Search results for: Jaroslav V. Burda

Items from 1 to 20 out of 54 results

article

Quantum mechanical study of transition metal hydrides: Comparison of determined molecular properties with experimental data

Adam Vavrečka, Kateřina Fatková, Jaroslav V. Burda

Journal of Computational Chemistry > 45 > 20 > 1727 - 1736

This study compares results of four relativistic pseudopotential basis sets, which differ mainly by their size: double‐zeta introduced by Hay and Wadt from Los Alamos National Laboratory (LANL2DZ), triple‐zeta based on Stuttgart energy‐consistent scalar‐relativistic pseudopotential (SDD3), its extension with 2fg polarization functions, and combination of Stuttgart pseudopotentials with quintuple‐zeta...

article

The vertical excitation energies and a lifetime of the two lowest singlet excited states of the conjugated polyenes from C2 to C22: Ab initio, DFT, and semiclassical MNDO‐MD simulations

Kateřina Fatková, Radim Cajzl, Jaroslav V. Burda

Journal of Computational Chemistry > 44 > 6 > 777 - 787

Electronic excited states in the series of polyene molecules were explored. Optimal ground‐state geometry was used for the evaluation of vertical excitation energies. Results of a chosen set of functionals were compared to post‐HF methods (EOM‐CCSD, NEVPT2, CASPT2, and MRCI). In addition, the semiempirical OM2/MNDO method using MRCISD computational level was confronted with the above‐mentioned techniques...

article

QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

Filip Šebesta, Jakub Šebera, Vladimír Sychrovský, Yoshiyuki Tanaka, more

Journal of Computational Chemistry > 41 > 16 > 1509 - 1520

The formation of the Hg–N3(T) bond between the 1‐methylthymine (T) molecule and the hydrated Hg²⁺ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H₂O)...

article

A Dogma in Doubt: Hydrolysis of Equatorial Ligands of Pt^IV Complexes under Physiological Conditions

Alexander Kastner, Isabella Poetsch, Josef Mayr, Jaroslav V. Burda, more

Angewandte Chemie International Edition > 58 > 22 > 7464 - 7469

Due to their high kinetic inertness and consequently reduced side reactions with biomolecules, Pt^IV complexes are considered to define the future of anticancer platinum drugs. The aqueous stability of a series of biscarboxylato Pt^IV complexes was studied under physiologically relevant conditions. Unexpectedly and in contrast to the current chemical understanding, especially oxaliplatin and satraplatin...

article

Zweifel an einem Dogma: Hydrolyse äquatorialer Liganden von Pt^IV‐Komplexen unter physiologischen Bedingungen

Alexander Kastner, Isabella Poetsch, Josef Mayr, Jaroslav V. Burda, more

Angewandte Chemie > 131 > 22 > 7542 - 7547

Pt^IV‐Komplexe gelten aufgrund ihrer hohen kinetischen Inertheit und der folglich reduzierten Nebenreaktionen mit Biomolekülen als die Zukunft der Platintherapeutika. In dieser Arbeit wurde unter physiologisch relevanten Bedingungen die Stabilität einer Reihe von Pt^IV‐Biscarboxylatokomplexen in wässriger Lösung untersucht. Entgegen des derzeitigen chemischen Kenntnisstandes zeigten (sogar in Zellkulturmedium...

article

Correction to: Exploration of selected electronic characteristics of half-sandwich organoruthenium(II) β-diketonate complexes

Zuzana Sochorová Vokáčová, Iztok Turel, Jaroslav V. Burda

Journal of Molecular Modeling > 2018 > 24 > 5 > 1-1

We would like to apologize for a wrong conclusion on the fourth page where the correlation of the Ru-P bond length and possible anticancer activity is discussed.

article

Cover Feature: Interactions of Ascorbic Acid with Satraplatin and its trans Analog JM576: DFT Computational Study (Eur. J. Inorg. Chem. 13/2018)

Filip Šebesta, Jaroslav V. Burda

European Journal of Inorganic Chemistry > 2018 > 13 > 1448 - 1448

The Cover Feature shows the theoretical possibility that a satraplatin–platinum(IV) complex can be reduced by ascorbic acid in a cellular environment. According to the performed calculations, the transfer of two electrons from ascorbic acid to the platinum(IV) complex can occur spontaneously especially under pH 7. The reduced platinum(II) metabolite is generally accepted to be an active metallodrug,...

article

Interactions of Ascorbic Acid with Satraplatin and its trans Analog JM576: DFT Computational Study

Filip Šebesta, Jaroslav V. Burda

European Journal of Inorganic Chemistry > 2018 > 13 > 1481 - 1491

Knowledge of the mechanisms for the reduction of Pt^IV anticancer prodrugs is of great importance, since the reduction process is considered as a necessary step for their activation. Therefore, in this study, we investigate the reduction of satraplatin {JM216, cis,trans,cis‐[PtCl₂(OAc)₂(cha)(NH₃)], cha = cyclohexylamine} by ascorbic acid (AA) where proton‐assisted electron‐transfer and outer‐sphere...

article

Exploration of selected electronic characteristics of half-sandwich organoruthenium(II) β-diketonate complexes

Zuzana Sochorová Vokáčová, Iztok Turel, Jaroslav V. Burda

Journal of Molecular Modeling > 2018 > 24 > 4 > 1-10

Based on experimental work, 12 half-sandwich organoruthenium(II) complexes with p-cymene and various substituted β-diketonates (acac) modified by several functional groups were explored. These complexes were optimized at the B3PW91/6–31 + G(d)/PCM/UFF computational level with the Ru atom described by Stuttgart pseudopotentials. The electron density analysis was performed using the B3LYP/ 6–311++G(2df,2pd)/DPCM/scaled-UAKS...

article

Formation of chelate structure between His-Met dipeptide and diaqua-cisplatin complex; DFT/PCM computational study

Michal Maixner, Helio F. Santos, Jaroslav V. Burda

JBIC Journal of Biological Inorganic Chemistry > 2018 > 23 > 3 > 363-376

Interaction of cisplatin in activated diaqua-form with His-Met dipeptide is explored using DFT approach with PCM model. First the conformation space of the dipeptide is explored to find the most stable structure (labeled 0683). Several functionals with double-zeta basis set are used for optimization and obtained order of conformers is confirmed by the CCSD(T) single-point calculations. Supermolecular...

article

The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study

Filip Šebesta, Mateusz Z. Brela, Silvia Diaz, Sebastian Miranda, more

Journal of Computational Chemistry > 38 > 31 > 2680 - 2692

This study involves the intramolecular proton transfer (PT) process on a thymine nucleobase between N3 and O2 atoms. We explore a mechanism for the PT assisted by hexacoordinated divalent metals cations, namely Mg²⁺, Zn²⁺, and Hg²⁺. Our results point out that this reaction corresponds to a two‐stage process. The first involves the PT from one of the aqua ligands toward O2. The implications of this...

article

Study on electronic properties, thermodynamic and kinetic parameters of the selected platinum(II) derivatives interacting with guanine

Filip Šebesta, Jaroslav V. Burda

Journal of Inorganic Biochemistry > 2017 > 172 > C > 100-109

Interaction of hydrated forms of several potential anticancer agents (PtCl₂(diaminocyclohexane), trans-[PtCl₂(NH₃)(thiazole)], cis-[PtCl₂(NH₃)(piperidine)], and cis-PtCl₂(NH₃)(cyclohexylamine) complexes) with guanine are explored and compared with an analogous interaction of cisplatin. Basic electronic properties, binding and stabilization energies are determined and energy profiles for the aquation...

article

Interactions of the “piano‐stool” [ruthenium(II)(η⁶‐arene)(quinolone)Cl]⁺ complexes with water; DFT computational study

Tereza Zábojníková, Radim Cajzl, Jakob Kljun, Zdeněk Chval, more

Journal of Computational Chemistry > 37 > 19 > 1766 - 1780

Full optimizations of stationary points along the reaction coordinate for the hydration of several quinolone Ru(II) half‐sandwich complexes were performed in water environment using the B3PW91/6‐31+G(d)/PCM/UAKS method. The role of diffuse functions (especially on oxygen) was found crucial for correct geometries along the reaction coordinate. Single‐point (SP) calculations were performed at the B3LYP/6‐311++G(2df,2pd)/DPCM/saled‐UAKS...

article

Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study

Filip Šebesta, Jaroslav V. Burda

Chemistry – A European Journal > 22 > 3 > 1037 - 1047

The reduction mechanism of [Pt^IV(dach)Cl₄] (dach=diaminocyclohexyl) in the presence of dGMP was studied. The first step is substitution of a chloro ligand by dGMP, followed by nucleophilic attack of a phosphate or sugar oxygen atom to the C8‐position of guanine. Subsequent reduction forms the [Pt^II(dach)Cl₂] complex. The whole process is completed by a hydrolysis. Two different pathways for the substitution...

article

International conference on “Modeling Interaction in Biomolecules VII”, held in Prague, 14–18 September 2015

Jaroslav V. Burda, Andrzej W. Sokalski, Jerzy Leszczynski

Journal of Molecular Modeling > 2016 > 22 > 5 > 1-1

This paper belongs to Topical Collection MIB 2015 (Modeling Interaction in Biomolecules VII)

article

The IR and Raman spectra of polyaniline adsorbed on the glass surface; comparison of experimental, empirical force field, and quantum chemical results

Jonáš Tokarský, Michal Maixner, Pavlína Peikertová, Lenka Kulhánková, more

European Polymer Journal > 2014 > 57 > Complete > 47-57

Vibrational spectra of the oligomeric models of polyaniline (PANI) were explored by quantum chemical and molecular mechanical tools. First, calibration calculations were performed on aniline sample where several computational models were compared with measured IR and Raman spectra. Based on this ‘calibration’, the ωB97XD/6-31G(d,p) level was used for optimization and spectra determination of powder...

article

Reaction mechanism of Ru(II) piano‐stool complexes: Umbrella sampling QM/MM MD study

Zdeněk Futera, Jaroslav V. Burda

Journal of Computational Chemistry > 35 > 19 > 1446 - 1456

Biologically relevant interactions of piano‐stool ruthenium(II) complexes with ds‐DNA are studied in this article by hybrid quantum mechanics—molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases: (i) hydration of the [Ru^II(η⁶‐benzene)(en)Cl]⁺ complex, (ii) monoadduct formation between the resulting aqua‐Ru(II) complex and N7 position of one...

article

The influence of arene-ring size on stacking interaction with canonical base pairs

Martin Formánek, Jaroslav V. Burda

Chemical Physics Letters > 2014 > 598 > Complete > 28-34

Stacking interactions between aromatic molecules (benzene, p-cymene, biphenyl, and di- and tetra-hydrogen anthracene) and G.C and A.T canonical Watson–Crick (WC) base pairs are explored. Two functionals with dispersion corrections: ω-B97XD and B3LYP-D3 are used. For a comparison also the MP2 and B3LYP-D3/PCM methods were used for the most stable p-cymene…WC geometries. It was found that the stacking...

article

Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study

Ondřej Bradáč, Tomáš Zimmermann, Jaroslav V. Burda

Journal of Molecular Modeling > 2013 > 19 > 11 > 4669-4680

Hydration reactions of two anticancer Pt(IV) complexes JM149 and JM216 (Satraplatin) were studied computationally together with the hydration of the Pt(II) complex JM118, which is a product of the Satraplatin reduction. Thermodynamic and kinetic parameters of the reactions were determined at the B3LYP/6-311++G(2df.2pd)//B3LYP/6-31 + G(d)) level of theory. The water solution was modeled using the COSMO...

article

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

Jaroslav V. Burda, Zdeněk Futera, Zdeněk Chval

Journal of Molecular Modeling > 2013 > 19 > 12 > 5245-5255

In the study behavior of molecular electrostatic potential, averaged local ionization energy, and reaction electronic flux along the reaction coordinate of hydration process of three representative Ru(II) and Pt(II) complexes were explored using both post-HF and DFT quantum chemical approximations. Previously determined reaction mechanisms were explored by more detailed insight into changes of electronic...

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Search results for: Jaroslav V. Burda

Quantum mechanical study of transition metal hydrides: Comparison of determined molecular properties with experimental data

The vertical excitation energies and a lifetime of the two lowest singlet excited states of the conjugated polyenes from C2 to C22: Ab initio, DFT, and semiclassical MNDO‐MD simulations

QM and QM/MM umbrella sampling MD study of the formation of Hg(II)–thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH

A Dogma in Doubt: Hydrolysis of Equatorial Ligands of Pt^IV Complexes under Physiological Conditions

Zweifel an einem Dogma: Hydrolyse äquatorialer Liganden von Pt^IV‐Komplexen unter physiologischen Bedingungen

Correction to: Exploration of selected electronic characteristics of half-sandwich organoruthenium(II) β-diketonate complexes

Cover Feature: Interactions of Ascorbic Acid with Satraplatin and its trans Analog JM576: DFT Computational Study (Eur. J. Inorg. Chem. 13/2018)

Interactions of Ascorbic Acid with Satraplatin and its trans Analog JM576: DFT Computational Study

Exploration of selected electronic characteristics of half-sandwich organoruthenium(II) β-diketonate complexes

Formation of chelate structure between His-Met dipeptide and diaqua-cisplatin complex; DFT/PCM computational study

The influence of the metal cations and microhydration on the reaction trajectory of the N3 ↔ O2 thymine proton transfer: Quantum mechanical study

Study on electronic properties, thermodynamic and kinetic parameters of the selected platinum(II) derivatives interacting with guanine

Interactions of the “piano‐stool” [ruthenium(II)(η⁶‐arene)(quinolone)Cl]⁺ complexes with water; DFT computational study

Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study

International conference on “Modeling Interaction in Biomolecules VII”, held in Prague, 14–18 September 2015

The IR and Raman spectra of polyaniline adsorbed on the glass surface; comparison of experimental, empirical force field, and quantum chemical results

Reaction mechanism of Ru(II) piano‐stool complexes: Umbrella sampling QM/MM MD study

The influence of arene-ring size on stacking interaction with canonical base pairs

Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study

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

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