1
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Šebesta F, Sovová Ž, Burda JV. Determination of Amino Acids' p Ka: Importance of Cavity Scaling within Implicit Solvation Models and Choice of DFT Functionals. J Phys Chem B 2024; 128:1627-1637. [PMID: 38345944 PMCID: PMC10895671 DOI: 10.1021/acs.jpcb.3c07007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Protonation states of molecules significantly influence the thermodynamics and kinetics of chemical reactions. This is especially important in biochemical processes, where appropriate protonation states of amino acids control the exo/endoergicity of practically all biochemical cycles. This paper is focused on appraisal of the impact of DFT functionals and PCM solvation models on the accuracy of pKa evaluations for all proteinogenic amino acids. Eight functionals (B3LYP, PBE0, revPBE0, M06-2X, M11, M11-L, TPSSh, and ωB97X-D) and four basis sets are considered, together with four kinds of implicit solvation models when additional attention is paid to a cavity construction. An influence of nonelectrostatic contributions and Wertz's corrections on Gibbs free energy is investigated together with accuracy of provided proton solvation energy. The best model is based on the M06-2X/6-311++G**/D-PCM/UAKS computational level. The fitting procedure is utilized to improve the accuracy of the evaluated models. All of these results are also compared with values obtained from the COSMOtherm program and CCSD(T) calculations. Results for cysteine and histidine are discussed individually, as they can be found in different protonation states at neutral pH.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Žofie Sovová
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics
and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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2
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Fatková K, Cajzl R, Burda JV. 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. J Comput Chem 2023; 44:777-787. [PMID: 36444915 DOI: 10.1002/jcc.27040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 12/03/2022]
Abstract
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. Despite the fact that the first excited state has a significant double-excitation character some functionals were able to qualitatively determine the correct state order (where the lowest excited state has a A g - character). The most successful functionals in transition energies predictions were PBE, TPSS and BLYP in Tamm-Dancoff approach (TDA), which had the smallest root-mean-square deviation (RMSD) scoring towards the experimental values. Regarding RMSD scoring, the OM2/MNDO method performed fairly well, too. Besides absorption spectra, lifetimes of the first two excited states were estimated based on a stochastic approach exploring a swarm of OM2/MNDO hopping dynamics using the Tully fewest switch algorithm for each molecule. The longest lifetime of the first excited state (S1 ) was found for decapentaene (about 5 ps). Further elongation of the conjugated chain caused a mild decrease of this value to ca 1.5 ps for docosaundecaene.
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Affiliation(s)
- Kateřina Fatková
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Radim Cajzl
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
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3
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Zimmermann T, Šebesta F, Burda JV. A new grand-canonical potential for the thermodynamic description of the reactions in solutions with constant pH. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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4
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Šebesta F, Šebera J, Sychrovský V, Tanaka Y, Burda JV. 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. J Comput Chem 2020; 41:1509-1520. [PMID: 32208552 DOI: 10.1002/jcc.26194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 01/01/2023]
Abstract
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(H2 O)6 ]2+ , (2) T + [Hg(H2 O)5 (OH)]+ , (3) T + Hg(H2 O)4 (OH)2 , and (4) N3-deprotonated T + Hg(H2 O)4 (OH)2 . The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4-5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg2+ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Japan
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
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5
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Šebesta F, Burda JV. Interactions of Ascorbic Acid with Satraplatin and its trans
Analog JM576: DFT Computational Study. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201701334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics; Faculty of Mathematics and Physics; Charles University; Ke Karlovu 3 121 16 Prague 2 Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics and Optics; Faculty of Mathematics and Physics; Charles University; Ke Karlovu 3 121 16 Prague 2 Czech Republic
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Formation of chelate structure between His-Met dipeptide and diaqua-cisplatin complex; DFT/PCM computational study. J Biol Inorg Chem 2018; 23:363-376. [DOI: 10.1007/s00775-018-1536-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/23/2018] [Indexed: 02/01/2023]
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Šebesta F, Baxová K, Burda JV. Redox Potentials for Tetraplatin, Satraplatin, Its Derivatives, and Ascorbic Acid: A Computational Study. Inorg Chem 2018; 57:951-962. [DOI: 10.1021/acs.inorgchem.7b01894] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics,
Faculty of Mathematics and Physics, Charles University, Ke Karlovu
3, 121 16 Prague
2, Czech Republic
| | - Katarína Baxová
- Department of Chemical Physics and Optics,
Faculty of Mathematics and Physics, Charles University, Ke Karlovu
3, 121 16 Prague
2, Czech Republic
| | - Jaroslav V. Burda
- Department of Chemical Physics and Optics,
Faculty of Mathematics and Physics, Charles University, Ke Karlovu
3, 121 16 Prague
2, Czech Republic
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8
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Study on electronic properties, thermodynamic and kinetic parameters of the selected platinum(II) derivatives interacting with guanine. J Inorg Biochem 2017; 172:100-109. [DOI: 10.1016/j.jinorgbio.2017.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/06/2017] [Accepted: 04/08/2017] [Indexed: 11/23/2022]
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9
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Šebesta F, Burda JV. Side Reactions with an Equilibrium Constraint: Detailed Mechanism of the Substitution Reaction of Tetraplatin with dGMP as a Starting Step of the Platinum(IV) Reduction Process. J Phys Chem B 2017; 121:4400-4413. [PMID: 28394593 DOI: 10.1021/acs.jpcb.7b01427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two possible pathways of the substitution reaction within the reduction process of the PtIV(DACH)Cl4 by dGMP are compared: associative reaction course and autocatalytic Basolo-Pearson mechanisms. Since two forms: single-protonated and fully deprotonated phosphate group of dGMP are present in equilibrium at neutral and mildly acidic solutions, consideration of a side reactions scheme with acido-basic equilibrium-constraint is a very important model for obtaining reliable results. The examined complexes are optimized at the B3LYP-GD3BJ/6-31G(d) level with the COSMO implicit solvation model and Klamt's radii used for cavity construction. Energy characteristics and thermodynamics for all reaction branches are determined using the B3LYP-GD3BJ/6-311++G(2df,2pd)/IEF-PCM/scaled-UAKS level with Wertz's entropy corrections. Rate constants are estimated for each individual branch according to Eyring's transition state theory (TST), averaged according to equilibrium constraint and compared with available experimental data. The determined reaction barriers of the autocatalytic pathway fairly correspond with experimental values. Furthermore, autocatalytic reaction of tetraplatin and its two analogues complexes [PtIV(en)Cl4 and PtIV(NH3)2Cl4] are explored and compared with measured data in order to examined general reaction descriptors.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University , Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University , Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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Paciotti R, Corinti D, De Petris A, Ciavardini A, Piccirillo S, Coletti C, Re N, Maitre P, Bellina B, Barran P, Chiavarino B, Elisa Crestoni M, Fornarini S. Cisplatin and transplatin interaction with methionine: bonding motifs assayed by vibrational spectroscopy in the isolated ionic complexes. Phys Chem Chem Phys 2017; 19:26697-26707. [DOI: 10.1039/c7cp05203k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
IRMPD spectroscopy discloses N- versus S-platination.
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11
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Chattopadhyaya M, Murugan NA, Rinkevicius Z. Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study. J Phys Chem A 2016; 120:7175-82. [DOI: 10.1021/acs.jpca.6b07660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- M. Chattopadhyaya
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - N. Arul Murugan
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Zilvinas Rinkevicius
- Division of Theoretical Chemistry & Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Swedish
e-Science Research Center (SeRC), KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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12
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Zábojníková T, Cajzl R, Kljun J, Chval Z, Turel I, Burda JV. Interactions of the "piano-stool" [ruthenium(II)(η(6) -arene)(quinolone)Cl](+) complexes with water; DFT computational study. J Comput Chem 2016; 37:1766-80. [PMID: 27185047 DOI: 10.1002/jcc.24373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 12/12/2022]
Abstract
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 level. In the first part, two possible reaction mechanisms-associative and dissociative were compared. It was found that the dissociative mechanism of the hydration process is kinetically slightly preferred. Another important conclusion concerns the reaction channels. It was found that substitution of chloride ligand (abbreviated in the text as dechlorination reaction) represents energetically and kinetically the most feasible pathway. In the second part the same hydration reaction was explored for reactivity comparison of the Ru(II)-complexes with several derivatives of nalidixic acid: cinoxacin, ofloxacin, and (thio)nalidixic acid. The hydration process is about four orders of magnitude faster in a basic solution compared to neutral/acidic environment with cinoxacin and nalidixic acid as the most reactive complexes in the former and latter environments, respectively. The explored hydration reaction is in all cases endergonic; nevertheless the endergonicity is substantially lower (by ∼6 kcal/mol) in basic environment. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tereza Zábojníková
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Radim Cajzl
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
| | - Jakob Kljun
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - Zdeněk Chval
- Department of Laboratory Methods and Information Systems, Faculty of Health and Social Studies, University of South Bohemia, J. Boreckého 27, České Budějovice, 370 11, Czech Republic
| | - Iztok Turel
- Faculty of Chemistry and Chemical Technologyn University of Ljubljana, Večna pot 113, Ljubljana, 1000, Slovenia
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, 121 16, Czech Republic
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13
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Šebesta F, Burda JV. Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study. Chemistry 2015; 22:1037-47. [PMID: 26663432 DOI: 10.1002/chem.201503555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/15/2015] [Indexed: 01/01/2023]
Abstract
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 reaction were examined: a direct associative and a Basolo-Pearson autocatalytic mechanism. All the explored structures were optimized at the B3LYP-D3/6-31G(d) level and by using the COSMO solvation model with Klamt's radii. Single-point energetics was determined at the B3LYP-GD3BJ/6-311++G(2df,2pd)/PCM/scaled-UAKS level. Activation barriers were used for an estimation of the rate constants and these were compared with experimental values. It was found that the rate-determining step is the nucleophilic attack with a slightly faster performance in the 3'-dGMP branch than in the case of 5'-dGMP with activation barriers of 21.1 and 20.4 kcal mol(-1) (experimental: 23.8 and 23.2 kcal mol(-1) ). The reduction reaction is connected with an electron flow from guanine. The product of the reduction reaction is a chelate structure, which dissociates within the last reaction step, that is, a hydrolysis reaction. The whole redox process (substitution, reduction, and hydrolysis) is exergonic by 34 and 28 kcal mol(-1) for 5'-dGMP and 3'-dGMP, respectively.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.
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Haloui A, Haloui E. Proton affinity of para-substituted acetophenones in gas phase and in solution: a theoretical study. J Mol Model 2012; 19:631-46. [PMID: 22996912 DOI: 10.1007/s00894-012-1585-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
Abstract
The gas phase proton affinities PA and basicities GB for a series of para-substituted acetophenones weak bases (B) p.X-C(6)H(4)CO*CH(3) with X=H, F, Cl, Br, I, Me, CF(3), CN, NO(2), OCH(3), NH(2), CH(2)OH, N(CH(3))(2), OH, [Formula: see text], … have been calculated at 298.15 K at the density functional theory DFT/B3LYP level with a 6-311++G (2d,2p) basis set. Conformational results lead to only one stable planar conformer for both unprotonated compounds and their O*-protonated forms. Satisfactory accuracy and computational efficiency could be reached if the computed PAs are scaled by a factor 0.983. Protonation at more than one site is discussed and the carbonyl oxygen atom is found to be the preferential protonated site rather than the substituent X. The calculated gas phase PAs show a good agreement with the experimental available data. The electron-donating/electron-withdrawing nature of the substituents has an enormous influence upon the thermochemical and structural properties. The influence of environment on the proton affinity has been studied by means of SCRF solvent effect computations using PCM solvation model for two solvents: water and SO(2)CI(2). Confrontation between computed and experimental pK(B) values exhibits better agreement in aqueous solution than in organic solvent.
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Affiliation(s)
- Abir Haloui
- Department of Chemistry, Faculty of Sciences, Manar 2, 2092, Tunis, Tunisia.
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15
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Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study. J Mol Model 2012; 19:4669-80. [DOI: 10.1007/s00894-012-1442-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 04/18/2012] [Indexed: 11/26/2022]
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16
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Michera L, Nekadová M, Burda JV. Reactions of cisplatin and glycine in solution with constant pH: a computational study. Phys Chem Chem Phys 2012; 14:12571-9. [DOI: 10.1039/c2cp41016h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Kizek R, Adam V, Hrabeta J, Eckschlager T, Smutny S, Burda JV, Frei E, Stiborova M. Anthracyclines and ellipticines as DNA-damaging anticancer drugs: Recent advances. Pharmacol Ther 2012; 133:26-39. [DOI: 10.1016/j.pharmthera.2011.07.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 07/22/2011] [Indexed: 12/21/2022]
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18
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Activation of the cisplatin and transplatin complexes in solution with constant pH and concentration of chloride anions; quantum chemical study. J Mol Model 2011; 17:2385-93. [DOI: 10.1007/s00894-011-1031-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/06/2011] [Indexed: 10/18/2022]
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19
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Chval Z, Futera Z, Burda JV. Comparison of hydration reactions for “piano-stool” RAPTA-B and [Ru(η6− arene)(en)Cl]+ complexes: Density functional theory computational study. J Chem Phys 2011; 134:024520. [DOI: 10.1063/1.3515534] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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20
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Truflandier LA, Sutter K, Autschbach J. Solvent Effects and Dynamic Averaging of 195Pt NMR Shielding in Cisplatin Derivatives. Inorg Chem 2011; 50:1723-32. [DOI: 10.1021/ic102174b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Kiplangat Sutter
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
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Zhang D, Ren X, Zhou L. Theoretical analysis of trans-[PtCl2(NH3)(thiazole)] and trans-[PtCl2(thiazole)2] binding to biological targets — Factors influence binding kinetics and adduct stability. CAN J CHEM 2010. [DOI: 10.1139/v10-139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Full reaction energy profiles for trans-[PtCl2(NH3)(thiazole)] and trans-[PtCl2(thiazole)2] binding to sulfur- and nitrogen-containing biorelevant ligands were constructed by the density functional theory (DFT) method. Calculated results demonstrate that trans-platinum complexes can interact with biological targets, affording cis and trans products via very similar transition states. For different substituents, sulfur-containing ligands constitute kinetically preferred targets for platination, whereas the platination of nitrogen-containing ligands is more favorable thermodynamically. This is consistent with previous experimental studies. Calculated results also suggest that the trans effect, the influence of the ligand, the size of the ligand, and hydrogen bonding play important roles in binding kinetics and stabilizing adducts.
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Affiliation(s)
- Dongdong Zhang
- Department of Chemistry, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Xiuli Ren
- Department of Chemistry, Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Lixin Zhou
- Department of Chemistry, Jinan University, Guangzhou, Guangdong 510632, P.R. China
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Zimmermann T, Burda JV. Cisplatin interaction with amino acids cysteine and methionine from gas phase to solutions with constant pH. Interdiscip Sci 2010; 2:98-114. [PMID: 20640800 DOI: 10.1007/s12539-010-0094-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 10/19/2022]
Abstract
This work is focused on the computational studies of reactions of hydrated forms of cisplatin with sulphur-containing amino acids cysteine and methionine. First, the appropriate model for solvation of the examined complexes was searched for. The suggested procedure employs the B3LYP density functional, 6-311++G(2df,2pd) basis set with Stuttgart-Dresden pseudopotentials on heavy atoms, the D-PCM solvation model and the UAKS cavity which uses more realistic NPA partial charges instead of formal partial charges for platinum ligands. In the second part this model is applied to the evaluation of the Legendre transformed reaction Gibbs free energy of cisplatin with cysteine and methionine in solution at constant pH.
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Affiliation(s)
- Tomás Zimmermann
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, Prague 2, Czech Republic
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23
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Zimmermann T, Burda JV. Reactions of cisplatin with cysteine and methionine at constant pH; a computational study. Dalton Trans 2010; 39:1295-301. [DOI: 10.1039/b913803j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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