atoms - A molecular-dynamics study with abinitio intermolecular potential. Journal of Physical Chemistry 1995, 99, (47), 17088
17092. 123. Tesarova, E.; Gilar, M.; Hobza, P.; Kabelac, M.; Deyl, Z.; Smolkova-Keulemansova, E., Correlation between structure of dihydropyridine calcium-antagonists and their retention behavior and enantioseparation on the βcyclodextrin stationary-phase in HPLC. HRC-Journal of High Resolution Chromatography 1995, 18, (9), 597
601. 122. Hobza, P.; Sponer, J.; Reschel, T., Density-functional theory and molecular clusters. Journal of Computational Chemistry 1995, 16, (11), 1315
1325. 121. Hobza, P.; Sponer, J.; Polasek, M., H-bonded and stacked DNA-base pairs: Cytosine dimer. An ab-initio second-order Moller
Plesset study. Journal of the American Chemical Society 1995, 117, (2), 792
798. 120. Zahradnik, R.; Hobza, P.; Burcl, R.; Hess, B. A.; Radziszewski, J. G., Strained unsaturated molecules
Theoreticalstudy of acyclic and cyclic cumulenes and acetylenes. Journal of Molecular Structure: THEOCHEM 1994, 119, (3), 335
349. 119. Wright, T. G.; Spirko, V.; Hobza, P., Ab-Initio calculations on Ar
No+
Structure and vibrational frequencies. Journal of Chemical Physics 1994, 100, (8), 5403
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118. Vondrasek, J.; Sponar, J.; Hobza, P., An empirical potential study of the interaction of L-lysine
L-alanine
L-alanine tripeptide with 4 models of B-DNA with different compositions. Journal of Biomolecular Structure and Dynamics 1994, 11, (4), 869
880. 117. Vacek, J.; Konvicka, K.; Hobza, P., A molecular-dynamics study of the benzene 3 3 3 Ar2 Complex
Application of the nonempirical ab-initio and empirical Lennard-Jones 6
12 potentials. Chemical Physics Letters 1994, 220, (1
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92. 116. Vacek, J.; Hobza, P., A molecular-dynamics study of the benzene 3 3 3 Arn (n = 3
5) complex using the ab-initio intermolecular potential. Journal of Physical Chemistry 1994, 98, (43), 11034
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714. 114. Sponer, J.; Hobza, P., G 3 C base-pair in parallel-stranded DNA: A novel type of base-pairing. An ab-initio quantumchemical study. Journal of Biomolecular Structure and Dynamics 1994, 12, (3), 671
680. 113. Sponer, J.; Hobza, P., Nonplanar geometries of DNA bases. Ab-initio second-order Moller
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An ab-initio quantum-chemical analysis. Journal of Molecular Structure: THEOCHEM 1994, 110, (1), 35
40. 111. Sponer, J.; Burcl, R.; Hobza, P., Interactions between amino-groups in DNA
An ab-initio study and a comparison with empirical potentials. Journal of Biomolecular Structure and Dynamics 1994, 11, (6), 1357
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102. Zahradnik, R.; Hobza, P.; Wichterlova, B.; Cejka, J., Isomorphous substitution of Si for Al, Ga, Fe, In and B in molecular-sieves of MFI Structure
A quantum-chemical, ammonia desorption and catalytic activity study of framework Si
OH
M acid site strength. Collection of Czechoslovak Chemical Communications 1993, 58, (10), 2474
2488. 101. Hrouda, V.; Florian, J.; Hobza, P., Structure, energetics, and harmonic vibrational-spectra of the adenine
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6), 497
502. 99. Hobza, P.; Zahradnik, R., World of van der Waals species. Collection of Czechoslovak Chemical Communications 1993, 58, (7), 1465
1475. 98. Hobza, P.; Selzle, H. L.; Schlag, E. W., New structure for the most stable isomer of the benzene dimer: A quantumchemical study. Journal of Physical Chemistry 1993, 97, (16), 3937
3938. 97. Hobza, P.; Selzle, H. L.; Schlag, E. W., Properties of fluorobenzene 3 3 3 Ar and p-difluorobenzene 3 3 3 Ar complexes. Ab initio study. Journal of Chemical Physics 1993, 99, (4), 2809
2811. 96. Hobza, P.; Bludsky, O.; Selzle, H. L.; Schlag, E. W., Ground-state potential surface for van der Waals complexes: Ab initio second-order Moller
Plesset study on benzene 3 3 3 N2 van der Waals molecule. Journal of Chemical Physics 1993, 98, (8), 6223
6226. 95. Cespiva, L.; Bonacic-Koutecky, V.; Koutecky, J.; Jensen, P.; Hrouda, V.; Carsky, P.; Spirko, V.; Hobza, P., Abinitio calculations of the rotation
vibration spectrum of Na3+. Collection of Czechoslovak Chemical Communications 1993, 58, (1), 24
28. 94. Burcl, R.; Hobza, P., Ab-initio study on the methanol
water cation-radical potential-energy surface. Theoretica Chimica Acta 1993, 87, (1
2), 97
105. 93. Hobza, P.; Zahradnik, R., Associates, clusters, intermolecular complexes, supramolecular systems
van der Waals species. Berichte Der Bunsen-Gesellschaft-Physical Chemistry Chemical Physics 1992, 96, (9), 1294
1298. 92. Hobza, P.; Zahradnik, R., An essay on the theory and calculations of intermolecular interactions. International Journal of Quantum Chemistry 1992, 42, (4), 581
590. 91. Hobza, P.; Selzle, H. L.; Schlag, E. W., High-level ab initio calculations on acetylene dimer: A prototype for estimation of the accuracy of the benzene dimer stabilization energy. Collection of Czechoslovak Chemical Communications 1992, 57, (6), 1186
1190. 90. Hobza, P.; Bludsky, O.; Selzle, H. L.; Schlag, E. W., Ab initio second-order and fourth-order Moller
Plesset study on structure, stabilization energy, and stretching vibration of benzene 3 3 3 X (X = He, Ne, Ar, Kr, Xe) van der Waals molecules. Journal of Chemical Physics 1992, 97, (1), 335
340. 89. Hobza, P., On the different characteristics of mediumsized van der Waals molecules obtainable from ab initio calculations. Croatica Chemica Acta 1992, 65, (1), 11
15. 88. Bludsky, O.; Spirko, V.; Hrouda, V.; Hobza, P., Vibrational dynamics of the benzene 3 3 3 argon complex. Chemical Physics Letters 1992, 196, (5), 410
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394. 86. Hobza, P.; Nachtigallova, D.; Havlas, Z.; Malon, P.; Sponar, J., Interaction of lysine
alanine
alanine tripeptide with a fragment of DNA: An empirical potential study. Journal of Computational Chemistry 1991, 12, (1), 9
16. 85. Zahradnik, R.; Havlas, Z.; Hess, B. A.; Hobza, P., Properties and reactivity of first and second row hydrides: Introductory remarks, isomerizations, and inversion barriers of the AH2, AH3, AH4 and related systems. Collection of Czechoslovak Chemical Communications 1990, 55, (4), 869
889. 84. Stibor, I.; Holy, P.; Hobza, P.; Carsky, P., MM2 study of 20-hydroxy-4,7,13,16-tetraoxa-1,10-diazabicyclo [8,8,3] heneicosane and its formation controlled by hydrogenbonding. Journal of Computational Chemistry 1990, 11, (7), 837
847. 83. Sannigrahi, A. B.; Kar, T.; Niyogi, B. G.; Hobza, P.; Schleyer, P. V., The lithium bond reexamined. Chemical Reviews 1990, 90, (6), 1061
1076. 82. Hobza, P.; Selzle, H. L.; Schlag, E. W., Floppy structure of the benzene dimer: Ab initio calculation on the structure and dipole-moment. Journal of Chemical Physics 1990, 93, (8), 5893
5897. 81. Hobza, P., Correction. Chemical Physics Letters 1990, 167, (4), 378
378. 80. Hofmann, H. J.; Hobza, P.; Cammi, R.; Tomasi, J.; Zahradnik, R., Metal
ion interactions with water and ammonia. Journal of Molecular Structure:THEOCHEM 1989, 60, 339
350. 79. Hobza, P.; Havlas, Z., An empirical potential for interactions of large molecules: Application to binding of dipeptides to DNA. International Journal of Quantum Chemistry 1989, 36, (3), 287
298. 78. Zahradnik, R.; Hobza, P., On the role of van der Waals interactions in organic-chemistry. Pure and Applied Chemistry 1988, 60, (2), 245
252. 77. Szczesniak, M. M.; Scheiner, S.; Hobza, P., Effects of electron correlation upon molecular-interactions: Correction of the electrostatic interaction between DNA bases. Journal of Molecular Structure: THEOCHEM 1988, 48, 177
184. 76. Schneider, B.; Hobza, P.; Zahradnik, R., Potential-energy surface of the (H2)2 Dimer: An MP2 study. Theoretica Chimica Acta 1988, 73, (2
3), 201
206. 75. Petrusova, H.; Havlas, Z.; Hobza, P.; Zahradnik, R., A theoretical-study on acetylene dimer, acetylene-stetrazine and acetylene benzene associates. Collection of Czechoslovak Chemical Communications 1988, 53, (11A), 2495
2502. 74. Hobza, P.; Zahradnik, R., Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies. Successes and failures. Chemical Reviews 1988, 88, (6), 871
897. 73. Hobza, P.; Schleyer, P. V., On the nature of the bonding in He
Be
O, Ne
Be
O, Ar
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O molecules. Collection of Czechoslovak Chemical Communications 1988, 53, (10), 2230
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guanine. Collection of Czechoslovak Chemical Communications 1988, 53, (9), 1943
1945. Sauer, J.; Hobza, P.; Carsky, P.; Zahradnik, R., Applicability of the supermolecule MP2 approach to intermolecular interactions: He2 and Ne2. Chemical Physics Letters 1987, 134, (6), 553
559. Hobza, P.; Schneider, B.; Sauer, J.; Carsky, P.; Zahradnik, R., MP4 interaction energies and basis set superposition errors for the (H2)2 dimer. Chemical Physics Letters 1987, 134, (5), 418
422. Hobza, P.; Sandorfy, C., Nonempirical calculations on all the 29 possible DNA base pairs. Journal of the American Chemical Society 1987, 109, (5), 1302
1307. Foucrault, M.; Hobza, P.; Sandorfy, C., Nonempirical calculations on hydrogen-bonded and stacked structures of para-benzoquinone
hydroquinone, pyridine
pyrrole and pyridine
phenol complexes. Journal of Molecular Structure: THEOCHEM 1987, 37, (1
2), 11
18. Foucrault, M.; Hobza, P.; Sandorfy, C., Quantum chemical study of the site of protonation in conjugated Schiff bases. Journal of Molecular Structure: THEOCHEM 1987, 37, (3
4), 231
240. Zahradnik, R.; Hobza, P., Weak intermolecular interactions: Statics and dynamics. International Journal of Quantum Chemistry 1986, 29, (4), 663
676. Schleyer, P. V.; Sawaryn, A.; Reed, A. E.; Hobza, P., The remarkable structure of lithium cyanide isocyanide. Journal of Computational Chemistry 1986, 7, (5), 666
672. Hobza, P.; Schneider, B.; Carsky, P.; Zahradnik, R., The superposition error problem: The (HF)2 and (H2O)2 complexes at the SCF and MP2 levels. Journal of Molecular Structure: THEOCHEM 1986, 31, (3
4), 377
385. Hobza, P.; Mehlhorn, A.; Carsky, P.; Zahradnik, R., Stacking interactions: Ab initio SCF and MP2 study on (H2O)2, (H2S)2, (HCN)2, (CH2O)2 and (C2H4)2. Journal of Molecular Structure: THEOCHEM 1986, 31, (3
4), 387
399. Zahradnik, R.; Schneider, B.; Hobza, P.; Havlas, Z.; Huber, H., Discriminative interactions between chiral molecules: Internal discrimination in 1,2-difluorohydrazine. Canadian Journal of Chemistry-Revue Canadienne De Chimie 1985, 63, (7), 1639
1641. Hobza, P.; Sandorfy, C., Perturbation of hydrogen-bonds in the adenine 3 3 3 thymine base pair by Na+, Mg2+, Ca2+ and NH4+ cations. Journal of Biomolecular Structure and Dynamics 1985, 2, (6), 1245
1254. Szczesniak, M. M.; Hobza, P.; Latajka, Z.; Ratajczak, H.; Skowronek, K., The methylation effect in amine 3 3 3 HF hydrogen-bonded systems. Quantum chemical and statistical thermodynamic study. Journal of Physical Chemistry 1984, 88, (24), 5923
5927. Sauer, J.; Hobza, P., The minimal basis set MINI-1 powerful tool for calculating intermolecular interactions 0.2. Ionic complexes. Theoretica Chimica Acta 1984, 65, (4), 291
302. Sandorfy, C.; Buchet, R.; Hobza, P.; Ruelle, P., Theoretical and experimental studies of biologically important hydrogen-bonds. Journal of Molecular Structure: THEOCHEM 1984, 16, (FEB), 251
256. Hobza, P.; Zahradnik, R.; Ladik, J., Origin of high-efficiency and specificity of biochemical reactions. International Journal of Quantum Chemistry 1984, 26, (5), 857
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56. Hobza, P.; Schleyer, P. V., On the nature of LiH2. Chemical Physics Letters 1984, 105, (6), 630
634. 55. Hobza, P.; Sauer, J., Minimal basis set MINI-1 powerful tool for calculating of molecular-interactions 0.1. Neutral complexes. Theoretica Chimica Acta 1984, 65, (4), 279
290. 54. Hobza, P.; Sandorfy, C., Quantum chemical and statistical thermodynamic investigations of anesthetic activity 0.3. The interaction between CH4, CH3Cl, CH2Cl2, CHCl3, CCl4, and an O
H 3 3 3 O Hydrogen-Bond. Canadian Journal of Chemistry-Revue Canadienne De Chimie 1984, 62, (3), 606
609. 53. Hobza, P.; Sandorfy, C., A quantum chemical study of the effect of Na+ on the hydrogen-bonds in the adenine
thymine base-pair. Biophysical Chemistry 1984, 19, (3), 201
209. 52. Hobza, P.; Mercier, P.; Sandorfy, C., Hydrogen-bonding in mechanisms of anesthesia tested with chloroform and deuterated chloroform. British Journal of Anaesthesia 1984, 56, (12), 1447
1448. 51. Szczesniak, M. M.; Hobza, P., Search for a simplified procedure for the evaluation of the Gibbs free-energy of hydrogen-bond formation. Journal of Physical Chemistry 1983, 87, (14), 2608
2614. 50. Huber, H.; Hobza, P.; Zahradnik, R., On the applicability of the FOGO procedure to van der Waals molecules. Journal of Molecular Structure: THEOCHEM 1983, 12, (AUG), 245
257. 49. Hobza, P.; Zahradnik, R., van der Waals molecules: Quantum-chemistry, physical-properties, and reactivity. International Journal of Quantum Chemistry 1983, 23, (1), 325
338. 48. Hobza, P.; Sandorfy, C., Perturbation of hydrogen-bonds in the adenine 3 thymine base pair by Na+: A quantum chemical study. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 1983, 80, (10), 2859
2860. 47. Hobza, P.; Hofmann, H. J.; Zahradnik, R., Influence of local electric-fields on the properties and reactivity of hydrogen-bonds. Complexes between (HF)2 and (HCl)2 and M (M = Li+, Na+, Mg2+). Journal of Physical Chemistry 1983, 87, (4), 573
578. 46. Zahradnik, R.; Hobza, P.; Sauer, J., Selected topics in biological catalysis. Chemicke Listy 1982, 76, (3), 312
329. 45. Hobza, P.; Zahradnik, R., Calculation of weak intermolecular van der Waals interactions in biologically important systems. Chemicke Listy 1982, 76, (7), 673
694. 44. Hobza, P.; Mulder, F.; Sandorfy, C., Quantum chemical and statistical thermodynamic investigations of anesthetic activity. 2. The interaction between chloroform, fluoroform, and a N
H 3 3 3 OdC hydrogen bond. Journal of the American Chemical Society 1982, 104, (4), 925
928. 43. Hobza, P.; Zahradnik, R., Formation of hydrogen-bonded van der Waals molecules: Applicability of 3-21G intermolecular interaction energies. Chemical Physics Letters 1981, 82, (3), 473
477. 42. Hobza, P.; Szczesniak, M. M.; Latajka, Z., HF
C1F: Minima on the 4-31G and 4
31G* energy hypersurfaces and thermodynamics of formation. Chemical Physics Letters 1981, 82, (3), 469
472. 41. Hobza, P.; Sauer, J.; Morgeneyer, C.; Hurych, J.; Zahradnik, R., Bonding ability of surface sites on silica and their

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39.

38. 37. 36.

35.

34.

33. 32.

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30. 29.

28. 27.

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effect on hydrogen-bonds: A quantum-chemical and statistical thermodynamic treatment. Journal of Physical Chemistry 1981, 85, (26), 4061
4067. Hobza, P.; Mulder, F.; Sandorfy, C., Quantum chemical and statistical thermodynamic investigations of anesthetic activity. 1. The interaction between chloroform, fluoroform, cyclopropane, and an O
H 3 3 3 O hydrogen bond. Journal of the American Chemical Society 1981, 103, (6), 1360
1366. Hobza, P.; Hofmann, H. J.; Zahradnik, R., The CO2 3 3 3 HF Complex: A theoretical study (4-31G,6-31G* + dispersion energy) of the stationary-points and thermodynamics of formation. Journal of Molecular Structure: THEOCHEM 1981, 2, (3
4), 241
247. Urban, M.; Hrivnakova, S.; Hobza, P., Ab initio study of the (BH)2 Dimer. Collection of Czechoslovak Chemical Communications 1980, 45, (12), 3270
3282. Sauer, J.; Hobza, P.; Zahradnik, R., Quantum chemical investigation of interaction sites in zeolites and silica. Journal of Physical Chemistry 1980, 84, (24), 3318
3326. Hobza, P.; Zahradnik, R., van der Waals systems: Molecular orbitals, physical properties, thermodynamics of formation and reactivity. Topics in Current Chemistry 1980, 93, 53
90. Hobza, P.; Szczesniak, M. M.; Latajka, Z., HH
HCl: Stationary points on the SCF energy hypersurface and thermodynamics of formation. Chemical Physics Letters 1980, 74, (2), 248
251. Hobza, P.; Pancir, J.; Zahradnik, R., Nature of stationary points on CNDO-2 energy hypersurfaces of van der Waals molecules formed by polar molecules. Collection of Czechoslovak Chemical Communications 1980, 45, (5), 1323
1330. Lochmann, R.; Hobza, P., PCILO calculations on true van der Waals complexes. International Journal of Quantum Chemistry 1979, 15, (1), 73
81. Hobza, P.; Carsky, P.; Zahradnik, R., Clusters of hydrogen molecules: Ab initio SCF calculations corrected semiempirically for correlation energies. Theoretica Chimica Acta 1979, 53, (1), 1
7. Hobza, P.; Carsky, P.; Zahradnik, R., Dimer (HCl)2: Stationary points on the SCF 4-31G energy hypersurface and the role of entropy in the dimer formation. Collection of Czechoslovak Chemical Communications 1979, 44, (12), 3458
3463. Hobza, P.; Carsky, P.; Zahradnik, R., Role of entropy in formation of van der Waals complexes. International Journal of Quantum Chemistry 1979, 16, (2), 257
260. Thang, N. D.; Hobza, P.; Pancir, J.; Zahradnik, R., Semiempirical energy hypersurface of formaldehyde
water complex and methyl-derivatives thereof. Collection of Czechoslovak Chemical Communications 1978, 43, (5), 1366
1374. Hobza, P.; Hurych, J., Quantum chemical study of properties and reactivity of quartz dust. 1. Electronic-structure of α-quartz. Environmental Research 1978, 15, (3), 432
442. Hobza, P.; Carsky, P.; Zahradnik, R., Semi-empirical EPCE-F2σ correlation energies for van der Waals complexes and energies of reaction. Collection of Czechoslovak Chemical Communications 1978, 43, (3), 676
680. Hobza, P.; Bocek, K.; Hofmann, H. J.; Slanina, Z.; Zahradnik, R., Gas-phase and liquid-phase hydration of dx.doi.org/10.1021/jp208270u |J. Phys. Chem. A 2011, 115, 11121–11135

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13. 12.

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SPECIAL ISSUE PREFACE

methanol: Enthalpy and entropy calculations. Collection of Czechoslovak Chemical Communications 1978, 43, (3), 665
675. Heidrich, D.; Hobza, P.; Carsky, P.; Zahradnik, R., Effect of correlation energy on stability of classical and non-classical structures of protonated benzene. Collection of Czechoslovak Chemical Communications 1978, 43, (11), 3020
3023. Havlas, Z.; Hobza, P.; Zahradnik, R., Weak inter-molecular interactions 0.8. Attempt to construct a hybrid intermolecular potential. Collection of Czechoslovak Chemical Communications 1978, 43, (5), 1356
1365. Hobza, P.; Zahradnik, R., Electronic-structure of established and potential oxidizing-agents in biological-systems. Journal of Theoretical Biology 1977, 66, (3), 461
474. Hobza, P.; Zahradnik, R., Selected chapters from applied quantum chemistry 0.27. Environmental effects on properties of molecules: Solvation energy and physical characteristic. Chemicke Listy 1977, 71, (8), 807
821. Hobza, P.; Zahradnik, R., Weak intermolecular interactions 0.6. Estimates of geometry of molecular complexes based on analysis of intermolecular forces. Collection of Czechoslovak Chemical Communications 1976, 41, (4), 1111
1120. Hobza, P.; Struzinsky, R.; Ducthang, N.; Zahradnik, R., Weak intermolecular interactions 0.7. Empirical calculations on interaction energies of clusters of molecules: Correlation with heats of vaporization. Collection of Czechoslovak Chemical Communications 1976, 41, (6), 1727
1739. Zahradnik, R.; Hobza, P.; Slanina, Z.; Carsky, P., Hydrogen and its aggregates: Review of results of quantum chemical studies. Chemicke Listy 1975, 69, (9), 897
914. Zahradnik, R.; Hobza, P.; Slanina, Z., Calculations of Henry constants and partition-coefficients. Collection of Czechoslovak Chemical Communications 1975, 40, (3), 799
808. Urban, M.; Hobza, P., Weak intermolecular interaction 0.3. Ab-initio SCF calculation of interaction energy and its components near van der Waals minimum. Theoretica Chimica Acta 1975, 36, (3), 207
214. Urban, M.; Hobza, P., Weak intermolecular interaction 0.4. Application of function counterpoise method to calculation of interaction energy and its components. Theoretica Chimica Acta 1975, 36, (3), 215
220. Horak, M.; Hilgard, S.; Hobza, P., Studies of solute
solvent interactions 0.7. Stabilization energy of collision complexes and its semiempirical calculations. Collection of Czechoslovak Chemical Communications 1975, 40, (6), 1801
1810. Hobza, P.; Zahradnik, R., Semiempirical variation calculations on interaction energy of 2 identical nonpolar systems. Collection of Czechoslovak Chemical Communications 1975, 40, (3), 809
814. Carsky, P.; Zahradnik, R.; Hobza, P., Semiempirical estimates of correlation energy in small clusters of hydrogen atoms. Theoretica Chimica Acta 1975, 40, (4), 287
295. Slanina, Z.; Hobza, P.; Zahradnik, R., Calculation of absolute values of equilibrium and rate constants 0.2. Dimerization of homonuclear biatomic molecules. Collection of Czechoslovak Chemical Communications 1974, 39, (1), 228
235. Hobza, P.; Zahradnik, R., Selected chapters from applied quantum chemistry 0.10. Weak interactions in chemistry. Chemicke Listy 1974, 68, (7), 673
695.

10. Hobza, P.; Zahradnik, R., Weak intermolecular interactions: Introductory remarks and methods used. Collection of Czechoslovak Chemical Communications 1974, 39, (10), 2857
2865. 9. Hobza, P.; Zahradnik, R., Weak intermolecular interactions 0.2. Perturbation treatment of interactions between nonpolar molecule nonpolar molecule and polar molecule polar molecule. Collection of Czechoslovak Chemical Communications 1974, 39, (10), 2866
2876. 8. Nykl, I.; Rejholec, V.; Hobza, P.; Carsky, P.; Zahradnik, R.; Hafner, K., Conjugated radicals 0.17. Electronic-spectra of radical ions derived from pentaleno[6,6a,1,2-def]heptalene and 2-phenylcyclopent[cd]azulene and semiempirical open-shell PPP-like calculations. Collection of Czechoslovak Chemical Communications 1973, 38, (5), 1463
1465. 7. Nykl, I.; Fojtik, A.; Hobza, P.; Carsky, P.; Zahradnik, R.; Shida, T., Electronic spectra of azulene mononegative and monopositive ions and semiempirical open-shell PPP-like calculations. Collection of Czechoslovak Chemical Communications 1973, 38, (5), 1459
1462. 6. Hobza, P.; Nykl, I.; Uhlir, K., Electrochemical equipment for generation of radicals and recording electronic-spectra. Collection of Czechoslovak Chemical Communications 1973, 38, (4), 994
997. 5. Hobza, P.; Hurych, J.; Zahradnik, R., Quantum chemical study of mechanism of collagen proline hydroxylation. Biochimica et Biophysica Acta 1973, 304, (2), 466
472. 4. Hobza, P.; Carsky, P.; Zahradnik, R., Conjugated radicals 0.16. Electronic spectra of ortho-semiquinones and a remark on applicability of LCI-CNDO method to quinones and semiquinones. Collection of Czechoslovak Chemical Communications 1973, 38, (3), 641
644. 3. Zahradnik, R.; Carsky, P.; Rejholec, V.; Hafner, K.; Hobza, P., Conjugated radicals 0.14. Electronic spectra and semiempirical calculations on radical anions of acenaphthylene, fluoranthene and aceheptylene. Collection of Czechoslovak Chemical Communications 1972, 37, (6), 1983. 2. Zahradnik, R.; Hobza, P.; Hurych, J., Molecular-orbital study of hydroxylation of collagenous proline and lysine. Biochimica et Biophysica Acta 1971, 251, (3), 314. 1. Carsky, P.; Hobza, P.; Zahradnik, R., Conjugated radicals 0.11. Para semiquinones. Collection of Czechoslovak Chemical Communications 1971, 36, (3), 1291.

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