The magnetic coupling in manganese-based dinuclear superhalogens and their analogues. A theoretical characterization from a combined DFT and BS study

The structures, relative stabilities, vertical detachment energies and magnetic coupling properties of a series of manganese-based dinuclear superhalogens and their isoelectronic analogues are explored via a combined density functional theory and broken symmetry study. Both the capabilities of various exchange-correlation functionals and basis set effects are investigated. The large magnitudes of the calculated exchange coupling constants indicate clearly the apparent molecular magnetism of these new types of superhalogen. Encouragingly, the high possibility of the coexistence of both high stability and strong magnetic coupling in these new polynuclear superhalogens is also confirmed. Besides these, the larger magnitudes of the calculated coupling constants of iron-based clusters here, compared with the homodinuclear [Mn(2)Cl(5)](-) cluster, demonstrate the possibility of the existence of strong magnetic coupling in potential iron-based homo- and heterodinuclear superhalogens. The analysis of spin density distribution is also performed in order to understand the coupling mechanisms.     

A DFT study of the degradation mechanism of anticancer drug carmustine in an aqueous medium

Structural Chemistry - Density functional theory calculations were carried out to study the degradation mechanism of anticancer drug carmustine in an aqueous medium. The calculations indicate that...     

杂环反铂(Ⅱ)抗癌药物水解反应机理的DFT研究

用DFT-B3LYP方法和IEF-PCM溶剂化模型研究了反铂抗癌药物trans-[PtCl2(piperidine)(Am)](Am=2-picoline(1),3-picoline(2),4-picoline(3)),trans-[PtCl2(piperidine)(piperazine)](4),trans-[PtCl2(pipera-zine)2](5)and trans-[PtCl2(iminoether)2](6)的水解过程.水解反应是药物与DNA靶分子作用的关键活化步骤.全优化和表征了一水解和二水解反应经由一般的SN2路径过程所有物种的势能面稳定点.结果发现反应过程遵循已经建立的平面正方形配合物的配体取代反应理论,即取代反应通常通过一个三角双锥过渡态结构的铂配体交换反应发生.得到的过渡态结构与以前的相关工作一致,所有反应都是吸热反应;所有体系的二水解能垒都高于一水解.与顺铂相比,这些配合物都有更快的水解反应速率;并与以前类似的反铂配合物的研究做了比较.研究结果提供了这些配合物水解反应过程的详细能量变化,对理解药物与DNA靶分子的作用机理和新型反铂抗癌药物的设计有帮助.     

DFT computational study towards investigating Cladribine anticancer drug adsorption on the graphene and functionalized graphene

Structural Chemistry - Density functional theory calculations at the M06-2X/6-31G** level have been carried out to examine the adsorption behavior of Cladribine drug on the graphene and graphene...     

The anticancer drug cisplatin can cross-link the interdomain zinc site on human albumin

Cisplatin, cis-[Pt(Cl(2)(NH(3))(2)], can crosslink residues His67 of domain I and His247 of domain II in human albumin, occupying the major binding site for the essential metal zinc on the protein.     

Factors governing the protonation state of Zn-bound histidine in proteins: a DFT/CDM study

We have performed systematic theoretical studies to elucidate the factors governing the His protonation/deprotonation state in Zn-binding sites, especially those containing the ubiquitous Zn-His-Asp/Glu triad. Specifically, we have addressed the following three questions: (1) How does the transfer of the Zn-bound His imidazole proton to the second-shell Asp/Glu carboxylate oxygen depend on the composition of the other first-shell ligands and the solvent accessibility of the metal-binding site? (2) Can any second-shell ligand with a proton acceptor group such as the backbone carbonyl oxygen also act as a proton acceptor? (3) What is the effect of the Asp/Glu in the Zn-His-Asp/Glu triad on the Zn-bound water protonation state? To address these questions, we used a combination of quantum mechanical and continuum dielectric methods to compute the free energies for deprotonating a Zn-bound imidazole/water in various Zn complexes. The calculations show that whether the Zn-bound His is protonated or deprotonated depends on (1) the solvent accessibility of the metal-binding site, and (2) the Lewis acid ability of Zn, which is indirectly determined by both the first- and the second-shell Zn ligands. The calculations also show that the effect of the Zn-His-Asp/Glu interaction on the nucleophilicity of the Zn-bound water depends on the solvent accessibility of the catalytic Zn site. Furthermore, they show that the Asp/Glu side chain in the Zn-His-Asp/Glu triad can increase the negative charge of its partner, His, and create an anionic hole that may stabilize a cation in buried cavities, provided that the Zn complex is cationic/neutral. The findings of this work are in accord with available experimental data.     

Tautomerism of the antiepileptic drug Felbamate: A DFT study

The Felbamate is a novel anticonvulsant and neuropathic pain drug that can exist as three possible tautomers. Herein, employing density functional theory (DFT) and handling the solvent effects with the PCM model, the structural parameters, energy behavior, natural bond orbital analysis (NBO), as well as the tautomerism of Felbamate are investigated. F1 is the kinetically and thermodynamically most stable tautomer of Felbamate, which contains the amide group in each of the carbamate moieties. The calculated NMR chemical shifts and IR vibrational frequencies are in good agreement with the experimental values, confirming the suitability of the optimized geometry for Felbamate. The tautomerization reaction of F1 to each of the other tautomers occurs via an intramolecular proton transfer. This reaction affects considerably the structural parameters and atomic charges of the Felbamate molecule. A large HOMO-LUMO energy gap implies a high stability of the F1 tautomer.     

A DFT study of reactions of Ru(III) anticancer drug KP1019 with 8-oxoguanine and 8-oxoadenine

Structural Chemistry - The cytotoxic activities of KP1019 and other Ru(III) drugs are believed to be associated with their binding with DNA. Here, we report the density functional theory (DFT)...     

Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study

Many of the essential metalloproteins are located in the cell, whose cytoplasmic fluid contains several small inorganic anions, such as Cl-, NO2-, NO3-, H2PO4-, and SO4(2-), that play an indispensable role in determining the cell's volume, regulating the cell's pH, signal transduction, muscle contraction, as well as cell growth and metabolism. However, the physical principles governing the competition between these abundant, intracellular anions and protein or nucleic acid residues in binding to cytoplasmic metal cations such as Na+, K+, Mg2+, and Ca2+ are not well understood; hence, we have delineated the physicochemical basis for this competition using density functional theory in conjunction with the continuum dielectric method. The results show that the metal cation can bind to its target protein against a high background concentration of inorganic anions because (i) desolvating a negatively charged Asp/Glu carboxylate in a protein cavity costs much less than desolvating an inorganic anion in aqueous solution and (ii) the metal-binding site acts as a polydentate ligand that uses all its ligating entities to bind the metal cation either directly or indirectly. The results also show that the absolute hydration free energy of the "alien" anion as well as the net charge and relative solvent exposure of the metal-binding protein cavity are the key factors governing the competition between protein and inorganic ligands for a given cytoplasmic metal cation. Increasing the net negative charge of the protein cavity, while decreasing the number of available amide groups for metal binding, protects the metal-bound ligands from being dislodged by cellular anions, thus revealing a "protective" role for carboxylate groups in a protein cavity, in addition to their role in high affinity metal-binding.     

An electroanalytical study of the anticancer drug dacarbazine

The electrochemical behaviour of dacarbazine [5-(3,3-dimethyl-1-triazenyl) imidazole-4-carboxamide; DTIC] was investigated by Tast and differential pulse polarography (d.p.p.) at the dropping mercury electrode, by cyclic and differential pulse voltammetry at the hanging mercury drop electrode and by anodic voltammetry at the glassy carbon electrode. Calibration graphs were obtained for 2×10^?8?2×10^?5 M DTIC by d.p.p., for 5×10^?9?1×10^?5 M by adsorptive stripping voltammetry ar a hanging mercury drop electrode, and for 1?10×10^?5 M by high-performance liquid chromatography with oxidative amperometric detection at a glassy carbon electrode. The methods are compared and applied to determine DTIC added to blood serum after a simple clean-up procedure.     

Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters

The thermodynamic and kinetic aspects of hydration reactions of cis-/transplatin were explored. The polarizable continuum model was used for estimation of solvent effects. Using the B3LYP/6-31+G(d) method, the structures were optimized and vibrational frequencies estimated. Interaction energies and activation barriers were determined at the CCSD(T)/6-31++G(d,p) level within the COSMO approach. An associative mechanism was assumed with a trigonal-bipyramidal structure of the transition state. Within the applied model, all the hydration reactions are slightly endothermic. The Gibbs energies of cisplatin hydration amount to 7.0 and 14.2 kcal/mol for the chloride and ammonium replacement, respectively. Analogous values for the transplatin reactions are 6.8 and 11.9 kcal/mol. The determined rate constants are by several (three to four) orders of magnitude larger for the dechlorination process than for deammination. The cisplatin dechlorination rate constant was established as 1.3 x 10(-4) s(-1) in excellent accord with the experiment.     

A structure-based 3D-QSAR study of anthrapyrazole analogues of the anticancer agents losoxantrone and piroxantrone

A series of 13 anthrapyrazole compounds that are analogues of piroxantrone and losoxantrone were synthesized, and their cell growth inhibitory effects, DNA binding, topoisomerase IIalpha mediated (EC 5.99.1.3) cleavage of DNA, and inhibition of DNA topoisomerase IIalpha decatenation catalytic activities were determined. Cell growth inhibitory activity was well-correlated with DNA binding, suggesting that these compounds may act by targeting DNA. However, cell growth inhibition was not well-correlated with the inhibition of topoisomerase IIalpha catalytic activity, suggesting that these anthrapyrazoles did not act solely by inhibiting the catalytic activity of topoisomerase II. Most of the analogues were able to induce DNA cleavage, and thus, it was concluded that they acted, at least in part, as topoisomerase II poisons. Structure-based three-dimensional quantitative structure-activity analyses (3D-QSAR) were carried out on the aligned structures of the anthrapyrazoles docked into DNA using comparative molecular field analysis (CoMFA) and comparative molecular similarity index (CoMSIA) analyses in order to determine the structural features responsible for their activity. Both CoMFA and CoMSIA yielded statistically significant models upon partial least-squares analyses. The 3D-QSAR analyses showed that hydrogen-bond donor interactions and electrostatic interactions with the protonated amino side chains of the anthrapyrazoles led to high cell growth inhibitory activity.     

A DFT/CDM Study of metal-carboxylate interactions in metalloproteins: factors governing the maximum number of metal-bound carboxylates

The number of negatively charged metal-bound Asp/Glu residues determines the net charge of the carboxylate-rich metal-binding site, which has been found to play a role in enhancing the affinity and/or selectivity of a protein cavity for a given metal cofactor. Therefore, it is of interest to know the maximum number of carboxylates that could bind to a given metal (M(q)()(+)) of charge q and the key factors determining this upper limit in protein cavities, which are usually relatively buried. Using density functional theory combined with the continuum dielectric method to compute the H(2)O --> CH(3)COO(-) exchange free energies, the maximum number of carboxylates bound to M(q)()(+) in a relatively buried metal-binding site is found to depend on (i) the metal charge, q, (ii) the carboxylate-binding mode, and (iii) the first-shell carboxylate-second-shell ligand interactions. The maximum number of carboxylates bound to M(q)()(+) in a fully/partially solvent inaccessible protein cavity would not likely exceed q + 2 if (a) the metal-bound Asp/Glu side chains are hydrogen bonded to a Lys/Arg side chain or several peptide backbone amides/Asn/Gln side chains in the metal's second coordination shell or (b) at least one acidic residue binds bidentately, as opposed to monodentately, to the metal cofactor. This number is reduced to q + 1 in the absence of stabilizing interactions from outer-shell ligand(s) and if all the carboxylates are bound monodentately to the metal cofactor in a buried cavity. The computational results are consistent with findings from a PDB survey of uni-, di-, and trivalent metal-binding sites containing Asp/Glu residues.     

The nature of the DNA template (single- versus double-stranded) affects the rate of aquation of a dinuclear Pt anticancer drug

The rate of aquation of a dinuclear platinum anticancer agent is altered in the presence of template DNA with enhancement of hydrolysis in the presence of single-stranded over double-stranded DNA, emphasising how the alteration of chemical properties of small molecules in the presence of large host interactions is also dependent on the conformation and nature of that host.     

DFT study of the asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex

We report the mechanism of asymmetric nitroaldol (Henry) reaction catalyzed by a dinuclear Zn complex using density functional theory. The experimentally proposed catalytic cycle is validated, in which the first step is the deprotonation of nitromethane by the ethyl anion of the catalyst, subsequently a C? C bond formation step, and then the protonation of the resulting alkoxide. Three mechanistic scenarios (differing in binding modes) have been considered for the C? C bond formation step. The origin of the enantioselectivity is discussed. Our calculations supported that the S configurations are the major products, which is in agreement with the experimental observations. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Optical absorption and emission properties of benzene-expanded Janus AT nucleobase analogues: A DFT study

We design benzene-expanded Janus AT bases (J-AT1, J-AT2, BF1 and BF2) and investigate the structural and optical properties of these bases using DFT and TDDFT methods and also consider the effect of water solution and base pairing. The results show that J-AT1 has a nonplanar structure and its amino group is more asymmetric than the other three bases. J-AT1 and BF1 exist intramolecular H-bonds. The Janus AT base pairs exist three intermolecular H-bonds: NH···N has the largest energy, followed by NH···O and CH···O. The Janus AT base pairs retain the strength of H-bonds and maintain the stability of the base pair. The lowest absorption and emission wavelengths of the benzene-expanded Janus AT bases are all assigned to ππ* character arising from HOMO to LUMO transition, and they exhibit redshift due to the increase in effective conjugation length with the introduction of benzene. The excited state assignments in water solution are one-to-one correspondence to those in gas phase. The lowest absorption and emission wavelength of J-AT1 is blueshift, while J-AT2, BF1 and BF2 bases are redshift as compared to those in gas. The TD-B3LYP method predicts that the first excitation wavelengths of Janus AT base pairs are local excitation on the Janus AT base moieties, which is coincident with the result of CAM-B3LYP and M062X functional. Base pair can influence the excitation properties of base monomer. The results obtained from this theoretical investigation confirm that the position of benzene ring significantly influences the structure and optical properties of the Janus AT bases.     

In silico evolution of substrate selectivity: comparison of organometallic ruthenium complexes with the anticancer drug cisplatin

A comparative quantum chemical approach helps to clarify how the selectivity of anticancer metallopharmaceuticals towards potential biological targets can be controlled by metal and ligands.     

Macrocyclic vs. dendrimeric effect. A DFT study

Macrocycles up to 15 members with different heteroatoms (N, O, and S) and dendrimeric functionalized branches were assembled, resulting in unique "collective" supramolecular hosts with several active sites for transition metal ions complexation. The nature of the interactions between these kinds of systems and metal ions of the first transition series (Fe, Ni, Cu, Zn) was evaluated by calculations of the binding energies at the B3LYP/LACVP* level of theory, resulting in a preference of metal ions for macrocyclic cavity in terms of complexation; however, there is a favorable contribution in energy due to the cooperative effect of dendrimeric branches (DBs) in the inclusion process by means of long-range interactions between metal ions and the heteroatoms present in DBs. According to calculated binding energies, even when the complexation in the middle of DBs appears as a less favored situation, still competes with the complexation occurred in several known macrocycles traditionally used in the formation of inclusion complexes. The capability of macrocycles as host entities is related to some criteria like: (1) the compatibility in orbital symmetry between host and guest molecules; (2) the cavity dimensions and the negative charge inside; and (3) the hardness-softness affinity between host and guest molecules. When DBs are included in host systems, their flexibility seems to be very important, in addition to localized negative charge, which permits the occurrence of long-range interactions.     

A spectroscopic study on the interaction between the anticancer drug erlotinib and human serum albumin

The interaction between erlotinib and human serum albumin (HSA) in simulated physiological conditions was investigated by spectroscopic methods. The results revealed that erlotinib caused the fluorescence quenching of HSA through a static quenching procedure. The binding constants at 293, 298, 303 and 308 K were obtained as 2.53 × 10⁵, 8.13 × 10⁴, 3.59 × 10⁴ and 1.93 × 10⁴ M^?1, respectively. There may be one binding site of erlotinib on HSA at 298 K. The thermodynamic parameters indicated that the interaction between erlotinib and HSA was driven mainly by hydrogen bonding or van der Waals forces. Synchronous fluorescence spectra, UV–Vis spectra, circular dichroism and Fourier Transform infrared spectroscopy results showed erlotinib binding slightly changed the conformation of HSA with secondary structural content changes. Förster resonance energy transfer study revealed high possibility of energy transfer with erlotinib-Trp-214 distance of 3.48 nm. The results of the present study may provide valuable information for studying the distribution, toxicological and pharmacological mechanisms of erlotinib in vivo.