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Simin Aghmasheh, Anita Abedi. A DFT Investigation on Two Proposed Anticancer Platinum(IV) Drugs. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420070031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chipman A, Gouranourimi A, Farshadfar K, Olding A, Yates BF, Ariafard A. A Computational Mechanistic Investigation into Reduction of Gold(III) Complexes by Amino Acid Glycine: A New Variant for Amine Oxidation. Chemistry 2018; 24:8361-8368. [PMID: 29655208 DOI: 10.1002/chem.201800403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/02/2018] [Indexed: 01/10/2023]
Abstract
Density functional theory (DFT) was utilized to explore the reduction of gold(III) complexes by the amino acid glycine (Gly). Interestingly, when the nitrogen atom of Gly coordinates to the gold(III) center, its Cα -hydrogen atom becomes so acidic that it can be easily deprotonated by a mild base like water. The deprotonation converts the amino acid into a potent reductant by which gold(III) is reduced to gold(I) with a moderate activation energy. To our knowledge, this is the first contribution suggesting that primary amines are oxidized to imines via direct α-carbon deprotonation. This finding may provide new insights into the mechanistic interpretation of amine oxidations catalyzed/mediated by a center with high cathodic reduction potential. This work also provides a rationalization behind why gold(III) complexes with amine-based polydentate ligands are reluctant to undergo a redox process. Gold(III) reduction occurs most efficiently if the Cα proton leaves in the plane of the Cα , N and Au atoms. Chelation prevents this alignment, resulting in the gold(III) complex being unreactive toward reduction. It has been experimentally found that gold(III) is capable of oxidizing Gly to glyoxylic acid (GA) as the initial product. The latter, in the presence of another gold(III) complex, has been reported to undergo oxidative decarboxylation to afford CO2 and HCOOH. This process is found to be mediated by formation of a geminal diol intermediate produced by reaction of water with the aldehyde functional group of the coordinated GA.
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Affiliation(s)
- Antony Chipman
- School of Physical Sciences (Chemistry), University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia
| | - Ali Gouranourimi
- School of Physical Sciences (Chemistry), University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia
| | - Kaveh Farshadfar
- Department of Chemistry, Islamic Azad University, Central Tehran Branch, Shohrak Gharb, Tehran, Iran
| | - Angus Olding
- School of Physical Sciences (Chemistry), University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia
| | - Brian F Yates
- School of Physical Sciences (Chemistry), University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia
| | - Alireza Ariafard
- School of Physical Sciences (Chemistry), University of Tasmania, Private Bag 75, Hobart, TAS, 7001, Australia.,Department of Chemistry, Islamic Azad University, Central Tehran Branch, Shohrak Gharb, Tehran, Iran
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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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Wu RR, He CC, Hamlow LA, Nei YW, Berden G, Oomens J, Rodgers MT. Protonation induces base rotation of purine nucleotides pdGuo and pGuo. Phys Chem Chem Phys 2018; 18:15081-90. [PMID: 27197049 DOI: 10.1039/c6cp01354f] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of 2'-deoxyguanosine-5'-monophosphate and guanosine-5'-monophosphate, [pdGuo+H](+) and [pGuo+H](+), are measured over the IR fingerprint and hydrogen-stretching regions using the FELIX free electron laser and an OPO/OPA laser system. Electronic structure calculations are performed to generate low-energy conformations of [pdGuo+H](+) and [pGuo+H](+) and determine their relative stabilities at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) and MP2(full)/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) levels of theory. Comparative analyses of the measured IRMPD action spectra and B3LYP/6-311+G(d,p) linear IR spectra computed for the low-energy conformers are performed to determine the most favorable site of protonation and the conformers present in the experiments. These comparisons and the computed energetics find that N7 protonation is considerably preferred over O6 and N3, and the N7 protonated ground-state conformers of [pdGuo+H](+) and [pGuo+H](+) are populated in the experiments. The 2'-hydroxyl substituent does not significantly impact the stable low-energy conformers of [pdGuo+H](+)vs. those of [pGuo+H](+). The effect of the 2'-hydroxyl substituent is primarily reflected in the relative intensities of the measured IRMPD bands, as the IRMPD profiles of [pdGuo+H](+) and [pGuo+H](+) are quite similar. Comparisons to previous IRMPD spectroscopy investigations of the protonated forms of the guanine nucleosides, [dGuo+H](+) and [Guo+H](+), and deprotonated forms of the guanine nucleotides, [pdGuo-H](-) and [pGuo-H](-), provide insight into the effects of the phosphate moiety and protonation on the conformational features of the nucleobase and sugar moieties. Protonation is found to induce base rotation of the guanine residue to an anti orientation vs. the syn orientation found for the deprotonated forms of the guanine nucleotides.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - C C He
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - L A Hamlow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Y-W Nei
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - G Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands
| | - J Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7c, 6525 ED, Nijmegen, The Netherlands and van't Hoff Institute for Molecular Sciences, University of Amsterdam, 1090 GD, Amsterdam, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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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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Ejehi Z, Ariafard A. A computational mechanistic investigation into the reduction of Pt(iv) prodrugs with two axial chlorides by biological reductants. Chem Commun (Camb) 2017; 53:1413-1416. [DOI: 10.1039/c6cc07834f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reduction of the Pt(iv) prodrugs with two axial chlorido ligands by biological reductants does not always proceed via the chloride-bridge inner-sphere mechanism.
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Affiliation(s)
- Zeinab Ejehi
- Department of Chemistry
- Islamic Azad University
- Central Tehran Branch
- Shahrak Gharb
- Iran
| | - Alireza Ariafard
- Department of Chemistry
- Islamic Azad University
- Central Tehran Branch
- Shahrak Gharb
- Iran
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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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Oxidation of 5'-dGMP, 5'-dGDP, and 5'-dGTP by a platinum(IV) complex. J Biol Inorg Chem 2015; 20:1327-41. [PMID: 26588933 DOI: 10.1007/s00775-015-1312-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 11/02/2015] [Indexed: 10/22/2022]
Abstract
We previously reported that a Pt(IV) complex, [Pt(IV)(dach)Cl4] [trans-d,l-1,2-diaminocyclohexanetetrachloroplatinum(IV)] binds to the N7 of 5'-dGMP (deoxyguanosine-5'-monophosphate) at a relatively fast rate and oxidizes it to 8-oxo-5'-dGMP. Here, we further studied the kinetics of the oxidation of 5'-dGMP by the Pt(IV) complex. The electron transfer rate constants between 5'-dGMP and Pt(IV) in [H8-5'-dGMP-Pt(IV)] and [D8-5'-dGMP-Pt(IV)] were similar, giving a small value of the kinetic isotope effect (KIE: 1.2 ± 0.2). This small KIE indicates that the deprotonation of H8 in [H8-5'-dGMP-Pt(IV)] is not involved in the rate-determining step in the electron transfer between guanine (G) and Pt(IV). We also studied the reaction of 5'-dGDP (deoxyguanosine-5'-diphosphate) and 5'-dGTP (deoxyguanosine-5'-triphosphate) with the Pt(IV) complex. Our results showed that [Pt(IV)(dach)Cl4] oxidized 5'-dGDP and 5'-dGTP to 8-oxo-5'-dGDP and 8-oxo-5'-dGTP, respectively, by the same mechanism and kinetics as for 5'-dGMP. The Pt(IV) complex binds to N7 followed by a two-electron inner sphere electron transfer from G to Pt(IV). The reaction was catalyzed by Pt(II) and occurred faster at higher pH. The electron transfer was initiated by either an intramolecular nucleophilic attack by any of the phosphate groups or an intermolecular nucleophilic attack by free OH(-) in the solution. The rates of reactions for the three nucleotides followed the order: 5'-dGMP > 5'-dGDP > 5'-dGTP, indicating that the bulkier the phosphate groups are, the slower the reaction is, due to the larger steric hindrance and rotational barrier of the phosphate groups.
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Ariafard A. A Density Functional Theory (DFT) Mechanistic Study of Gold(I)-Catalyzed Alkynylation of the Indole and Pyrrole Substrates, Using a Hypervalent Iodine Reagent. ACS Catal 2014. [DOI: 10.1021/cs500613t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alireza Ariafard
- Department of Chemistry,
Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran, Iran
- School of Chemistry, University of Tasmania, Private Bag 75, Hobart TAS 7001, Australia
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Ariafard A, Ghohe NM, Abbasi KK, Canty AJ, Yates BF. Theoretical investigation into the mechanism of 3'-dGMP oxidation by [Pt(IV)Cl4(dach)]. Inorg Chem 2012; 52:707-17. [PMID: 23270414 DOI: 10.1021/ic3018425] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism for the oxidation of 3'-dGMP by [PtCl(4)(dach)] (dach = diaminocyclohexane) in the presence of [PtCl(2)(dach)] has been investigated using density functional theory. We find that the initial complexation, i.e., the formation of [PtCl(3)(dach)(3'-dGMP)], is greatly assisted by the reaction of the encounter pair [PtCl(2)(dach)···3'-dGMP] with [PtCl(4)(dach)], leading to migration of an axial chlorine ligand from platinum(IV) to platinum(II). A dinuclear platinum(II)/platinum(IV) intermediate could not be found, but the reaction is predicted to pass through a platinum(III)/platinum(III) transition structure. A cyclization process, i.e., C8-O bond formation, from [PtCl(3)(dach)(3'-dGMP)] occurs through an intriguing phosphate-water-assisted deprotonation reaction, analogous to the opposite of a proton shuttle mechanism. Followed by this, the guanine moiety is oxidized via dissociation of the Pt(IV)-Cl(ax) bond, and the cyclic ether product is finally formed after deprotonation. We have provided rationalizations, including molecular orbital explanations, for the key steps in the process. Our results help to explain the effect of [PtCl(4)(dach)] on the complexation step and the effect of a strong hydroxide base on the cyclization reaction. The overall reaction cycle is intricate and involves autocatalysis by a platinum(II) species.
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Affiliation(s)
- Alireza Ariafard
- Department of Chemistry, Faculty of Science, Central Tehran Branch, Islamic Azad University, Shahrak Gharb, Tehran, Iran.
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