Untitled Document

List of papers:

1. Burda J.V., Lukáš R.:
Structure of Poly(Vinyl Chloride) Chain. I. Conformation of 2,4-dichloropentane.
Makromol. Chem., Macromol.Symp.29,321 (1989).

2. Špirko V., Kraemer W.P., Burda J.V.:
Anharmonic Potential Function, Geometry, and Energy Level of SiH3.
J.Mol. Spectrosc., 147, 478 (1991).

3. Burda J.V., Lukáš R.:

Thermal Dehydrochlorination of Poly(Vinyl Chloride) in Syndiotactic Systems.
Collect. Czech. Chem. Commun, 57, 93 (1992).

4. Burda J.V.,Bureš M., Černý Č.:
An Investigation of the Surface Growth of Silicon Crystal by the CNDO/2 Method. I. Effect of the Cluster Size on the Properties of Chemisorption.
Collect. Czech. Chem. Commun., 57, 241 (1992).

5. Burda J.V.,Bureš M., Černý Č.:
An Investigation of the Surface Growth of Silicon Crystal by the CNDO/2 Method. II. Interaction of the SiH x Cl y Silicon Species with theSi4H9 Cluster.
Collect. Czech. Chem. Commun., 57, 248 (1992).

6. Brát J., Burda J.V., Zajíc J., Lukáš R.:
Simulation der Spaltung von partiellen Estern des Glucerins.
Fat Sci.Technol., 94,73(1992).

7. Brát J., Burda J.V., Zajíc J.:
Vergleich der Spaltmechanismen bei den Partialestern des Glycerins.
Fat Sci.Technol., 94,594(1992).

8. Burda J.V., Lánská B.:
Oxidability and Structure of Lactams.
Collect. Czech. Chem. Commun., 58, 354 (1993).

9. Burda J.V., Lukáš R.:
Thermal Dehydrochlorination of Poly(Vinyl Chloride) in Isotactic System.
Collect. Czech. Chem. Commun., 58, 343 (1993).

10. Burda J.V., Lukáš R., Prádová O.:
Differential and Integral Form of Copolymerization Equation. I. Copolymerization System Vinyl Chloride/2-(Octanoyloxy)Ethyl Acrylate.
J. Macromol.Sci., Pure and Applied Chemistry, A32, 251 (1995).

11. Cincotti S., Burda J.V., Hentschke R., Rabe J.P.:
Calculation of monolayer structures of chain molecules at the solid liquid interface: Dotriacontane (C 32 H 66 ) on MoSe2.
Phys. Rev. E 51(3): 2090-2098 (1995).

12. Burda J.V., Lukáš R.:
Thermal Dehydrochlorination of Poly(Vinyl Chloride) Initiated by Tertiary Chlorine Gouping.
Collect. Czech. Chem. Commun., 60, 1303 (1995).

13. Burda J.V.:
Thermal Dehydrochlorination of Poly(Vinyl Chloride) Containing Aldehyde Group.
Collect. Czech. Chem. Commun., 60, 1310 (1995).

14. Burda J.V., Šponer J., Hobza P.:
An ab initio Study Interaction of Guanine and Adenine with Various Mono- and Bivalent Metal Cations (Li + , Na + , K + , Rb + , Cs + ; Cu + , Ag + , Au + ; Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ ; Zn 2+ , Cd 2+ , and Hg 2+ ).
J.Phys.Chem., 100, 7250 (1996).

15. 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 calculation on the (Ne)2 dimer, and CCSD(T) all-electron and pseudopotential calculations on the dimers from (Ne)2 through (Xe)2.
Mol. Phys., 89, 425-432 (1996).

16. Burda J.V., Hobza P., Zahradnik R.:
Properties and Reactivity in Groups of the Periodic System: Ion-Molecule Reactions HX + HX + · (X = F, Cl, Br, I, At).
J.Phys.Chem.A, 101, 1134-1139 (1997).

17. Burda J.V., Šponer J., Leszczynski J., Hobza P.:
Ab initio Study of the Interaction of DNA Base Pairs with Metal Cations (Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ , Cu + , Ag + , Au + , Zn 2+ , Cd 2+ , and Hg 2+ ): Structures, Energies, and Nonadditivity of the Interaction.
J. Phys. Chem.B, , 101, 9670-9677 (1997).

18. Šponer J., Burda J.V., Mejzlík P., Leszczynski J., Hobza P.:
Hydrogen-bonded Trimers DNA Bases and their Interaction with Metal Cations: Ab initio Quanum-chemical and Empirical Potential Study.
J. of Biomol. Struct. And Dyn. 14, 613 (1997).

19. Hobza P., Burda J.V., Zahradnik R.:
Isoelectronic dimers [(XH 3 ) 2 , (YH 2 ) 2 , (ZH) 2 , and (Rg) 2 ] in the Groups of the Periodic Systems: Ab initio Quantum Chemical Calculations.
Pol. J. Chem. 72, 1497-1504 (1998).

20. Burda J.V., Lánská B.:
supplement to Oxidability of Lactams and Lactam-based Polyamides.
Angewant. Makromol. Chemie 252, 139-151 (1997).

21. Burda J.V.:
A quantum chemical ab initio study of the interaction between Co + and Ni + ions with CO2 and N2O.
Phys.Chem., 230, 13-22 (1998).

22. Burda J.V., Hobza P., Zahradnik R.:
The (XH) 2 Species (X=F through At) in the Groups of the Periodic System: MP2 and CCSD(T) Ab initio Quantum Chemical Calculations.
Chem. Phys. Letters, 288, 20-24 (1998).

23. Burda J.V., Runeberg N., Pyykkö P.:
Chemical bonds between noble metals and noble gases: Ab initio study of the neutral diatomics NiXe, PdXe, and PtXe.
Chem. Phys. Letters, 289, 635-641 (1998).

24. Šponer J., Burda J.V, Sabat M., Leszczynki J., Hobza P.:
Interaction between the Guanine-Cytosine Watson-Crick DNA Base Pair and Hydrated Group IIa (Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ ) and Group IIb (Zn 2+ , Cd 2+ , Hg 2+ ) Metal Cations.
J. Phys. Chem., 102, 5951-5957 (1998).

25. Burda J.V., Šponer J., Hobza P., Leszczynski J.:
Ab initio Study of the Interaction of DNA Bases and Base Pairs with Various Mono- and Bivalent Metal Cations.
Bulletin de la Société des Sciences et Lettres de Lódz 49, 65-76 (1999).

26. Šponer J., Sabat M., Burda J.V., Doody A.M., Leszczynki J., Hobza P.:
Stabilization of the Purine .Purine.Pyrimidine DNA Base Triplets by Divalent Metal Cations.
J. Biomol. Struct. Dyn., 16, 139-143 (1998).

27. Capková P., Burda J.V., Weiss Z., Schenk H.:
Modelling of Aniline-Vermiculite and Tetramethylammonium-Vermiculite; Test of Force Fields.
J. Mol. Model., 5, 8-16 (1999).

28. Šponer J., Sabat M., Burda J., Leszczynski J., Hobza P.:
Interaction of the Adenine-Thymine Watson-Crick and Adenine-Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ ) and IIb (Zn 2+ , Cd 2+ , Hg 2+ ) Metal Cations: Absence of the Base Pair Stabilization by Metal-Induced Polarization Effects.
J.Phys.Chem. B 103(13), 2528-2534 (1999).

29. Šponer, J.; Burda, J. V.; Leszczynski, J.; Hobza, P.:
Interactions of Hydrated IIa and IIb Group Metal Cations with Thioguanine-Cytosine DNA Base Pair: Ab initio and Density Functional Theory Investigation of Polarization Effects, Differences among Cations, and Flexibility of the Cation Hydration Shell.
Journal of Biomolecular Structure and Dynamics, 17, 631-642 (1999).

30. Šponer J., Sabat M., Burda J.V., Leszczynski J., Hobza P., Lippert B.:
Metal ions in non-complementary DNA base pairs. Ab initio study of Cu(I), Ag(I) and Au(I) complexes with the cytosine - adenine base pair.
Journal of Biological Inorganic Chemistry 4, 537-545, (1999).

31. Burda J.V., Šponer J., Leszczynski J.:
Interaction of square platinum(II) complexes with guanine and adenine. Quantum chemical ab initio study of metalated tautomer forms.
J.Biological Inorganic Chemistry, 5(2), 178-188 (2000).

32. Burda, J. V.; Zeizinger, M.; Šponer J., Leszczynski, J.:
Pseudopotential treatment in the frame of G3-like theory for platinum complexes. Hydratation of cisplatin.
J. Chemical Physics 113(6), 2224-2232 (2000).

33. Zeizinger, M.; Burda, J. V.; Šponer J., Kapsa, V.; Leszczynski, J.:
A Systematic ab Initio Study of the Hydration of Selected Palladium Square-Planar Complexes. A Comparison with Platinum Analogues.
J. Physical Chemistry A, 105(34), 8086-8092 (2001).

34. Burda, J. V. ; Šponer, J.; Leszczynski, J.:
The influence of square planar platinum complexes on DNA base pairing. An ab initio DFT study.
Phys. Chem. Chem. Phys., 3(19), 4404-4411 (2001).

35. Burda, J. V. ; Lánská, B.:
An ab initio quantum chemical study of reactions ofhexano-6-lactam peroxy radicals with phenoxy or diphenyl radicals.
Polymer Degradation and Stability 74 (2001) 569-577.

36. Kopecký Jr., V. Mojzes, P.; Burda, J. V.; Dostál, L.:
Raman Spectroscopy Study of Acid–Base and Structural Properties of 9-[2-(Phosphonomethoxy)ethyl]adenine in Aqueous Solutions.
Biopolymers, 67(4-5), 285-288, (2002).

37. Bonacic-Koutecký, V ; Burda, J.; Mitric, R.; Ge, Maofa; Zampella, G.; Fantucci P.:
Density functional study of structural and electronic properties of bimetallic silver–gold clusters: Comparison with pure gold and silver clusters.
J.Chem.Phys. 117, 3120 (2002).

38. Mitric R., Burgel C., Burda J., Bonacic-Koutecky V., Fantucci P.:
Structural properties and reactivity of bimetallic silver-gold clusters.
Europ. Phys. J. D, 24 (1-3): 41-44 (2003).

39. Burda, J.V.; Šponer, J.; Hrabáková, J.; Zeizinger, M.; Leszczynski, J.:
The Influence of N 7 Guanine Modifications on the Strength of Watson - Crick Base Pairing and Guanine N 1 Acidity: Comparison of Gas-Phase and Condensed-Phase Trends.
J. Phys. Chem. B, 107(22), 5349-5356 (2003).

40. Burda, J.V.; Leszczynski J.:
Deformations of the DNA helix: the influence of cisplatin as revealed by ab initio study of platinum(II) bridged DNA purine bases.
Inorg. Chem. 42(22) 7162-7172(2003) .

41. Burda, J.V.; Zeizinger, M.; Leszczynski, J.:
Activation barriers and rate constants for hydration of platinum and palladium square-planar complexes: An ab initio study.
J. Chem.Phys. 120, 1253-1262 (2004).

42. Zeizinger, M; Burda,J.V.; Leszczynski, J.:
The influence of sugar-phosphate backbone on the cisplatin bridged BpB' models of the DNA purine bases. Quantum chemical calculations of the Pt(II) bonding characteristics.
PCCP, 2004, 6, 3585 - 3590 (2004).

43. Šeda, J.; Burda, J.V.; Brázdová, V.; Kapsa, V.:
Estimation of Electron Spectra Transitions of Free-Based Porphin and Mg-Porphin Using Various Quantum Chemical Approaches.
International Journal of Molecular Science , 5, 196-204 (2004 ).

44. Burda, J.V.; Pavelka, M; Šimanek, M.:
Theoretical model of copper Cu(I)/Cu(II) hydration. DFT and ab initio quantum chemical study.
J. Mol. Struct. THEOCHEM, 683, 183-193 (2004).

45. Šeda, J.; Burda, J.V.; Leszczynski, J.:
Computational Study of Electronic Spectra of Free-Base Porphin and Mg-Porphin: Comprehensive Comparison of the Application of Variety of Ab Initio, DFT and Semiempirical Methods.
J. Comput. Chem., 26, 294-303 (2005).

46. Pavelka, M; Burda, J.V.:
Theoretical description of copper Cu(I)/Cu(II) complexes in mixed ammino-aqua environment. DFT and ab initio quantum chemical study.
Chem. Phys., 312,193-204 (2005).

47. Burda, J.V.; Zeizinger, M.; Leszczynski, J.:
Hydration process as an activation step of trans- and cisplatin. DFT and ab initio computational study of thermodynamic and kinetic parameters.
J. Comput. Chem., 26, 907-914 (2005).

48. Burda, J.V.; Shukla, M.K.; Leszczynski, J.:
Theoretical model of the interaction aqua-copper [Cu(H2O)5] + cations with guanine. DFT and MP2 quantum chemical study.
J. Mol. Model., 11 , 362-369 (2005).

49. Zimmerman, T.; Zeizinger, M.; Burda, J.V.:
Cisplatin Interaction with Cysteine and Methionine; theoretical DFT study.
J. Inorg. Biochem. 11, 2184-2196 (2005).

50. Politzer, P.A.; Burda, J.V.; Concha, M.C.; Lane, P.; Murray , J.S.:
Analysis of the Reaction Force for a Gas Phase S N 2 Process: CH3Cl + H2O CH3OH + HCl.
J. Phys. Chem. A.; 110 (2); 756-761 ( 2006).

51. Pavelka, M; Šimánek, M., Šponer, J., Burda, J.V.:
Copper Cations Interactions with Biologically Essential Types of Ligands: Computational DFT Study.
J. Phys. Chem. A, 110, 4795-4809 (2006).

52. Allen, R.N.; Shukla, M.K.; Burda, J.V.; Leszczynski, J.:
Theoretical Study of Interaction of Urate with Li + , Na + , K + , Be 2+ , Mg 2+ , and Ca 2+ Metal Cations.
J. Phys. Chem. A, 110, 6139-6144 (2006).

53. Mrázek; J.Burda, J.V.:
Is it possible to predict the pH value of water from autodissociation energies of small clusters? Quantum chemical study of potential energy sufaces.
J. Chem. Phys. 125, 194518 (2006).

54. Pavelka, M; Burda, J.V.:
Pt-bridges in the Single-strand and Interstrand DNA sequences. DFT and MP2 study of the cisplatin coordination with guanine, adenine, and cytosine.
J. Mol. Model., 13, 367-379 (2007).

55. Burda, J. V.; Toro-Labbe, A.; Gutierrez-Oliva, S.; Murray, J. S.; Politzer, P.:
Reaction Force Decomposition of Activation Barriers To Elucidate Solvent Effects.
J. Phys. Chem. A.; (Letter); 111(13); 2455-2457 (2007).

56. Vokáčová, Z.; Burda, J.V.:
Computational study on the spectral properties of the selected pigments from the photosystems: Structure – transition energy relationship with TD DFT approach.
J. Phys. Chem. A 1111, 5864-5878 (2007).

57. Burda, J.V.; Gu, J.:
A computational study on DNA bases interactions with dinuclear tetraacetato-diaqua-dirhodium(II,II) complex
J. Inorg. Biochem. 102, 53-62 (2008).

58. Bradáč, O., Zimmermann, T.; Burda, J.V.
Comparison of activity and properties of selected cisplatin derivatives
J. Mol. Model., 14, 705-716(2008).

59. Pavelka, M.; Shukla, M. K.; Leszczynski, J.; Burda, J. V.
Theoretical Study of Hydrated Copper(II) Interactions with Guanine: A Computational Density Functional Theory Study
J. Phys. Chem. A.; 112 (2); 256-267(2008).

60. Chval, Z.; Ší p, M.; Burda, J.V.
The Trans Effect in Square-Planar Platinum(II) Complexes- a Density Functional Study.
J. Comput. Chem . 29, 2370–2381(2008).

61. Pavelka, M; Burda, J.V.
Theoretical Study of Redox Active Centers of Blue Copper Proteins: A Computational DFT Study.
Mol. Phys. 106, 2733-2748 (2008).

62. Futera, Z.; Klenko, J., Šponer, J.E.; Šponer, J.; Burda, J.V.
Computational model for Ru(II) interactions with water, guanine, and adenine.
J. Comput.. Chem. 30, 1758-1770 (2009).

63. Zimmermann, T.; Chval, Z.; Burda, J.V.
Cisplatin Interaction with Cysteine and Methionine in Aqueous Solution: Computational DFT/PCM Study
J. Phys. Chem. B ,113, 3139–3150 (2009).

64. Burda, J.V.; Murray, J.S.; Toro-Labbé, A.; Gutiérrez-Oliva, S.; Politzer, P.A.
Reaction Force Analysis of Solvent Effects in the Addition of HCl to Propene
J. Phys. Chem. A , 113, 6500–6503 (2009)

65. Zimmermann, T.; Burda, J.V.
Charge-Scaled Cavities in Polarizable Continuum Model; Determination of acid dissociation constants for platinum – amino acid complexes.
J.Chem. Phys. 131, 135101(2009)

66. Zimmermann, T.; Burda, J.V.
Reactions of cisplatin with cysteine and methionine at constant pH; a computational study
Dalton Transaction, Dalton Trans., 1295-1301 (2010)

67. Zimmermann, T. Burda, J.V.
Cisplatin interaction with amino acids cysteine and methionine from gas phase to solutions with constant pH
Interdisc.Sci. Comput.Life Sci., 2, 98-114 (2010)

68. Futera, Z; Kovaľ, T.; Leszczynski, J.; Gu, J.; Srebro, M.; Mitoraj, M.; Burda J.V.
Exploring a reaction mechanism for Acetato ligand replacement in Paddlewheel Tetrakisacetatodirhodium (II) Complex by Ammonia; Computational DFT Study,
J.Phys.Chem. A, 115, 784–794 (2011)

69. Chval, Z.; Futera, Z.; Burda, J.V.
Comparison of hydration reactions for "piano-stool" RAPTA-B and [Ru(η6−arene)(en)Cl+ complexes; DFT computational study.
J.Chem. Phys. 134, 024520 (2011)

70. Zimmermann, T.; Leszczynski, J.; Burda; J.V.
Activation of the cisplatin and transplatin complexes in solution with constant pH and concentration of Cl- anions; quantum chemical study.
J. Mol. Model., 17(9) 2385-2393 (2011)

71. Tokarský, J.; Čapková, P.; Burda, J.V.
Structure and stability of kaolinite/TiO2 nanocomposite: DFT and MM computations.
J Mol Model, 18, 2689-2698 (2012).

72. Kizek, R.; Adam, V.; Hraběta, J.; Eckschlager, T.; Smutný, S.; Burda, J.V. ; Frei, E.; Stiborová, M.
Anthracyclines and ellipticines as DNA-damaging anticancer drugs: Recent advances.
Pharmacology & Therapeutics 133 26–39 (2012).

73. Futera, Z.; Platts, J.A.; Burda, J.V.
Binding of Ru(II) Complexes to DNA; QM/MM Study.
J. Comput. Chem. 33, 2092-2101 (2012).

74. Michera, L.; Nekardová, M.; Burda, J.V.
Reactions of cisplatin and glycine in solution with constant pH; a computational study.
Phys.Chem.Chem.Phys 14, 12571-12579 (2012).

75. S. Ishihara, J. Labuta, T. Šikorský, J.V. Burda, N. Okamoto, H. Abe, K. Ariga, J.P. Hill
Colorimetric detection of trace water in tetrahydrofuran using N,N0-substituted oxoporphyrinogens.
Chem. Commun., 48, 3933–3935 (2012).

76. Alster, J.; Kabeláč, M.; Tuma, R.; Pšencík, J.; Burda, J.V.
Computational study of short-range interactions in bacteriochlorophyll aggregates.
Comput.& Theor. Chem. 998, 87–97 (2012).

77. Dos Santos, H. F.; Paschoal, D.; Burda, J.V.
Exploring the potential energy surface for interaction of a trichloro (diethylenetriamine)gold(III) complex with strong nucleophiles.
Chemical Physics Letters 548, 64-70 (2012).

78. Dos Santos, H.F.; Paschoal, D.; Burda, J.V.
Exploring the Potential Energy Surface for the Interaction of Sterically Hindered Trichloro(diethylenetriamine)gold(III) Complexes with Water.
J. Phys. Chem. A, 116, 11015–11024 (2012)

79. Bradáč, O.; Zimmermann, T.; Burda, J.V.
Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study
J. Mol.Model. 19, 4669-4680,(2013)

80. Šebera, J.; Burda, J.V.; Straka, M.; Ono, A.; Kojima, C.; Tanaka, Y.; Sychrovský, V;
Formation of the T-HgII-T Metal-Mediated DNA Base Pair; Proposal and Theoretical Calculation of the Reaction Pathway.
Chem. Eur. J. 19 , 9884–9894 (2013).

81. Chval, Z.; Kabelac, M.; Burda, J.V.
Mechanism of the cis-[Pt(1R,2R-DACH)(H2O)(2)](2+) Intrastrand Binding to the Double-Stranded (pGpG)center dot(CpC) Dinucleotide in Aqueous Solution: A Computational DFT Study.
Inorg. Chem. 52, 5801-5813 (2013)

82. Labuta, J. Ishihara, S., Šikorsky´, T.; Futera, Z.; Shundo, A.; Hanykova´, L.; Burda, J.V.; Ariga, K.; Hill1, J.P.
NMR spectroscopic detection of chirality and enantiopurity in referenced systems without formation of diastereomers.
Nature Commun. (2013) DOI: 10.1038/ncomms3188.

83 Burda, J.V.; Futera, Z.; Chval, Z.
Exploration of various electronic properties along the reaction coordinate for hydration of Pt(II) and Ru(II) complexes; the CCSD, MPx, and DFT computational study
J Mol Model (2013) 19:5245–5255.

84. Futera, Z.; Burda, J.V.
Reaction Mechanism of Ru(II) Piano-Stool Complexes; Umbrella Sampling QM/MM MD Study
J. Comput. Chem. (2014) 35. 1446-1456.

85. Tokarský, J.; Maixner, M.; Peikertová, P.; Kulhánková, L.; Burda, J.V.
The IR and RAMAN spectra of polyaniline adsorbed on the glass surface; comparison of experimental, empirical force field, and quantum chemical results.
Eur Polymer. J. (2014) 57, 47-57.

86. Yamaguchi, H. ; Šebera, J.; Kondo, J.; Oda, S.; Komuro, T.; Kawamura, T.; Daraku, T.; Kondo, Y.; Okamoto, I.; Ono, A.; Burda, J.V.; Kojima, C.; Sychrovský, V.; Tanaka, Y.
The structure of metallo-DNA with consecutive T-HgII-T base-pairs ex-plains positive reaction entropy for the metallo-base-pair formation.
Nucleic Acid Research (NAR) (2014), 42, 4096-4099.

87. Futera, Z.; Sodeyama, K.; Burda, J.V.; Einaga, Y.; Tateyama, Y.
Double-QM/MM Method for Donor-Acceptor Electron Transfer in Solution.
Phys.Chem.Chem.Phys., (2014), 16, 19530-19539.

88. Formánek, M.; Burda, J.V.
The Influence of Arene-Ring Size on Stacking Interaction with Canonical Base Pairs
Chem. Phys. Letters, 598 (2014) 28–34.

89. Matěnová, M.; Horhoiu, V. L.; Pospíšil, P.; Alster, J.;. Burda, J.V.; Balaban, T.S.; Pšenčík, J.;
Energy transfer in aggregates of bacteriochlorophyll c self-assembled with azulene derivatives.
Phys. Chem.Chem.Phys, (2014), 16, 16755-16764.

90 Šebesta F. Burda, J.V.
Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study.
Chemistry Eur. J. (2016) 22, 1037-1047.

91. Zábojníková, T.; Futera, Z.; Kljun, J.; Turel, I.; Burda, J.V.
Thermodynamic and Kinetic parameters for Aquation of Various Quinolone Ru(II) Complexes; DFT Study.
J. Comput. Chem. (2016) 37, 1766–1780,

92. Šebesta, F.; Sláma, V.; Melcr, J.; Futera, Z.; Burda, J.V.
Estimation of transition-metal empirical parameters for molecular mechanical force fields.
J. Chem. Theor. Comput. (2016) 12, 3681-8.

93. Šebesta, F.; Burda, J.V.
Study on Electronic Properties, Thermodynamic and Kinetic Parameters of the Selected Platinum(II) Derivatives Interacting With Guanine.
J. Inorg. Biochem. (2017) 172, 100-109.

94. Šebesta, F.; Burda, J.V.
Side Reactions with an Equilibrium Constraint: Detailed Mechanism of the Substitution Reaction of Tetraplatin with dGMP as a Starting Step of the Pt(IV) Reduction Process.
J. Phys. Chem. B (2017) 121, 4400−4413.

95. Šebesta, F.; Brela, M.Z.; Diaz, S.; Miranda, S.; Murray, J. S.; Gutiérrez-Oliva, S.; Toro-Labbé, A.; Michalak, A.; Burda, J.V.
The Influence Of The Metal Cations and Microhydration On The Reaction Trajectory Of The N3 ↔ O2 Thymine Proton Transfer. Quantum Mechanical Study.
J.Comput.Chem. (2017) 38, 2680–2692. DOI: 10.1002/jcc.24911

96. Šebesta, F.; Burda, J.V.
Interactions of Ascorbic Acid with Satraplatin and Its Trans Analog JM576; DFT Computational Study.
Eur. J. Inorg. Chem. (2018), 1481–1491 10.1002/ejic.201701334

97. Šebesta, F.; Baxová, K.; Burda, J.V.
Redox Potentials for Tetraplatin, Satraplatin, Its Derivatives and Ascorbic Acid; Computational Study.
Inorg.Chem. (2018) 57, 951-962, DOI 10.1021/acs.inorgchem.7b01894

98. Maixner, M.; Dos Santos, F. H.; Burda, J.V.
Formation of Chelate Structure Between His-Met dipeptide and diaqua-cisplatin complex; DFT/PCM computational study.
J.Biol.Inorg. (2018) 23, 363–376, doi.org/10.1007/s00775-018-1536-x

99. Sochorová Vokáčová, Z.; Turel, I.; Burda, J.V.
Exploration of selected electronic characteristics of the half-sandwich organoruthenium(II) β-diketonate complexes.
J. Mol. Model. (2018), 24, 98, https://doi.org/10.1007/s00894-018-3598-7

100. Špačková, N.; Trošanová, Z.; Šebesta,F.; Jansen,S. Burda, J.V.; Srb, P.; Zachrdla, M.; Žídek, L.; Kozelka, J.
Protein environment affects the water-tryptophan binding mode. MD, QM/MM, and NMR studies of Engrailed homeodomain mutants.
Phys. Chem. Chem. Phys. (2018), 20, 12664-12677

101. Šebesta, F.; Šebera, J.; Sychrovský, V.; Tanaka, Y; Burda, J.V
QM/MM Umbrella sampling MD Study of Thymine Interaction with Mercury Cation in Explicit Water Solution.
In prep.

Chapters in v books:

1. Chapter 6: Towards the Elucidation of the Activation of Cisplatin in Anticancer Treatment

Jaroslav V. Burda, Jiří Šponer , and Jerzy Leszczynski
in Computational Chemistry: Reviews of Current Trends Vol. 10
Jerzy Leszczynski (Ed.)
World Scientific, Singapore
ISBN 981-256-742-9

2. Interaction of metal cations with Nucleic acids and their building units
A comprehensive view from quantum chemical calculations

Judit E. Šponer, Jaroslav V. Burda, Jerzy Leszczynki and Jiří Šponer
in Computational studies of RNA and DNA
Series: Challenges and Advances in Computational Chemistry and Physics , Vol. 2
Šponer, Jiří; Lankaš, Filip (Eds.)
2006, XII, 640 p., Hardcover
ISBN-10: 1-4020-4794-0
ISBN-13: 978-1-4020-4794-7