密度泛函方法研究气相胞嘧啶的互变异构化

By comparing the ready experimental results with the calculated results obtained at 7 basis sets and 3 theoretical levels, respectively, for the tautomeric form Cyt1 of cytosine, the relatively accurate B3LYP/6-311+G** theoretical method to study the tautomerism of cytosine was chosen. The ground-state structures of 8 tautomers of cytosine were fully optimized at B3LYP/6-311+G** level, and the tautomerism of 6 relatively stable tautomers of cytosine was studied. The frequency analysis was performed on all the optimized structures. For the ground state geometries, all the calculated frequencies are real; for the transition-state geometries, there is only one imaginary frequency for each structure. Detailed Intrinsic Reaction Coordination calculations were carried out to guarantee the optimized transition-state structures being connected to the related tautomers. All the energies given include the zero-point energy corrections. The theoretical results can give a reasonable interpretation for the experimental results.     

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.     

Prototropic tautomerism and microsolvation in antitumor drug imexon: a DFT study

Density functional theory method, at the B3LYP/6–311+G(d, p) level has been used to explore the geometries, relative energies, and electronic properties of all hypothetically possible prototropic tautomers of imexon. The specific interactions of the tautomeric forms of imexon with one and two solvating water molecules have been investigated. The relative stability order of the complexes remains unchanged upon interaction with one water molecule. The addition of a second water molecule, however, stabilizes the oxo-amino form more than the oxo-imino structure. The bulk water environment has been simulated by a combination of microhydration and the conductor-like polarizable continuum model. The energy profile corresponding to the prototopic tautomerisms connecting oxo-imino form with oxo-amino, hydroxyl-amino, and one rare tautomer has been studied. We found that the tautomerism activation barriers are high enough as to conclude that only the oxo-imino tautomer should be found in the gas phase. Our results present clear evidence that microhydration with one and two solvating water molecules considerably lower these barriers by a concerted multiple proton transfer mechanism.

     

The chemistry of dinuclear analogues of the anticancer drug cisplatin. A DFT/CDM study

The mechanism of the formation of dinuclear platinum(II) mu-hydroxo complexes from cisplatin hydrolysis products, their interconversion, decomposition, and reactions with biomolecules has been explored using a combined DFT/CDM approach. All activation barriers for the formation of [cis-{Pt(NH(3))(2)(X)}-(mu-OH)-cis-{Pt(NH(3))(2)(Y)}](n)()(+) (X, Y = Cl, OH(2), OH) via nucleophilic attack of a hydroxo complex on an aqua complex are lower than the activation barriers for cisplatin hydrolysis. Considering therapeutic Pt(II) concentrations in tumors, however, only the reaction between two molecules of cis-[Pt(NH(3))(2)(OH(2))(OH)](+) (E) yielding [cis-{Pt(NH(3))(2)(OH(2))}-(mu-OH)-cis-{Pt(NH(3))(2)(OH)}](2+) (5) remains kinetically superior to cisplatin hydrolysis. 5 is strongly stabilized by intramolecular hydrogen bonding between the terminal aqua and hydroxo ligands, resulting in an unusually high pK(a) of 5 and a low pK(a) of its conjugate acid. Unimolecular cyclization of 5 yields the dimers [cis-{Pt(NH(3))(2)}(mu-OH)](2)(2+) (7a with antiperiplanar OH groups and 7b with synperiplanar OH groups). The electronic structure of several diplatinum(II) complexes has been analyzed to clarify whether there are metal-metal interactions. The overall reactivity to guanine (Gua) and dimethyl sulfide (Met, representing the thioether functional group of methionine) increases in the order 5 < 7a approximately 7b < mononuclear complexes, whereas the kinetic selectivity to Gua relative to Met increases in the order 7a approximately 5 < 7b approximately monocationic mononuclear complexes < dicationic mononuclear complex. The results of this work (i) help assess whether dinuclear metabolites play a role in cisplatin chemotherapy, (ii) elucidate the toxicity and pharmacological inactivity of [cis-{Pt(NH(3))(2)}(mu-OH)](2)(2+), and (iii) suggest future investigations of dinuclear anticancer complexes that contain one mu-hydroxo ligand.     

A DFT study of the domino inter

The molecular mechanism of the domino inter [4 + 2]/intra [3 + 2] cycloaddition reactions of nitroalkenes with enol ethers to give nitroso acetal adducts has been characterized using density functional theory methods with the B3LYP functional and the 6-31G basis set. The presence of Lewis acid catalyst and solvent effects has been taken into account to model the experimental environment. These domino processes comprise two consecutive cycloaddition reactions: the first one is an intermolecular [4 + 2] cycloaddition of the enol ether to the nitroalkene to give a nitronate intermediate, which then affords the final nitroso acetal adduct through an intramolecular [3 + 2] cycloaddition reaction. The intermolecular [4 + 2] cycloaddition can be considered as a nucleophilic attack of the enol ether to the conjugated position of the nitroalkene, with concomitant ring closure and without intervention of an intermediate. For this cycloaddition process, the presence of the Lewis acid favors the delocalization of the negative charge that is being transferred from the enol ether to the nitroalkene and decreases the activation energy of the first cycloaddition. The [4 + 2] cycloaddition presents a total regioselectivity, while the endo/exo stereoselectivity depends on the bulk of the Lewis acid used as catalyst. Thus, for small Lewis acid catalyst, modeled by BH(3), the addition presents an endo selectivity. The [3 + 2] cycloaddition reactions present an total exo selectivity, due to the constraints imposed by the tether. Inclusion of Lewis acid catalyst and solvent effects decrease clearly the barrier for the first [4 + 2] cycloaddition relative to the second [3 + 2] one. Calculations for the activation parameters along this domino reaction allow to validate the results obtained using the potential energy barriers.     

A DFT study of the hydrolysis of hydantoin

Density functional theory (DFT) calculations were made on the hydrolysis of hydantoin (2,4-imidazolidinedione). In the neutral hydrolysis, reacting systems composed of hydantoin and (H₂O)_n with n = 1+3, 2+3, 3+3, and 4+3 were adopted. Three water molecules (“+3”) participate in the in-plane hydrogen-bond circuit, and the n–3 = 1, 2, 3 or 4 water cluster works for the out-of-plane nucleophilic attack onto the carbonyl carbon of hydantoin. Transition states (TSs) involving bond interchanges prompted by proton transfers were determined. The reaction path with n = 3+3 containing N-carbamoyl glycine, N-carboxy glycine and three tetrahedral intermediates was found to be most likely. In the acid-catalyzed hydrolysis, a reacting system composed of hydantoin and H₃O⁺(H₂O)₇ was employed. Ten TSs and nine intermediates were obtained. N-carbamoyl glycine and N-carboxy glycine were confirmed to be detectable stable species. The product consists of glycine, carbonic acid (not CO₂), NH₄⁺, and (H₂O)₅. It has the exothermic energy, whereas the product in the neutral hydrolysis is of the endothermic one for all n values. For both neutral (n = 3+3) and acid-catalyzed hydrolyses, the rate-determining steps were calculated to be for formation of the tetrahedral intermediate, HOOC-CH₂-NH-C(OH)₂NH₂. The pattern of proton transfers along hydrogen bonds was carefully investigated.     

Molecular electrostatic potential studies on antiepileptic drug: Troxidone

Ab initio SCF -MO -LCAO calculations of the molecular electrostatic potential (MEP ) have been carried out on a seven-member series related to the antiepileptic drug troxidone. The effect of the substituted alkyl groups on the bioactivity of these molecules is discussed. The substituted alkyl groups increase the negative potential found near the oxygen atoms in the molecular plane.     

A DFT study on the geometry,spectroscopic properties,and tautomerization of the local anaesthetic drug prilocaine

The prilocaine is a significant amino amide local anaesthetic. This drug can exist as three possible tautomers. Herein, by using density functional theory (DFT), and handling the solvent effects with the PCM model, the structure, energetic behavior, kinetics and mechanism of tautomerization, as well as the natural bond orbital analysis (NBO) of the prilocaine are reported. P1 is the most stable tautomer of the prilocaine, which can be tautomerized to two other tautomers via the intramolecular-proton transfer. Good agreement between the calculated NMR chemical shifts and IR vibrational frequencies with the experimental values approves the suitability of the optimized geometry for the prilocaine. A large HOMO-LUMO energy gap implies a high stability of the prilocaine.     

Tautomerism of peroxyacetic acid derivatives: a quantum chemical study

The electronic and molecular structures and the relative stabilities of organic peracids X=C(R)-COOH and their cyclic tautomers, dioxiranes

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, with R = Me, CF₃; X = O, NH, were studied using the ab initio Hartree-Fock method and the density functional theory (B3LYP version) as well as at the MP2-MP4 Møller-Plesset levels of perturbation theory. Geometry optimization was performed by the UHF and B3LYP methods with the 6-31G** basis set and at the MP2/cc-pvtz level of theory. The acyclic form of the peracid is more stable than the cyclic dioxirane form irrespective of the nature of the substituent. The energy difference between these tautomers increases as the CF₃ and NH groups are replaced by Me and O, respectively. Parameters of the activation barrier to tautomeric conversion increase in parallel with enhancement of the electron-accepting properties of both substituents. The transition state of tautomeric interconversion, which is topologically similar to the acyclic structure of the carbonyl oxide derivative R(HX)C=O⁺-O^?, was found and characterized taking peroxyacetic acid as an example. The characteristic features of the transition state are an intramolecular “multicenter” H-bond and the charge distribution that is inconsistent with the canonical structure mentioned above. An appropriate reaction coordinate for the transformation of the quasi-tetrahedral dioxirane structure into a planar peroxyacetic acid structure is provided by the dihedral angle. Deprotonated anionic systems are characterized by much smaller differences between the relative stabilities of the open and closed forms of isomers and by much lower activation barriers to isomeric conversions.

     

Analysis of the antiepileptic drug keppra by capillary electrophoresis

A simple and rapid method for determination of the new antiepileptic drug keppra (levetiracetam) by capillary electrophoresis in borate buffer containing sodium dodecyl sulfate is described. The serum was injected without any treatment. The method compared well to high performance liquid chromatography. The mean of keppra in the serum of 35 patients was 25 mg/l (range 7-77 mg/l).     

Tautomerism and thermal decomposition of tetrazole: high-level ab initio study

The mutual interconversion and decomposition reactions of four tetrazole isomers (1H-TZ, 2H-TZ, 5H-TZ, and an N-heterocyclic carbene 14H) have been studied theoretically using the W1 high-level procedure. Computations allowed resolution of the existing discrepancies in the mechanism and key intermediates of TZ thermolysis. The tautomeric equilibria between 1H-TZ, 2H-TZ, and 14H turned out to play a very important role in the mechanism of thermal decomposition. Although the barriers of monomolecular tautomeric transformations were found to be high (～50-70 kcal/mol), the concerted double H atom transfer reactions in the H-bonded complexes of TZ tautomers have profoundly lower barriers (～18-28 kcal/mol). These reactions lead to fast interconversion between 1H-TZ, 2H-TZ, and 14H. The carbene 14H has never been considered before; however, it was predicted to be a key intermediate in the mechanism of thermal decomposition of TZ. For all species considered, the unimolecular reactions of N(2) elimination were predicted to dominate over the elimination of hydrazoic acid. In agreement with existing experimental data, the effective activation energy of thermolysis was calculated to be 36.2 kcal/mol.     

Sensing the cathinone drug concentration in the human body by using zinc oxide nanostructures: a DFT study

Structural Chemistry - The capability of zinc oxide, ZnO, nanocage to adsorb cathinone (CA) drug was evaluated by density functional theory, DFT method. Having considered all energetically...     

Conformational study on dipeptides containing phenylalanine: A DFT approach

DFT calculations has been done applying 6-31G^* basis set on a series of dipeptides where the N-terminus position is fixed with phenylalanine and the C-terminus is varied with eight different amino acids. Different geometrical parameters (bond angle, bond length, geometry around -carbon atom) are thoroughly investigated to study the effect of amino acid sequence on dipeptide. Dihedral angle data analysis shows the deviation of amide plane from planarity, which is due to the combined effect of the steric hindrance of –R group and hydrogen bonding. The λ_max value for phenylalanine has been calculated, which shows good agreement with the experimental value. A rigid potential energy scan is performed on phenylalanine by rotating –CH₂Ph, –COOH and –NH₂ groups separately to get some idea about the conformational stability.     

β-Cyclodextrin—α-aminopyridine interaction: A DFT study

The energy changes for two opposite complexation orientations of β-cyclodextrin (β-CD) and α-aminopyridine were calculated by the semiempirical PM3 method. The complexes with the lowest energies obtained by the PM3 method were further investigated by the density functional theory at the B3LYP/3-21G* level. The DFT results indicate that the complexation orientation, in which the amino group is located near the secondary hydroxyl rim of the β-CD cavity, is much more favorable, probably, due to effective hydrophobic interactions. The results of statistical thermodynamics calculations for p = 1 atm and T = 298.15 K suggest that the inclusion complexation processes of two different orientations are driven by enthalpy. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 416–420, March, 2007.     

DFT study of SiO2 nanoparticles as a drug delivery system: structural and mechanistic aspects

Structural Chemistry - Adsorption and reaction mechanisms for the noncovalent and covalent functionalization of SiO2 nanoparticle (SiNP) with gemcitabine (GEM) anticancer drug have been...     

Cycloaddition mechanism for the resin-OsO_4-catalyzed of styrene: A DFT study

The postulated intermediates in the base-free and base-assisted addition of OsO4 to styrene have been investigated at the B3LYP/6-311G** level of the theory. N(CH3)2(Ph) was chosen as the base of the resin-OsO4. According to our model calculations the [2 3] addition was found to be favorable with an activation of <45.00 kJ/mol. In contract, the reaction barriers for the [2 2] cycloaddition remain high (>155.00 kJ/mol). In addition, the electronic structure analysis of the molecules was carried out by na- ture bond orbital (NBO). The computational results were in reasonable agreement with experimental results.     

Detection of NO2 by hexa-peri-hexabenzocoronene nanographene: A DFT study

It has been previously indicated that pristine graphene cannot detect NO₂ gas. Nanographene is a segment of graphene whose end atoms are saturated with hydrogen atoms and its properties are different from those of graphene. Herein, we investigated the reactivity, electronic sensitivity, and structural properties of hexa-peri-hexabenzocoronene (HBC) nanographene toward NO₂ gas using density functional theory calculations. It was found that the central and peripheral rings of HBC are aromatic but the middle rings are non-aromatic, following Clar's sextet rule of aromaticity. The NO₂ molecule prefers to be adsorbed on the central ring with a nitro configuration, releasing an energy of about 13.2 kJ/mol. The NO₂ molecule significantly stabilizes the LUMO level of the HBC, thereby reducing the HOMO–LUMO energy gap from 3.60 to 1.35 eV. This indicates that the HBC is converted from a semiconductor to a semimetal. It was shown that the adsorption of NO₂ gas by HBC can produce an electrical signal selectively in the presence of O₂, H₂, N₂, CO₂, and H₂O gases. A short recovery time about 1.9 ns is predicted and the effect of density functional is investigated.     

A physiochemical study of azo dyes: DFT based ESIPT process

Azo linked dye derivatives were synthesized and characterized by NMR, mass and elemental analysis. An excited state intramolecular proton transfer (ESIPT) in hydroxy Schiff base has been analyzed, and found that two distinct ground state isomers of I and II are responsible for the observed dual emission. DFT calculation on energy, dipole moment, charge distribution of the rotamers in the ground and excited states support the ESIPT process. PES calculation indicates that the energy barrier for the interconversion of two rotamers is too high in the excited state than the ground state. By varying the addition of base concentration to hydroxy Schiff base, two isobestic points were found which confirm the equilibrium among the trans enol form, anion and the cis enol form. Fluorescence quenching with metal ions reveal that hydroxy Schiff base can be used as a new fluorescence sensor to detect the Cu(2+) ion.