Co-reporter:Yanhua He, Lixin Zhou
Computational and Theoretical Chemistry 2016 Volume 1093() pp:20-28
Publication Date(Web):1 October 2016
DOI:10.1016/j.comptc.2016.08.008
•Explore AuCl3(Hpm) and AuCl2(pm) substitution reactions’ mechanisms.•Compare B3LYP and M06 methods on calculation results.•Compare gas phase/aqueous solution optimizations on calculation results.The mechanisms of gold (III) based complexes, AuCl3 (Hpm) and AuCl2 (pm), binding to cysteine (S/O), guanine and adenine (N7) were investigated by means of B3LYP and M06 functionals in density functional theory (DFT). The qualitative results obtained by the B3LYP and M06 functionals were generally similar, which suggested that hydrogen bonding interactions and proton transfers help to stabilize the configurations and reduce activation energies. Guanine showed stronger reactivity with gold (III) complexes compared with both adenine and cysteine (Cys). And reaction energies related to free amino acids were sensitive to chemical states (neutral molecules or zwitterions) and depended upon optimized environments. On the contrary, in aqueous solution reactions, Cys (O) exhibited better kinetic selectivity than Cys (S), while purine bases were unaffected by solvent and were practically independent on the substrate types.
Co-reporter:Ziping Huang, Lixin Zhou
Computational and Theoretical Chemistry 2016 Volume 1094() pp:47-54
Publication Date(Web):15 October 2016
DOI:10.1016/j.comptc.2016.09.003
•Explore trans-[Pt(P)NH3Cl2] (P = 3-pic or py) interacting with electrons reactions’ mechanisms.•Explore trans-[Pt(P)NH3Cl]trans-[Pt(P)NH3Cl] interacting with ribose or thymine(T) reactions’ mechanisms.•Compare purine bases and DNA skeleton which are easy to be attacked from radical free.•Compare B3LYP and M06 methods on calculation results.The interaction of cisplatin and low-energy electrons (LEEs) can excellently enhance the yield of DNA strand breaks, which is identified by experiments, as recently highlighted. Meanwhile, the mechanism of this action has been researched by density functional theory (DFT). The calculation found that the mechanism of the interaction between cisplatin and electrons is different from that of the hydrolysis of cisplatin. This discovery will certainly be expected to reduce the side effects of cisplatin importantly. However, the mechanism of the attachments and the dissociative electron transfer reactions of trans-[Pt(P)NH3Cl2] (P = 3-picoline or pyridine) with electrons currently is not clear yet. Thus, by using M06 and B3LYP functionals, we can obtain conclusion that one-electron attacks to trans-[Pt(P)NH3Cl2] and generates a Cl ions and T- shaped trans-[Pt(P)NH3Cl]trans-[Pt(P)NH3Cl] neutral radical, and then the combination of trans-[Pt(P)NH3Cl]trans-[Pt(P)NH3Cl] with the second electron can form a linear type trans-[Pt(P)NH3]trans-[Pt(P)NH3] radical. Our calculations found that trans-[Pt(P)NH3Cl]trans-[Pt(P)NH3Cl] binds with purines and will be lost high affinity but it might capture hydrogen from ribose (H4′/H5′/C3′O) or a hydrogen of methyl groups (CH3H′)on thymine(T) to improve the yield of DNA strand breaks. In summary, the results may have significance that the H4′ site on ribose or CH3H′ site on T might be the most dominant target from the trans-[Pt(P)NH3Cl]trans-[Pt(P)NH3Cl].
Co-reporter:Lixin Zhou
Inorganica Chimica Acta 2011 Volume 376(Issue 1) pp:44-56
Publication Date(Web):1 October 2011
DOI:10.1016/j.ica.2011.05.034
The monofunctional and bifunctional bindings of the potential anticancer drug trans-isopropylaminedimethylaminedichloroplatinum (trans-IPADMADP) and its cis isomer to purine base in DNA are explored by using density functional theory and IEF-PCM solvation models. The computed lowest free energy barrier in the aqueous solution is 14.0/11.6 kcal/mol (from trans-Pt-chloroaqua complex to trans-/cis-monoadduct) for guanine(G), and 11.7/13.3 kcal/mol (from trans-Pt-chloroaqua complex to trans-/cis-monoadduct) for adenine(A). Our calculations demonstrate that the trans reactant complexes (or isolated reactants) can generate trans- or cis-monoadducts via similar trigonal bipyramidal transition state structures, suggesting that the monoadducts can subsequently close to form the bifunctional intrastrand Pt–DNA adducts and simultaneously distort DNA in the similar way as cisplatin. Our calculations show that Pt(isopropylamine)(dimethylamine)G22+ head-to-head path has the lowest free energy of activation at 17.6 kcal/mol, closely followed by the Pt(isopropylamine)(dimethylamine)GA2+ head-to-head path at 19.6 kcal/mol when the monofunctional cis-Pt-G complex serves as the reactant; while the Pt(isopropylamine)(dimethylamine)G22+ head-to-tail adduct has the lowest barrier of 20.5 kcal/mol, closely followed by the Pt(isopropylamine)(dimethylamine)GA2+ head-to-tail adduct at 23.0 kcal/mol if the monofunctional trans-Pt-G complex is the reactant.The calculated relatively lower activation energy barrier than that of cisplatin theoretically confirm that trans-[PtCl2(isopropylamine)(dimethylamine)] is a potential anticancer drug as described by experiment.Graphical abstractReaction mechanisms: The trans reactant complexes (or isolated reactants) can generate trans- or cis-monoadducts via similar trigonal bipyramidal transition state structures, suggesting that the monoadducts can subsequently close to form the bifunctional intrastrand Pt–DNA adducts and simultaneously distort DNA in the same way as cisplatin.Highlights► The DNA binding modes of a novel trans platinum anticancer drug with two aliphatic amines. ► The trans reactant complexes (or isolated reactants) can generate trans/cis-monoadducts. ► Reaction barriers of the trans platinum anticancer agent are compared with that of cisplatin.
Co-reporter:Bo Jiang
Structural Chemistry 2011 Volume 22( Issue 6) pp:
Publication Date(Web):2011 December
DOI:10.1007/s11224-011-9833-9
The reaction mechanism of the binding of the completely hydrolyzed trans-[Pd(dmnp)2Cl2] (dmnp = 2,6-dimethyl-4-nitropyridine) complexes to DNA and peptides was investigated computationally using model molecules and density functional theory calculations at the B3LYP level. To test the solvent effect, single-point energy calculations for the structures optimized in all reactions were conducted by employing the polarizable continuum model (IEF-PCM). The pentammineruthenium fragment had been intensively studied and also constituted a good model for antitumor trans-[Pd(dmnp)2Cl2], while the considered bases/ligands had been chosen as models for the main binding sites of DNA, nucleobases, and phosphate backbone and proteins, nitrogen-containing histidyl, and sulfur-containing residue such as methionine or cysteine. The activation free energies had been calculated for all the considered metal binding sites both in the gas phase and in solution and allowed building a binding affinity order for the considered nucleic acid or protein binding sites. Additionally, to better understand the interactions between the compounds and binding sites, the natural orbital population analysis (NPA) was adopted for every stationary point to employ the mutative trend of the net charge on the three important atoms which directly related to the reactions.
Co-reporter:Chunqiang Deng, Lixin Zhou
Inorganica Chimica Acta 2011 370(1) pp: 70-75
Publication Date(Web):
DOI:10.1016/j.ica.2011.01.033
Co-reporter:Yanfang Wu, Lixin Zhou
Inorganica Chimica Acta 2010 Volume 363(Issue 13) pp:3274-3281
Publication Date(Web):25 October 2010
DOI:10.1016/j.ica.2010.06.012
The hydrolyzed α-[Ru(azpy)2Cl2] (azpy is 2-(phenylazo)pyridine; α indicates that the isomer in which the coordinating pairs Cl, N(py), and N(azo) are cis, trans, and cis, respectively) binding to guanine (G), adenine (A), methionine (Met), and histidine (His) residues were investigated by using density functional theory. Reactant complexes (RC), product complexes (PC), and transition states (TS) involved were fully characterized. The calculated energy profiles showed that the activation free energies for the substitutions of hydrolyzed α-[Ru(azpy)2Cl2] with Met was apparently lower than those of guanine and adenine. This indicate that the hydrolyzed α-[Ru(azpy)2Cl2] compounds may preferentially bind to the sulfur-containing amino acids residues in vivo. Moreover, the natural orbital population analysis (NPA) showed that the Ru atom gained the greatest negative charges in the reactions of hydrolyzed α-[Ru(azpy)2Cl2] with Met, which may contribute to their remarkably low activation free energies partially.The binding mechanism of the Ru-based antitumor complex α-[Ru(azpy)2Cl2] with DNA purine bases and amino acid residues has been investigated theoretically both in the gas and in aqueous solution. The calculation results indicated that the amino acid residues may be the preferential binding sites compared to DNA purine bases in the binding reactions with hydrolyzed α-[Ru(azpy)2Cl2] complexes in vivo.
Co-reporter:Chunqiang Deng
Structural Chemistry 2010 Volume 21( Issue 4) pp:735-744
Publication Date(Web):2010 August
DOI:10.1007/s11224-010-9603-0
The complexes [Ti(η5-C2H4{CMe2CH2CH2CH=CH2})2Cl2] (1) and [Ti{Me2Si(η5-C5Me4)(η5-C5H3{CMe2CH2CH2CH=CH2})}Cl2] (2) exhibited significant antitumor activity, but the detailed mechanism of antitumor effect remains unknown. In current research, we studied the hydrated 1 and 2 bindings to potential biological targets, purine bases, and phosphate group, using density functional theory and IEF-PCM solvation models. Our calculations reveal that the monoaquated complex binding to guanine shows the lowest activation free-energy with 15.3 and 21.5 kcal/mol for the complexes 1 and 2, respectively. In the diaquaed 1, the lowest activation-free energy is 16.7 kcal/mol for the guanine and closely followed by the phosphate group is 18.3 kcal/mol, while the lowest activation-free energy is 16.9 kcal/mol for the complex 2 binding to the phosphate group. In addition, natural orbital population analysis (NPA) method was performed for the investigation of major electronic characteristics.
Co-reporter:Xiang Chen, Lixin Zhou
Journal of Molecular Structure: THEOCHEM 2010 Volume 940(1–3) pp:45-49
Publication Date(Web):30 January 2010
DOI:10.1016/j.theochem.2009.10.007
This work reports an investigation of the hydrolysis of anticancer drug titanocene dichloride with the combined density functional theory and continuum dielectric model approach. The hydrolysis of titanocene dichloride includes three typical reactions, i.e., the first, second and third hydrolysis processes, which has been believed a key step before the titanocene complexes interaction with the target biomolecules. The detail knowledge of mechanism of the hydrolysis for titanocene dichloride is a prerequisite for clinical tests and for a successful application for permission as medication. With the analysis of thermodynamics and kinetics, the conclusions predict the activation energies (14–19 kcal/mol) and reaction free energies (0–13 kcal/mol) in aqueous solution for the three hydrolysis reactions, the predicted activation energy and reaction free energy for the second hydrolysis agree well with the available experimental data (the first hydrolysis is too rapid to measure with the experimental methods and the experimental values of thermodynamics and kinetics of the third hydrolysis reaction have not yet been occurred). We also discuss the variations of structural parameters of the three reactions in detail below. The results could contribute to the identification of the active compounds (titanocene dichloride or titanocene analogous) that interact with biological targets.
Co-reporter:Yan Gao
Theoretical Chemistry Accounts 2009 Volume 123( Issue 5-6) pp:455-468
Publication Date(Web):2009 August
DOI:10.1007/s00214-009-0557-5
The coordination of an activated novel anticancer drug, trans-[PtCl2(ipa)(3-pico)] (ipa = isopropylamine, 3-pico = 3-methylpyridine), to DNA in a two-step process has been studied using a combination of DFT theory and IEF–PCM approach. The computed free energy barrier for the first substitution is 16.9/16.9 kcal/mol for trans-Pt-chloroaqua → trans-/cis-Pt–guanine monoadduct, 18.7/18.7 kcal/mol for trans-Pt-chloroaqua → trans-/cis-Pt–adenine monoadduct. Barriers of 20.2/20.2 kcal/mol are evaluated for trans-Pt-diaqua → trans-/cis-Pt–guanine monoadduct, 26.0/26.0 kcal/mol for trans-Pt-diaqua → trans-/cis-Pt–adenine monoadduct. In the second substitution starting from trans-Pt–guanine monoadduct to trans-diadducts, the reaction barrier for (G–Pt–G) head-to-head formation is 22.2 kcal/mol, while 22.0 kcal/mol is evaluated for the head-to-tail configuration. Barriers for (A–Pt–G) head-to-head and head-to-tail formation are 25.7/28.9 kcal/mol, respectively. The observed preference for guanine is explained in terms of remarkable larger complexation energy for the initial reactant complex as well as the lower barrier height for the substitutions. In the competition reactions, cysteine residue stabilizes the transition state (ΔGaq/ZPE = 13.1 kcal/mol) for platination more efficiently than purine bases and other protein residues.
Co-reporter:Lixin Zhou
The Journal of Physical Chemistry B 2009 Volume 113(Issue 7) pp:2110-2127
Publication Date(Web):January 27, 2009
DOI:10.1021/jp806661g
The first and second substitution reactions between hydrolyzed trans/cis-[PtCl2(isopropylamine)2], trans/cis-[Pt(isopropylamine)2Cl(H2O)]+, and trans/cis- [Pt(isopropylamine)2(H2O)2]2+ and purine bases guanine and adenine are explored using the B3LYP hybrid functional and IEF-PCM solvation models. For the first substitution, the calculated lowest free energy barrier is 11.4/12.2kcal/mol (from trans-Pt−chloroaqua complex to trans/cis-monoadduct) for guanine, and 14.2/14.2kcal/mol (from trans-Pt−chloroaqua complex to trans/cis-monoadduct) for adenine. The computed lowest free energy barrier of monoaquated complexes is always lower than that of diaquated complexes in the first substitution. Our calculations for the first substitution demonstrate, for the first time, that the trans reactant complexes (or isolated reactants) can generate trans- or cis-monoadducts via identical or very similar trigonal-bipyramidal transition-state structures, suggesting that the monoadducts can subsequently close to form the bifunctional intrastrand Pt−DNA adducts and simultaneously distort DNA in the same way as cisplatin. Our calculations confirm that the transplatin analogue leads to conformational alterations in double-helical DNA similar to those induced by cisplatin. In other words, it is likely that the transplatin analogue has the same mechanism of action as cisplatin binding to DNA targets. For the second substitution, the Pt(isopropylamine)2GA2+ head-to-tail path has the lowest free energy of activation at 17.2 kcal/mol, closely followed by the Pt(isopropylamine)2GG2+ head-to-tail path at 23.7 kcal/mol when the monofunctional cis-Pt−G complex serves as the reactant, while the Pt(isopropylamine)2GA2+ head-to-head adduct has the lowest barrier of 13.3kcal/mol, closely followed by the Pt(isopropylamine)2GG2+ head-to-head adduct at 17.6 kcal/mol if the monofunctional trans-Pt−G complex is the reactant. The theoretically determined activation energy is lower than that of cisplatin, which confirms that trans-[PtCl2(isopropylamine)2] is a potential anticancer drug as suggested by experiment. The structural analysis for reactant complexes, product complexes, and transition states shows that hydrogen bonds play an important role in stabilizing these species for the first and second substitution.
Co-reporter:Qing-Hui YUAN;Li-Xin ZHOU
Chinese Journal of Chemistry 2007 Volume 25(Issue 11) pp:1604-1611
Publication Date(Web):13 NOV 2007
DOI:10.1002/cjoc.200790297
In the present work, the hydrolysis process of non-classical transplatin(II) with two same planar heterocycle amines has been studied using hybrid density functional theory (B3LYP) and IEF-PCM solvation models. Optimizations were performed at the B3LYP level using a combined basis set of (LanL2DZ+6-31+G(d,p)) with single-point energy evaluations using the B3LYP/6-31++G(3df,2pd) approach in vacuo and in aqueous solution. For the obtained structures of reactants, intermediates, transition states, and products, both thermodynamic (reaction energies and Gibbs energies) and kinetic (reaction barriers) characteristics were estimated. In comparison with cisplatin, decreased activation energies were obtained. The result implies that the non-classical transplatin with two same planar heterocycle amines increases the equatorial steric effect and lowers reaction barriers, which may assist in designing novel Pt-based anticancer drugs.
Co-reporter:Guan-Ru Chang;Li-Xin Zhou;Dong Chen
Chinese Journal of Chemistry 2006 Volume 24(Issue 11) pp:
Publication Date(Web):3 NOV 2006
DOI:10.1002/cjoc.200690286
A systematic quantum chemical characterization of intrinsic structure, energies and spectral properties of all the studied cross-link adducts formed by the novel trans platinum with thiazole ligand has been carried out at B3LYP/6-31G* level of theory with the Lanl2dz pseudo potential basis set for the Pt atom. Special attention has been paid to the relative stability of these complexes and the factors that probably alter the order of the relative stability. The important influence of hydrogen bond on the structures, the energies and the spectral property was revealed. Other factors that contribute to relative stability including solvation effect, entropy and electronic delocalization energy were taken into account. The stability energy of the whole complex, and the interaction energy between two purine bases and the [Pt-(NH3)thiazole]2+ group were adopted to study the interplay among subsystems and their contribution to relative stability of all the studied cross-link model. Finally, basic spectral properties of these complexes including H(8) chemical shifts of all the studied complexes and the VCD (vibrational circular dichroism) spectra of two pairs of GG chelate enantiomers, were provided in order to define the structure of the most possible duplex bearing novel trans platinum drug lesions.
Co-reporter:Qin He;Li-Xin Zhou;Zhi-Qiang Zhang
Chinese Journal of Chemistry 2005 Volume 23(Issue 10) pp:
Publication Date(Web):4 NOV 2005
DOI:10.1002/cjoc.200591355
The influence of a series of square planar metal adducts on the protonation ability of adenine has been investigated using ab initio calculation. The results showed that the protonation ability was mainly influenced by the long-range electrostatic effect in gas phase, no strong influence of different metals has been detected for the system studied, and the solvent effect calculations showed that the polar solvent could efficiently compensate for the long-range electrostatic effect dominant in gas phase. The NBO population analysis indicated that the protonation ability was mainly affected by changes of the electron density on selected atoms.
Co-reporter:Zhi-Qiang Zhang;Li-Xin Zhou;Qina He
Chinese Journal of Chemistry 2005 Volume 23(Issue 10) pp:
Publication Date(Web):4 NOV 2005
DOI:10.1002/cjoc.200591327
The influence of binding of cisplatin adducts on tautomeric equilibrium of guanine was investigated using quantum chemical method. The monoaqua adduct [Pt(NH3)2Cl(H2O)]+ and the diaqua adduct [Pt(NH3)2(H2O)2]2+were chosen for coordination to the N(7) site of guanine tautomers. The results demonstrate that the platinum adducts influence moderately on tautomeric equilibrium, but do not change the relative stability of tautomers whether in gas phase or in aqueous solution. The keto form having H atom at N(1) and N(9) was always the predominant structure when cisplatin adducts were bound to guanine. However, other forms could coexist in water. Meanwhile, our calculations suggest that the tautomeric equilibrium should be via the same intermediate.