Synthesis and density functional theoretical study of steroidal spiro-triazolidinone

The reaction of 3beta-chloro-5alpha-cholestan-6-one semicarbazone 1 with hydrogen peroxide at 0 degrees C gives 3beta-chloro-5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one 2 as a product. The structural assignment of the product was confirmed on the basis of its elemental, analytical and spectral data. The ab initio calculations were performed by using density functional theory (DFT) at B3LYP/6-31G* basis set in order to describe a free radical reaction mechanism. The reaction proceeds through two radical intermediates formation. The mechanism of the reaction was explained by using frontier molecular orbital (FMO), spin electronic density map, encoded electrostatic potential map and atomic charges. It was found that the localization of frontier orbitals and the flow of atomic charges of all the calculated structures support the present reaction mechanism. The molecular properties like total energy, dipole moment and hardness of each optimized structure, were also explained. Stability of all the optimized structures in this study was supported by their respective fundamental frequencies and energy minima.     

Oxidative degradation of quinazoline in supercritical water: a combined ReaxFF and DFT study

ABSTRACT

Quinazoline (Qu) is a representative heterocyclic compound in chemical wastewater. In this work, the supercritical water oxidation of Qu is investigated using molecular dynamics simulations based on the ReaxFF reactive force field combined with density functional theory (DFT) method. The detailed reaction pathways, transformation routes of nitrogen element, and kinetic behaviours are systematically analyzed at the atomistic level. Simulation results show that the increment of temperature and O₂ molecule accelerates the reaction rate and facilitates the complete destruction of Qu. The pyrimidine ring in Qu can be attacked by the OH radical, O₂ molecule, and H₂O molecule, thereby causing three main pathways for the pyrimidine ring-opening reaction. The aromatic ring undergoes a ring rearrangement process and opens under the attack of active O₂ molecules. DFT calculations demonstrate that the supercritical water cluster can decrease the cracking energy of chemical bonds and accelerate the degradation rate of Qu. In addition, the transformation routes of nitrogen element during reaction are described. NH₃ is found to be the primary N-containing product after ring-opening reactions and is an intermediate for the production of N₂. Finally, the value of activation energy is obtained as 123.0?kJ/mol, which is reasonably consistent with the experimental results.     

Effect of microsolvation on zwitterionic glycine: an ab initio and density functional theory study

The effect of microsolvation on zwitterionic glycine, considering both (-NH3(+)) as proton donor and (-COO(-)) as proton acceptor at correlated ab initio (MP2) level and density functional methods (B3LYP, PW91, MPW1PW91 and PBE) using 6-311++G** basis set has been reported. DFT methods have been employed so as to compare the performance/quality of different gradient-corrected correlation functionals (PW91, PBE), hybrid functionals (B3LYP, MPW1PW91) and to predict the near quantitative structural and vibrational properties, at reduced computational cost. B3LYP method outperforms among the different DFT methods for the computed hydrogen bond distances and found closer to the value obtained by correlated MP2 level, whereas MPW1PW91 and PBE methods shows very similar values but approximately 0.03 A less, compared to B3LYP method. MP2 calculation and single point CCSD(T)//MP2 calculation have been considered to decompose the interaction energy, including corrections for basis set superposition error (BSSE). Moreover, charge distribution analysis has also been carried out to understand the long raised questions, how and why the two body energies have significant contribution to the total binding energy.     

Effect of amino acids on X-ray-induced hydrogen peroxide and hydroxyl radical formation in water and 8-oxoguanine in DNA

Generation of hydrogen peroxide and hydroxyl radicals in L-amino acid solutions in phosphate buffer, pH 7.4, under X-ray irradiation was determined by enhanced chemiluminescence in the luminol-p-iodophenol-peroxidase system and using the fluorescent probe coumarin-3-carboxylic acid, respectively. Amino acids are divided into three groups according to their effect on the hydrogen peroxide formation under irradiation: those decreasing yield of H2O2, having no effect, and increasing its yield. All studied amino acids at 1 mM concentration decrease the yield of hydroxyl radicals in solution under X-ray irradiation. However, the highest effect is observed in the order: Cys > His > Phe = Met = Trp > Tyr. At Cys, Tyr, and His concentrations close to physiological, the yield of hydroxyl radicals decreases significantly. Immunoenzyme analysis using monoclonal antibodies to 8-oxoguanine (8-oxo-7,8-dihydroguanine) was applied to study the effect of amino acids with the most pronounced antioxidant properties (Cys, Met, Tyr, Trp, Phe, His, Lys, Arg, Pro) on 8-oxoguanine formation in vitro under X-ray irradiation. It is shown that amino acids decrease the content of 8-oxoguanine in DNA. These amino acids within DNA-binding proteins may protect intracellular DNA against oxidative damage caused by formation of reactive oxygen species in conditions of moderate oxidative stress.     

Hybrid density functional theory with a specific reaction parameter: hydrogen abstraction reaction of difluoromethane by the hydroxyl radical

Accurate potential energy surfaces for the OH + CH2F2 --> H2O + CHF2 reaction are constructed using hybrid and hybrid meta density functional theory methods (mPW1PW91, B1B95, and mPW1B95) with specific reaction parameters in conjunction with the 6-31 + G(d,p) basis set. The accuracy of a surface is examined by comparing the calculated rate constants with the experimental ones. The rate constants are calculated over the temperature range 200-1,500 K using variational transition state theory with multidimensional tunneling contributions. The hybrid density functional theory methods with specific-reaction-parameter Hartree-Fock exchange contributions (39.2-41.0% for mPW1PW91, 41.0-42.2% for B1B95, and 44.9-46.3% for mPW1B95, respectively) provide accurate rate constants over an extended temperature range. The classical barrier height for the hydrogen abstraction reaction on these potential energy surfaces is determined to be 5.0-5.3 kcal mol(-1), and the best estimate value is 5.14 kcal mol(-1).     

基于密度泛函理论研究Watson–Crick碱基对中的氢键特征(英文)

基于密度泛函理论(DFT)研究腺嘌呤、胸腺嘧啶、鸟嘌呤、胞嘧啶以及腺嘌呤胸腺嘧啶碱基对、鸟嘌呤胞嘧啶碱基对。在DFT-B3LYP/6-31G**水平上利用自然键轨道理论分析研究结果显示,互补碱基对的结构和电子特征有利于氢键的形成。本文中讨论几何结构、电子结构、分子轨道和能量对于氢键形成的影响。此研究结果将有助于更好的理解AT和GC碱基对中氢键与它们的结构特性之间的关系。     

Ion pair formation of phosphorylated amino acids and lysine and arginine side chains: A theoretical study

Protein phosphorylation is one of the major signal transduction mechanisms for controlling and regulating intracellular processes. Phosphorylation of specific hydroxylated amino acid side chains (Ser, Thr, Tyr) by protein kinases can activate numerous enzymes; this effect can be reversed by the action of protein phosphatases. Here we report ab initio (HF/6-31G* and Becke3LYP/6-31G*) and semiempirical (PM3) molecular orbital calculations pertinent to the ion pair formation of the phosphorylated amino acids with the basic side chains of Lys and Arg. Methyl-, ethyl-, and phenylphosphate, as well as methylamine and methylguanidinium were used as model compounds for the phosphorylated and basic amino acids, respectively. Phosphorylated amino acids were calculated as mono- and divalent anions. Our results indicate that the PSer/PThr ion pair interaction energies are stronger than those with PTyr. Moreover, the interaction energies with the amino group of Lys are generally more favorable than with the guanidinium group of Arg. The Lys amino groups form stable bifurcated hydrogen bonded structures; while the Arg guanidinium group can form a bidentate hydrogen bonded structure. Reasonable values for the interaction free energies in aqueous solution were obtained for some complexes by the inclusion of a solvent reaction field in the computation (PM3-SM3).     

Formation of two centre three electron bond by hydroxyl radical induced reaction of thiocoumarin: evidence from experimental and theoretical studies

Radiation chemical studies of thioesculetin (1), a thioketone derivative of coumarin, were performed by both pulse radiolysis technique and DFT calculations. Hydroxyl (^?OH) radical reaction with 1 resulted transients absorbing at 320, 360 and 500?nm. To identify the nature of the transients, the reaction was studied with specific one-electron oxidant (N₃^?) radical, where 360?nm band was absent. The transient absorption at 500?nm was concentration-dependent. The overall impression for ^?OH radical reaction was that the transient absorbing at 320, 360 and 500?nm was due to sulphur centred monomer radical, hydroxysulfuranyl and dimer radical of 1 respectively. The equilibrium constant between the monomer to dimer radical was 3.75?×?10⁴ M^?1. From the transients’ redox nature, it was observed that 57 and 24% of ^?OH radical yielded to oxidising and reducing products respectively. Further, the product analysis by HPLC suggested that the dimer radical disproportionate to esculetin and thioesculetin. DFT energy calculation for all the possible transients revealed that dimer radical has the lowest energy. The HOMO of 1 and its monomer radical suggested that the electron density was localised on the sulphur atom. The bond length between the two sulphur atoms in dimer radical was 2.88 Å which was less than the van der Waals distance. Bond order between the two sulphur atoms was 0.55, suggesting that the bond was two centre three electron (2c–3e). From TD-DFT calculation, the electronic transition of dimer radical was at 479?nm which was in close agreement with the experimental value. The nature of the electronic transition was σ → σ* from a 2c???3e bond.     

DFT study on the radical scavenging activity of β,β-dimethylacrylalkannin derivatives

The radical scavenging activity of β,β-dimethylacrylalkannin derivatives has been studied by using density functional theory. The hydrogen bond property of the studied structures was investigated using the atoms in molecules theory. It turned out that the hydrogen bond is important for good radical scavenging activity. The hydrogen atom transfer for β,β-dimethylacrylalkannin derivatives is difficult to occur compared with the zero compound phenol. However, β,β-dimethylacrylalkannin derivatives appear to be good candidates for the one-electron transfer, particularly for β,β-dimethylacrylalkannin derivatives with electron-donating groups. Their naphthoquinone planar conformation and the extended electronic delocalisation between adjacent substituent groups determine low adiabatic ionisation potential (IP_a) values. The IP_a values of β,β-dimethylacrylalkannin derivatives with –NHPh, –N(CH₃)Ph, –N(CH₂CH₂)O and –N(CH₃)₂ groups are lower than that of the parent compound β,β-dimethylacrylalkannin, suggesting that these derivatives are expected to be the promising candidates for radical scavenging activity compounds. Taking this system as an example, we present an efficient method for the investigation of radical scavenging activity from theoretical point of view.     

Improvement of the method to estimate the relative reaction rate constants of hydroxyl radical with polyphenols using ESR spin trap: X-ray irradiation of water with a flowing system

UV-photolysis of hydrogen peroxide is a useful technique to produce hydroxyl radical. However, it is not an appropriate method to estimate the reactivity of polyphenols with hydroxyl radicals because many of the polyphenol derivatives also absorb the UV-light to generate hydroxyl radicals. In this study, X-ray irradiation of water with a flowing system was applied to estimate the reactivity of hydroxyl radicals with polyphenols using electron spin resonance (ESR) spin trap. The obtained relative reaction rates reasonably agreed with previous data by pulse radiolysis. This method will be a useful technique to estimate the reactivity of antioxidants including polyphenols with hydroxyl radicals.     

On the application of 4-hydroxybenzoic acid as a trapping agent to study hydroxyl radical generation during cerebral ischemia and reperfusion

Aromatic hydroxylation from the reaction between hydroxyl radical and salicylate or its related compounds has been often utilized as a marker for the generation of hydroxyl radicals. We have investigated several technical aspects of applying this method to study hydroxyl radical production during cerebral ischemia and reperfusion using the hydroxylation of 4-hydroxybenzoic acid (4-HBA) to form 3,4-dihydroxybenzoic acid (3,4-DHBA). 4-HBA was administered to rats either through intravenous infusion, or by way of an in vivo microdialysis probe implanted in the brain. Dialysate containing 3,4-DHBA was collected and analyzed by HPLC with electrochemical detection. An endogenous compound was found to co-elute with 3,4 -DHBA but could be separated by varying the chromatographic conditions. Because of interrupted blood flow during cerebral ischemia and reperfusion, delivery of 4-HBA through the microdialysis probe is a preferred method to systemic administration such as intravenous infusion. It is concluded that the oxidation of 4-HBA to 3,4-DHBA can be a reliable and accurate indicator for the formation of hydroxyl radical in vivo if the experiments are well designed to avoid potential pitfalls associated with technical difficulties of the method.     

Computational studies on the water‐catalyzed stereoinversion mechanism of glutamic acid residues in peptides and proteins

In contrast with the common belief that all the amino acid residues in higher organisms are l ‐forms, d ‐amino acid residues have been recently detected in various aging tissues. Aspartic acid (Asp) residues are known to be the most prone to stereoinvert via cyclic imide intermediate. Although the glutamic acid (Glu) is similar in chemical structure to Asp, little has been reported to detect d ‐Glu residues in human proteins. In this study, we investigated the mechanism of the Glu‐residue stereoinversion catalyzed by water molecules using B3LYP/6‐31+G(d,p) density functional theory calculations. We propose that the Glu‐residue stereoinversion proceeds via a cyclic imide intermediate, i.e., glutarimide (GI). All calculations were performed by using a model compound in which a Glu residue was capped with acetyl and methylamino groups on the N‐ and C‐termini, respectively. We found that two water molecules catalyze the three steps involved in the GI formation: iminolization, cyclization, and dehydration. The activation energy required for the Glu residue to form a GI intermediate was estimated to be 32.3 kcal mol^?1, which was higher than that of the experimental Asp‐residue stereoinversion. This calculation result suggests that the Glu‐residue stereoinversion is not favored under the physiological condition.     

Excitation energy transfer and carotenoid radical cation formation in light harvesting complexes — A theoretical perspective

Light harvesting complexes have been identified in all chlorophyll-based photosynthetic organisms. Their major function is the absorption of light and its transport to the reaction centers, however, they are also involved in excess energy quenching, the so-called non-photochemical quenching (NPQ). In particular, electron transfer and the resulting formation of carotenoid radical cations have recently been discovered to play an important role during NPQ in green plants. Here, the results of our theoretical investigations of carotenoid radical cation formation in the major light harvesting complex LHC-II of green plants are reported. The carotenoids violaxanthin, zeaxanthin and lutein are considered as potential quenchers. In agreement with experimental results, it is shown that zeaxanthin cannot quench isolated LHC-II complexes. Furthermore, subtle structural differences in the two lutein binding pockets lead to substantial differences in the excited state properties of the two luteins. In addition, the formation mechanism of carotenoid radical cations in light harvesting complexes LH2 and LH1 of purple bacteria is studied. Here, the energetic position of the S₁ state of the involved carotenoids neurosporene, spheroidene, spheroidenone and spirilloxanthin seems to determine the occurrence of radical cations in these LHCs upon photo-excitation. An elaborate pump-deplete-probe experiment is suggested to challenge the proposed mechanism.     

Interaction of anticancer drug cisplatin with guanine: density functional theory and surface-enhanced Raman spectroscopy study

Surface-enhanced Raman spectroscopy (SERS) in a silver sol assisted by density functional theory (DFT) calculations is shown to be a promising tool in the characterization of platinum complexes and their interaction with nucleic acid bases. This is demonstrated using cisplatin and guanine as a model. The energies and geometric parameters of cisplatin, guanine, and their reaction products are calculated at Becke's nonlocal three parameter exchange and correlation functional and the Lee-Yang-Parr correlation functional level using the 6-31++G(d,p) basis set on the light elements and the effective core potential by Hay and Wadt on platinum. Available X-ray crystallography data are mostly in agreement with predictions within the experimental precision level, although Pt-N bond lengths tend to be systematically overestimated. The normal Raman spectrum of cisplatin is assigned. The SERS spectra of cisplatin and its reaction product with guanine are measured from 10(-6) M aqueous solution. The observed spectral changes in the SERS spectrum of guanine upon cisplatin binding are modeled by DFT calculations. The best agreement between theory and experiment is achieved when the adsorbed reaction product is assumed to be the 1:1 adduct cis-Pt(NH3)2ClG in which Pt is bound to N7 and guanine is deprotonated at N9.     

Conformational preferences of 1,4,7-trithiacyclononane: a molecular mechanics and density functional theory study

Conformational preferences of 1,4,7-trithiacyclononane were studied using a highly efficient sampling technique based on local nonstochastic deformations and the MM2(91) force field. The results show that conformers that the molecule adopts in the crystal state were found to be low-energy conformers (LECs) within 5 kcal mol(-1) of the global minimum. A conformation with C1 symmetry was the global minimum and the C3 and C2 conformations were calculated to be 0.03 and 1.78 kcal mol(-1) higher in energy, respectively. The structures were further minimized using Density Functional Theory (DFT) calculations with two different functionals. The C2 and the C1 conformations were found to be LECs with the C3 conformation more than 4.0 kcal mol(-1) above the global minimum. The relative energies and structural ordering obtained using the BP86 functional are in agreement with the previously reported relative energies calculated using second-order Moller-Plesset (MP2) ab initio calculations. With the energy ordering being dependent on the molecular mechanics force field used, the approach of MM-->DFT (searching exhaustively the available conformational space at the MM level followed by generating the energy ordering through DFT calculations) appears to be appropriate for thiacrown ethers.     

Structural and electronic properties of diazonium functionalized (4, 4) single walled carbon nanotube: an ab initio study

In this work, ab initio density functional theory (DFT) calculations are performed to study the structural and electronic properties of diazonium reagent functionalized (4, 4) single-walled carbon nanotube (SWCNT). We find the aryl group covalently bonds with SWCNT and prefers to be perpendicular to the side wall of nanotube. It has a rotational barrier of 0.35 eV around the formed aryl-tube bond axis and should be thermodynamically stable at room temperature. Additionally, new peaks appeared around the Fermi energy in the density of state (DOS) due to the weak band dispersion. Increasing of the coverage of the functional group will result in significant upshift of the Fermi level.     

Different mechanisms of hydroxyl radical production susceptible to purine P2 receptor antagonists between carbon monoxide poisoning and exogenous ATP in rat striatum

Abstract

Previous studies have suggested that carbon monoxide (CO) poisoning stimulates cAMP production via purine P2Y11-like receptors in the rat striatum, activating cAMP signaling pathways, resulting in hydroxyl radical (^?OH) production. Extracellular ATP was thought likely to trigger the cascade, but the present study has failed to demonstrate a clear increase in the extracellular ATP due to CO poisoning. The CO-induced ^?OH production was attenuated by the P2Y11 receptor antagonist NF157, in parallel with its abilities to suppress the CO-induced cAMP production. The ^?OH production was more strongly suppressed by a non-selective P2 receptor antagonist, PPADS, which had no effect on cAMP production. More selective antagonists toward the respective P2 receptors susceptible to PPADS, including NF279, had little or no effect on the CO-induced ^?OH production. The intrastriatal administration of exogenous ATP dose-dependently stimulated ^?OH production, which was dose-dependently antagonized by PPADS and NF279 but not by NF157. Exogenous GTP and CTP dose-dependently stimulated ^?OH production, though less potently. The GTP-induced ^?OH production was susceptible to both of NF279 and PPADS, but the CTP-induced ^?OH production was resistant to PPADS. The mechanism of ^?OH production may differ between CO poisoning and exogenous ATP, while multiple P2 receptors could participate in ^?OH production. The CO-induced ^?OH production was susceptible to the inhibition of NADPH oxidase, but not xanthine oxidase. Also, the NADPH oxidase inhibition suppressed ^?OH production induced by forskolin, a stimulator of intracellular cAMP formation. It is likely that ^?OH is produced by NADPH oxidase activation via cAMP signaling pathways during CO poisoning.     

Peroxidase-mediated binding of diethylstilbestrol analogs to DNA in vitro: A possible role for a phenoxy radical

In order to investigate the role of peroxidase-mediated metabolic activation in the mechanism of carcinogenicity of diethylstilbestrol (DES), a series of ¹⁴C-labelled analogs of DES was synthesized and their binding to DNA upon oxidation by peroxidases from horseradish or mouse uterus was studied in vitro. The compounds chosen for this study were the erythro and threo form of hexestrol (HES), the E,E- and Z,Z-isomer of dienestrol (DIES) and the mono- and dimethyl ether of DES.

Non-extractable binding to DNA was observed for all compounds with at least one free hydroxyl group independent of the stilbene structure. The extent of binding was highest for the HES isomers and for E,E-DIES, whereas Z,Z-DIES and the monomethyl ether were bound to about the extent of DES. These findings imply that the formation of a phenoxy free radical is sufficient for non-extractable DNA binding and the stilbene structure is not required for peroxidase-mediated activation of DES.     

Binding to DNA purine bases and amino acid residues of a ruthenium(II) antitumor complex: A density functional study

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.