Davood Ajloo

This study was designed to investigate the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin (BSA) by means of various spectroscopic and electrochemical methods along with molecular docking study and molecular dynamics simulations. Binding constants were estimated by fluorescence and UV-Vis spectroscopy. The results indicated a good affinity of the complexes for BSA in which furyl derivative had more activity. Molecular docking study showed that these complexes have the similar binding modes and located within subdomain IB in site III of BSA. The supporting of molecular docking and molecular dynamics results by experimental data, confirms the validity of the interactions data obtained by these methods. Biological activity against cancer cell showed that furyl derivative has higher activity than other complexes. Pharmaceutical analysis also showed that, these complexes potentially can be used as anticancer agents. © 2017, © 2017 Informa UK Limited, trading as Taylor & Francis Group.

Photconversion of an anthraquinone photochrome (AQP) from Trans to Ana forms were studied by different methods and techniques. Solution of AQP was irradiated under UV light in buffer condition, pH = 7.5, 10 mM phosphate buffer in the absence and presence of human serum albumin at 27 and 37 °C. The results showed that a new peak at higher wavelength was observed that indicative of producing the Ana form. Rate of Trans to Ana conversion increases in the presence of human serum albumin (HSA). Electron transport calculations were carried out from the first principles with a method based on non-equilibrium Green's functions (NEGF) combined with DFT. The results showed that electron transport is easier in Ana form due to increasing the resonance length and electron delocalization. Binding study by docking and spectroscopy showed that Trans form has more tendency to interact with HSA due to higher number of HSA-Trans hydrogen bond. Structural studies by circular dichroism and molecular dynamics results show that at lower concentration of AQP, percentage of helix was increased and then decreases at higher concentration. In addition structural parameters such as RMSD, accessible surface area, hydrogen bond, in associated with experimental results showed that protein folded at low concentration. © 2018

Methylglycine, also known sarcosine, is dramatically used in drug molecules and its metal complexes can interact to DNA and also do cleavage. Hence, to study the influence of methylglycine ligand on biological behavior of metal complexes, two water-soluble platinum (II) complexes with the formula cis-[Pt(NH3)2(CH3-gly)]NO3 and cis-[Pt(NH2-CH3)2(CH3-gly)]NO3 (where CH3-gly is methylglycine) have been synthesized and characterized by spectroscopic methods, molar conductivity measurements, and elemental analyzes. The anticancer activity of synthesized complexes was tested against human breast adenocarcinoma cell line of MCF7 using MTT assay and results showed excellent anticancer activity with Cc50 values of 126 and 292 μM after 24 h incubation time, for both complexes of cis-[Pt(NH3)2(CH3gly)]NO3 and cis-[Pt(NH2-CH3)2(CH3gly)]NO3, respectively. Also, the interaction between Pt(II) complexes with calf thymus DNA was extensively studied by means of absorption spectroscopy, fluorescence titration spectra displacement with ethidium bromide (EtBr), and circular dichroism studied in Tris-buffer. The obtained spectroscopic results revealed that two complexes can bind to highly polymerized calf thymus DNA cooperatively and denature at micromolar concentrations. The fluorescence data indicate that quenching effect for cis-[Pt(NH3)2(CH3gly)]NO3 (Ksv = 9.48 mM−1) was higher than that of cis-[Pt(NH2-CH3)2(CH3gly)]NO3 (Ksv = 1.98 mM−1). These results were also confirmed by circular dichrosim spectra. Consequently, docking data showed that cis-[Pt(NH3)2(CH3gly)]NO3 with more interaction energy binds on DNA via groove binding which is more compatible with experimental results. [Figure not available: see fulltext.]. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.

Electrochemical characterization of functionalized carbon nanotubes (f-CNT) including carboxyl (CNT-COOH), amine (CNT-NH2) and hydroxyl (CNT-OH) functional groups were studied using differential pulse voltammetry (DPV). The current-voltage (I-V) curves were obtained from each system and the effect of f-CNT on redox interaction of horseradish peroxidase (HRP) immobilized on the electrode surface was investigated. The non-equilibrium Green's function (NEGF) combined with density functional theory (DFT) were used to study the transport properties of f-CNT. Additionally, the effect of the number of functional groups on transport properties of CNT, I-V characteristics, electronic transmission coefficients and spatial distribution of f-CNTs have been calculated and analyzed. The results showed that the carboxyl derivative has larger transmission coefficients and current value than other f-CNTs. Then, the effect of functional groups on the electron transport in heme group of HRP is discussed. Finally, the effect of a covalent bond between active site amino acids and amine functional group of CNT was investigated and discussed. © 2018 Elsevier Ltd

Using nonequilibrium Green's function formalism combined first-principles density functional theory, we analyze the transport properties of a 4,4-dimethyl-6-(4-nitrophenyl)-2-phenyl-3,5-diaza-bicyclo[3.1.0]hex-2-ene molecular optical switch. The title molecule can convert between closed and open forms by visible or ultraviolet irradiation. The I-V characteristics, differential conductance, on-off ratio, electronic transmission coefficients, spatial distribution of molecular projected self-consistent Hamiltonian orbitals, HOMO-LUMO gaps, effect of electrode materials Y (111) (Y =Au, Ag and Pt) on electronic transport and different molecular geometries corresponding to the closed and open forms through the molecular device are discussed in detail. Based on the results, as soon as possible the open form translates to the closed form, and there is a switch from the ON state to the OFF state (low resistance switches to high resistance). Theoretical results show that the donor/acceptor substituent plays an important role in the electronic transport of molecular devices. The switching performance can be improved to some extent through suitable donor and acceptor substituents. © 2018 Chinese Physical Society and IOP Publishing Ltd.

A series of 4-arylmethylene-3-methylisoxazol-5(4H)-one derivatives are obtained via treating ethyl acetoacetate, hydroxylamine hydrochloride and variety of aromatic aldehyde compounds in the presence of antimony trichloride as an efficient catalyst in aqueous media. Mild conditions, safe, short reaction times, commercially available catalyst, environmentally friendly, no uses of organic solvent and high yields are remarkable advantages to this process. (Z)-4-(3-hydroxybenzylidene)-3-methylisoxazol-5(4H)-one, (HBIM), is characterized by theoretical (density functional theory) and experimental (IR, 1H NMR, CV and UV). The structural parameters, vibrational frequencies, molecular electrostatic potential, frontier molecular orbital analysis (HOMO–LUMO), thermodynamic properties and nonlinear optical properties are found and discussed. UV–Vis spectra are recorded in two organic solvents. Thermal stability of HBIM is studied by thermogravimetric analysis. The molecule orbital contributions are studied using the total and partial density of states (TDOS and PDOS). © 2017, Iranian Chemical Society.

We analyze the transport properties of 4-(6-(4-chlorophenyl)-4-phenyl-1,3-diaza-bicyclo[3.1.0]hex-3-en-2-yl)-2-nitrophenol molecular optical switch using first-principles calculations. Molecule consisting switch can transform among closed and open forms by visible or ultraviolet irradiation. We have studied multiple attributes such as I–V characteristics, electronic transmission coefficients T(E), the effect of electrode materials (Au, Ag, and Pt) on electronic transport properties, on-off ratio and spatial distribution of molecular projected self-consistent Hamiltonian (MPSH) orbitals corresponding to the closed and open forms. The physical origin of switching behavior is interpreted based on the different molecular geometries, location and size of the frontier molecular orbitals and the HOMO–LUMO gap. According to the theoretical results, one can found that when the open form converts to the closed form, there is a switch from low resistance (on state) to high resistance (off state). We hope that the results of this study can help researchers to design new functional molecular devices. © 2017 Elsevier GmbH

Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mono- and bis-spirooxindolehexahydropyrrolizines as the potent butyrylcholinesterase (BuChE) inhibitors was carried out using statistical methods, molecular dynamics and molecular docking simulation. QSAR methodologies include classification and regression tree (CART), multiple linear regression (MLR), principal component analysis (PCA) and principal component regression analysis (PCRA). Three descriptors in three classes: 3D-Morse, WHIM and GETAWAY descriptors were selected by SPSS software, and then applied in the final tree structure to describe the inhibitory activities. Docking simulations were carried out using AutoDock Vina software for all inhibitors. Docking results showed that the studied BuChE inhibitors have two commons binding modes. Molecular dynamics results obtained by Gromacs showed that the more potent inhibitor has the stronger interaction with the enzyme and higher effect on the enzyme structure. © 2018, Iranian Chemical Society.

This study was designed to investigate the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin (BSA) by means of various spectroscopic and electrochemical methods along with molecular docking study and molecular dynamics simulations. Binding constants were estimated by fluorescence and UV-Vis spectroscopy. The results indicated a good affinity of the complexes for BSA in which furyl derivative had more activity. Molecular docking study showed that these complexes have the similar binding modes and located within subdomain IB in site III of BSA. The supporting of molecular docking and molecular dynamics results by experimental data, confirms the validity of the interactions data obtained by these methods. Biological activity against cancer cell showed that furyl derivative has higher activity than other complexes. Pharmaceutical analysis also showed that, these complexes potentially can be used as anticancer agents. © 2017 Informa UK Limited, trading as Taylor & Francis Group

The aim of this study was synthesis of two new water-soluble fluorescent palladium and platinum complexes with formulas of [Pt(DACH)(FIP)](NO3)2 and [Pd(DACH)(FIP)](NO3)2, respectively, where FIP is 2-(furan-2-yl)-1H-imidazo[4,5-f][1,10] phenanthroline and DACH is 1R,2R-diaminocyclohexane. Fluorescence spectroscopy, circular dichroism (CD), thermal denaturation measurement, ionic strength, and kinetic study displayed groove binding of Pt complex on DNA, while due to binding of Pd complex, B form of DNA convert to Z form. Due to electrostatic interaction of Pd complex with DNA, the DNA form is converted and it provides enough space for Pd complex to insert between base stacking of DNA. UV–vis study shows two complexes could denature the DNA at low concentrations in exothermic process and Pt complex is more active than Pd complex. Finally, the anticancer and growth inhibitory activities of synthesized complexes were investigated against human colon cancer cell line HCT116 after incubation time of 24 h using MTT assay and higher activity was observed for the platinum complex. Interaction of the two metal derivative complexes was studied by molecular docking and molecular dynamics simulation. The results showed that Pt complexes have higher negative docking energy and higher tendency for interaction with DNA, and exert more structural change on DNA. © 2017 Informa UK Limited, trading as Taylor & Francis Group

A novel sensitive method for detection of DNA methylation was developed with thioglycollic acid (TGA)-capped CdTe quantum dots (QDs) as fluorescence probes. Recognition of methylated DNA sites would be useful strategy due to the important roles of methylation in disease occurrence and developmental processes. DNA methylation occurs most often at cytosine-guanine sites (CpG dinucleotides) of gene promoters. The QDs significantly interacted with hybridized unmethylated and methylated DNA. The interaction of CpG rich methylated and unmethylated DNA hybrid with quantum dots as an optical probe has been investigated by fluorescence spectroscopy and electrophoresis assay. The fluorescence intensity of QDs was highly dependent to unmethylated and methylated DNA. Specific site of CpG islands of Adenomatous polyposis coli (APC), a well-studied tumor suppressor gene, was used as the detection target. Under optimum conditions, upon the addition of unmethylated dsDNA, the fluorescence intensity increased in linear range from 1.0 × 10− 10 to 1.0 × 10− 6M with detection limit of 6.2 × 10− 11 M and on the other hand, the intensity of QDs showed no changes with addition of methylated dsDNA. We also demonstrated that the unmethylated and methylated DNA and QDs complexes showed different mobility in electrophoresis assay. This easy and reliable method could distinguish between methylated and unmethylated DNA sequences. © 2017, Springer Science+Business Media, LLC.

We study the transport properties of 4-((9,10-dioxo-9,10-dihydroanthracen-1-yl)oxy) benzaldehyde molecular optical switch by the first-principles calculations. Our molecule can reversibly switch between trans and ana forms by visible or UV irradiation. We studied many properties such as, I–V characteristics, the effect of electrode materials on electronic transport properties, on–off ratio and spatial distribution of molecular projected self-consistent Hamiltonian orbitals corresponding to both forms. The physical behavior of conductance interpret in terms of the HOMO–LUMO gap, the effective conjugation lengths, and size of the frontier molecular orbitals. Our results show, current through the ana form is higher than that the trans form. © 2017 Elsevier B.V.

A simple and efficient method has been developed for the synthesis of Quinazolines using SbCl3 as a heterogeneous catalysis at room temperature. This method provides a good pathway for the synthesis of 2,3-Dihydroquinazolin-4(1H)-ones derivatives in the terms of excellent yields and short reaction times. Also we studied theoretically and experimentally on 2-phenyl-2,3-dihydroquinazolin-4(1H)-one (PDQ). Using density functional theory (DFT), the tautomerism of PDQ was also studied. Thermal stability of PDQ was studied by thermo gravimetric analysis (TGA). The spectroscopic results and theoretical calculations indicate that the strength of intramolecular hydrogen bonding (IHB) of PDQ is stronger than that in 2-methyl-4-quinolinol (2MQ). The absorption spectra of the PDQ in solvents with different polarity were obtained and the results show that PDQ exists in both keto-amine and enol-imine forms in THF, while it has keto-amine form in other solvents. Theoretical results show that the conductance of the two tautomers (keto-amine and enol-imine) varies greatly, which offers that the potential usage of this molecule is as a molecular device. © 2017 Elsevier Ltd

The (Z)-4-(phenylamino) pent-3-en-2-one (PAPO) was synthesised applying carbon-based solid acid and described by experimental techniques. Calculated results reveal that its keto-amine form is more stable than its enol-imine form. A relaxed potential energy surface scan has been accomplished based on the optimised geometry of NH tautomeric form to depict the potential energy barrier related to intramolecular proton transfer. The spectroscopic results and theoretical calculations demonstrate that the intramolecular hydrogen bonding strength of PAPO is stronger than that in 4-amino-3-penten-2-one)APO(. In addition, molecular electrostatic potential, total and partial density of stats (TDOS, PDOS) and non-linear optical properties of the compound were studied using same theoretical calculations. Our calculations show that the title molecule has the potential to be used as molecular switch. © 2017 Informa UK Limited, trading as Taylor & Francis Group.

This study describes the thermodynamics of dissolution of flavonoid naringin in different aqueous solutions of dimethyl sulfoxide (DMSO) containing 0-100% (w/w) under atmospheric pressure and over a temperature range of 298.15 to 325.15 K. The temperature dependence of solubility of naringin was analyzed using the modified Apelblat equation model, ideal model, and the λH equation model. In a mean harmonic temperature, the dissolution thermodynamic parameters of naringin containing , and were also calculated. Furthermore, the effects of solvent composition on the solubility of this flavonoid were analyzed in terms of Hildebrand's solubility parameter (δH) and Kamlet, Abboud and Taft (KAT) solvatochromic parameters (α, β, and π*). Finally, the preferential solvation parameters of the flavonoid naringin by DMSO (δxDMSO,S) were determined from experimental solubility data using the inverse Kirkwood-Buff integrals (IKBIs). It was found that water preferentially solvates naringin in water-rich mixtures while DMSO forms local solvation shells in compositions from 50% (w/w) or xDMSO = 0.19 up to pure co-solvent. Moreover, the structure of solvation shells of naringin in the under study mixtures was obtained by molecular dynamics (MD) simulations. The computational results showed that in the compositions xDMSO > 0.20, the probability of presence of the DMSO molecules in vicinity of naringin is more than water molecules. These findings are compatible with the available IKBI data. © The Royal Society of Chemistry.

Studies on interaction of azo dyes with bovine serum albumin, as carrier protein, would be of particular importance in the field of toxicology that can help in better understanding of dye-protein interaction mechanism. In this regard, the interaction between the azo dye, trisodium (4E)-3-oxo-4-[(4-sulfonato-1-naphthyl) hydrazono] naphthalene-2,7-disulfonate (C20H11N2Na3O10S3), known as Amaranth, and bovine serum albumin (BSA) was studied using UV-Vis absorption, fluorescence spectroscopy, viscosity measurement and molecular docking studies. Also, the association behavior of Amaranth was investigated at its various concentrations and different ionic strengths (NaCl) in 5 mM aqueous phosphate buffer of pH 7.0 at 25 °C. From the spectrophotometric studies, the binding constant was determined. The value of the binding constant was Kb = 0.71 × 104 M-1 at 298 K. Thermodynamic parameters (ΔH > 0 and ΔS > 0) indicated that hydrophobic forces play a major role in the interaction between Amaranth and BSA. From the results of fluorescent experiments, the binding constants and the number of binding sites were obtained as Kb = 3.4 × 107 M-1 and 1.2901, respectively. By increasing the amount of Amaranth, a significant increase in viscosity of BSA was observed. The molecular docking method was employed to understand the interaction of Amaranth with BSA. The results showed that BSA has great affinity for interaction with Amaranth dye.

Alzheimer’s disease is causally linked to the aggregation of amyloid-β peptide and is one of the main causes of death in developed countries. Consumption of foods rich in polyphenolics is strongly correlated to reduced occurrence rate of Alzheimer’s disease. This paper compares the inhibition effect of amyloid-β aggregation in the presence of 25 polyphenolic compounds by quantitative structure–activity relationship (QSAR), molecular docking, and molecular dynamics simulation. The structure information such as solvent accessible surface area and radial distribution function was obtained at 300 K. The results showed that three compounds, luteolin, transilitin, and maritimetin, were identified as potent inhibitors of Aβ aggregation. Interaction energies between polyphenolic derivatives and β-amyloid were obtained using docking calculation. Computational docking studies offer a rational discussion for the observed inhibitory activity. Multiple linear regression method and principal component analysis were used to set up QSAR models for predicting anti-Alzheimer activity of 25 polyphenolics derivatives. These computational studies may facilitate in understanding the action mechanism and development of improved inhibitors of Aβ aggregation or modification of this series of the anti-Alzheimer agents. © 2016, Springer Science+Business Media New York.

This work presents a combined experimental and theoretical study on a photochromic compound, 2-([1,1’-biphenyl]-4-yl)-2-methyl-6-(4-nitrophenyl)-4-phenyl-1,3 diazabicyclo [3.1.0]hex-3-ene, existing in closed form (‘A’) and open form (‘B’). The spectroscopic properties of the title compound have been investigated by using IR, UV–Vis and 1H NMR techniques. The molecular geometry and spectroscopic data of the title compound have been calculated by using the density functional method (B3LYP) invoking 6-311G(d,p) basis set. UV-Vis spectra of the two forms were recorded. The excitation energies, oscillator strength, etc., were calculated by time-dependent density functional theory (TD-DFT). Furthermore, molecular electrostatic potential map (MEP), frontier molecular orbital analysis (HOMO–LUMO), total density of state (TDOS) and reactivity descriptors were found and discussed. We applied a first-principles computational approach to study a light-sensitive molecular switch. We find that the conductance of the two isomers varies dramatically, which suggests that this system has potential use as a molecular switch. [Figure not available: see fulltext.] © 2016, Indian Academy of Sciences.

4-((9,10-dioxo-9,10-dihydroanthracen-1-yl)oxy)-3-methoxybenzaldehyde has been synthesized in an attempt to obtain a new photochromic compound. The optimized molecular structure, mole fractions of title compound in trans and ana forms have been investigated. UV-visible spectra of the compound were also recorded. Upon irradiation with 300 nm light, the camel solid turned orange, in which a visible absorption band was observed at 475 nm. The electronic properties, such as HOMO, LUMO and band gap energies were obtained by the time-dependent DFT (TD-DFT) approach. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Transition structures were calculated by QST3 and IRC methods which yielded the potential energy surface and activation energy. © 2016, Pleiades Publishing, Ltd.

Effects of sodium (octyl, dodecyl, hexadecyl) sulfate and their cationic analogous on the structure of adenosine deaminase (ADA) were investigated by fluorescence and circular dichroism spectroscopy as well as molecular dynamics simulation and docking calculation. Root-mean-square derivations, radius of gyration, solvent accessible surface area, and radial distribution function were obtained. The results showed that anionic and cationic surfactants reduce protein stability. Cationic surfactants have more effect on the ADA structure in comparison with anionic surfactants. More concentration and longer surfactants are parallel to higher denaturation. Furthermore, aggregation in the presence of anionic surfactants is more than cationic surfactants. Docking data showed that longer surfactants have more interaction energy and smaller ones bound to the active site. © 2015 Informa UK Limited, trading as Taylor & Francis Group.

This paper presents a combined experimental and theoretical study on an ortho-hydroxy Schiff base compound, (E)-1-(4-(2-hydroxybenzylideneamino)phenyl)ethanone. The spectroscopic and electrochemical properties of the compound were determined using IR, UV–vis and 1H, 13C NMR as well as cyclic voltammetry techniques. The hydrogen bond strength was studied using the spectroscopic results, geometry calculations, topological and NBO analysis. The results showed that the predicted nonlinear optical (NLO) properties of the title compound are much greater than those of urea. Thermodynamic properties in the range from 100 to 505 K were obtained. Furthermore, molecular electrostatic potential, Fukui functions, thermodynamic, frontier molecular orbital analysis, reactivity descriptors and NLO properties were found and discussed. Theoretical results show that the conductance of the two tautomers varies seriously, which offers that this molecule has potential usage as a molecular device. © 2016 Informa UK Limited, trading as Taylor & Francis Group.

The experimental and theoretical studies on asymmetrical Schiff base, salicylideneimino-ethylimino-pentan-2-one (SEIPO) were studied. The tautomerism of SEIPO was also studied by calculations using density functional theory (DFT). Two of the four tautomers were shown to coexist. Tautomerism and the effect of solvent on the tautomeric equilibria in the gas phase and in different solvents were studied. According to calculated results, L3, L4 tautomers are more stable than the L1, L2 tautomers. The 1H NMR spectra give the additional evidence for the coexistence of the tautomers keto-amine and enol-imine for SEIPO. UV-vis spectra of SEIPO were recorded in various organic solvents to check the dependence of tautomerism on solvent types. The theoretical calculations and spectroscopic results indicate that the intramolecular hydrogen bonding (IHB) strength of SEIPO is stronger than that in 4-amino-3-penten-2-one)APO(. In addition, natural atomic charges, global reactivity parameters, and HOMO-LUMO gaps have also been discussed. © 2016 Elsevier B.V. All rights reserved.

The present study aimed to determine an efficient and solvent-free method to synthesize 2-methyl-4-quinolinol (2MQ, also known as 4-hydroxy-2-methylquinoline) and includes spectroscopic investigations and computational studies. Molecular geometry and vibrational wavenumbers of 2MQ were investigated using the density functional (DFT/B3LYP) method with 6-311++G(d,p) and 6-311++G(2d,p) basis sets. According to calculations, the keto form of 2MQ is more stable than the annual form, and the dimeric conformation is predicted to be more stable than the monomeric conformations. A detailed analysis of the nature of the hydrogen bonding, using topological parameters such as electronic charge density, Laplacian, kinetic and potential energy density evaluated at the bond critical point, is also presented. The 1H nuclear magnetic resonance chemical shifts of the molecule were calculated by the GIAO method. The molecule orbital contributions were studied by using total (TDOS) and partial (PDOS) density of states. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were investigated by the time-dependent DFT (TD-DFT) approach. The linear polarizability (α) and the first-order hyperpolarizability (β) values of the investigated molecule were computed using DFT quantum mechanical calculations. The results show that the 2MQ molecule may have a nonlinear optical comportment with non-zero values. The stability and charge delocalization of the molecule was studied by natural bond orbital analysis. In addition, a molecular electrostatic potential map of the title compound was studied for predicting the reactive sites. Local reactivity descriptors, such as Fukui functions, local softness and electrophilicity indices analyses, were studied to determine the reactive sites within the molecule. © 2015 Springer Science+Business Media Dordrecht.

To investigate the interaction and adsorption of drug and carbon nanotube on human serum albumin, three anti-cancer drugs ([Pd(phen)(R-gly)]NO3, R = methyl, propyl and amyl) with different hydrophobic tails and anticancer activities were selected. These drugs have better anti-tumor activity and less side effects than that known cis-platinum drug. Human serum albumin is also important for drug delivery and release and acts as carrier of internal biological molecules and external drugs that bind to many drugs in blood route and carry them. Drug binding to human serum albumin can change its helicity and this can affect on the drug release and distribution. Thus, study of this aspect can provide structural features determining the therapeutic efficiency of drug that has the least effect on human serum albumin helix structure. Interaction of three drugs with human serum albumin was investigated by molecular dynamics simulation and the best drug with the least denaturation effect was selected to compare its effect in the presence of nanotube. The structure of protein was again compared in the presence of drug and nanotube. The results revealed less denaturation effect of methyl on human serum albumin structure. The denaturation of protein also decreased more in the presence of nanotube. Carbon nanotube can be used as a cover for denaturation effect of drug and leads to better orientation and less random movement of drug around protein. It also reveals drug interaction with protein binding site facilitated in the presence of carbon nanotube.

In this study, we have investigated how to control the net flux of water molecules transported through a CNT using an orthogonal and axial electric field. The flow of water molecules through CNT decrease as the orthogonal electric field strength (E) increased from 1 to 3 V nm-1. When E increases over 3 V nm-1, the flow of water molecules through the CNT was turned off and zero water flow was observed. Both the number of water molecules in tube and free energy values was influenced by water flow. A reverse behavior was observed in the case of axial electric field by constantly maintaining electric field direction in the direction of the water flow. Increase of water flow with E of axial electric field was revealed and it can be concluded that water permeation through CNT is much sensitive to the axial electric field strength than the orthogonal electric field. © 2015 Pleiades Publishing, Ltd.

A three-component, NBS-promoted synthesis of α,β-unsaturated isoxazol-5(4H)-ones by reaction of aromatic aryl or hetero-aryl aldehydes, hydroxylamine hydrochloride, and 1,3-dicarbonyl compounds (ethyl acetoacetate or ethyl 4-chloroacetoacetate), under mild reaction conditions at room temperature is described. This simple, efficient, and clean reaction is an expeditious means of obtaining the corresponding isoxazol-5(4H)-one derivatives in good to high yields. Geometrical properties and vibrational wavenumbers of 3-methyl-4-(thiophen-2-ylmethylene)isoxazol-5(4H)-one (MTISO) were predicted by use of density functional theory (DFT) by use of the B3LYP level with the 6-311++G(d,p) and 6-311++G(2d,p) basis sets. Results indicate that the B3LYP method enables satisfactory prediction of vibrational frequencies and structural data. The absorption spectra of MTISO in solvents of different polarity were studied at room temperature. The UV-visible spectrum of the compound was recorded and such electronic properties as the energies of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) were determined by the time-dependent DFT (TD-DFT) approach. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization was studied by NBO analysis. A molecular electrostatic potential map (MEP) of the compound was also studied to predict reactive sites. Reactivity descriptors, Fukui functions, and electrophilic sites were found and are discussed. The thermal stability of MTISO was studied by thermogravimetric analysis (TGA). © 2014 Springer Science+Business Media Dordrecht.

Abstract The Schiff base compound (E)-1-(4-(4-(diethylamino)-2-hydroxybenzylideneamino)phenyl)ethanone has been synthesized and characterized by IR, UV-Vis, and 1H and 13C NMR techniques. These properties of title compound were also investigated from calculative point of view. UV-Vis spectra of the title compound were recorded in different organic solvents to investigate the dependence of tautomerism on solvent types. Calculated results reveal that its enol form is more stable than its keto form. A detailed analysis of the nature of the hydrogen bonding, using topological parameters, evaluated at bond critical points. © 2015 Springer Science+Business Media New York.

Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Followings are the observed changes in the spectral properties of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP), as a free-base porphyrin with no axial ligand, and its Fe derivative (FeTMAP) upon interaction with oligo(dA.dT)15 and oligo(dG.dC)15: (1) the substantial red shift and hypochromicity at the Soret maximum in the UV-vis spectra; (2) the increased RLS intensity by increasing the ionic strength; and (3) an intense bisignate excitonic CD signal. All of them are the reasons for TMAP and FeTMAP binding to oligo(dA.dT)15 and oligo(dG.dC)15 with the outside binding mode, accompanied by the self-stacking of the ligands along the oligonucleotide helix. The CD results demonstrated a drastic change from excitonic in monomeric behavior at higher ionic strengths, which indicates the groove binding of the ligands with oligonucleotides. Molecular docking also confirmed the groove binding mode of the ligands and estimated the binding constants and energies of the interactions. Their interaction trend was further confirmed by molecular dynamics technique and structure parameters obtained from simulation. It showed that TMAP reduced the number of intermolecular hydrogen bonds and increased the solvent accessible surface area in the oligonucleotide. The self-aggregation of ligands at lower concentrations was also confirmed. © 2014 © 2014 Taylor & Francis.

Interaction of 1,3-bis(2-hydroxy-benzylidene)-urea (H2L1), 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea (H2L2) and 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea nickel(II) (NiL2) with calf-thymus DNA were investigated by UV-vis absorption, fluorescence emission and circular dichroism (CD) spectroscopy as well as cyclic voltammetry, viscosity measurements, molecular docking and molecular dynamics simulation. Binding constants were determined using UV-vis absorption and fluorescence spectra. The results indicated that studied Schiff-bases bind to DNA in the intercalative mode in which the metal derivative is more effective than non metals. Their interaction trend is further determined by molecular dynamics (MD) simulation. MD results showed that Ni derivative reduces oligonucleotide intermolecular hydrogen bond and increases solvent accessible surface area more than other compounds. © 2015 Elsevier B.V.

The interaction of three novel synthesized complexes of [Pd(phen)(R-gly)]NO3, where R-gly is methyl-, propyl-, and amyl-glycine; and phen is 1,10-phenanthroline were synthesized and characterized by spectroscopic methods. The interaction of ct-DNA with different concentrations of these palladium(II) complexes were studied by UV-Vis, fluorescence, circular dichroism spectroscopy, viscometric, and voltammetric measurements in Tris-HCl buffer solution containing 10 mM sodium chloride (pH 7.2) at 27 and 37 °C as well as molecular dynamics (MD) simulation and molecular docking. The biological activity of the synthesized Pd(II) complexes was tested against chronic myelogenous leukemia cell line K562 at micromolar concentrations. Binding constants obtained by UV-Vis spectroscopy for methyl, propyl and amyl derivatives are as 5.08 × 105, 5.55 × 105, 7.08 × 105 at 27 °C and 5.53 × 105, 6.54 × 105, 10.01 × 105 M-1 at 37 °C, respectively. The experimental results suggested that these complexes cooperatively bind to DNA presumably via intercalation. Moreover, these Pd(II) complexes showed higher tendency to interact with DNA at higher concentrations and temperatures. These Pd complexes increase the Tm, viscosity, and helicity of DNA solution. The binding data shows that methyl-derivative has higher tendency for binding to DNA. The trend of changes in the structural parameters such as calculated ASA, RMSD, hydrogen bond, and experimental viscosity were amyl > propyl > methyl. The results suggest that the synthesized Pd(II) complexes have dose-response suppression on growing of K562 leukemia cell line. Also, according to Cc50 values, it is clear that the Pd(II) complex of methylglycine has higher cytotoxic or anti-proliferative effect against K562 leukemia cell line. © 2015 Elsevier B.V. All rights reserved.

Spontaneous encapsulation of drugs into carbon nanotubes (CNTs) has attracted great interest because of their importance in biological and biomedical devices. In this work, the diameter dependence of 20 drugs on the carbon nanotube size was explored via molecular dynamics (MD) simulation. Negative free energy of interaction, reduced potential of mean force, reduced CNT-drug distance, and reduced number of water molecules after encapsulation confirm the encapsulation of the drug into the smallest possible size of CNT. The variations of the radius of gyration of the CNTs and drugs were compared to explore the correlation trend. One of the factors influencing the encapsulation and insertion of drug is the size of the nanotube. In addition, the linear correlation between the drug and the nanotube size was confirmed by quantitative structure-property relationship (QSPR) analysis, and themultiple linear regression (MLR) method was applied to develop the correlation model. The regression parameter provided by the MLR method was R2 = 0.99 for prediction of the drug gyration radius. The MLR prediction confirms that the larger drug molecule prefers to locate inside a larger CNT, which agrees with MD data. It was found that there is π-π interaction between the oxygen atoms and the aromatic ring of some of the drugs and the aromatic rings of CNTs are conjugated; this helps the drug molecule to locate inside the CNT. These theoretical methods provide a simple, detailed, and alternative method to obtain optimal tube size for encapsulation. © 2015 Korean Chemical Society, Seoul & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular dynamics simulations at 270 and 310 K rationalized the effect of urea, temperature and the size of the carbon nanotube, on the insertion of Tretinoin into nanotubes with chirality (10, 7) and (8, 5). Concentrations of 0.9 mmol L-1 and 2 mol L-1 of urea are studied, that are less and more than the normal range of blood urea content, respectively. Results show that encapsulation of Tretinoin could be ascribed to the flow of the waters via hydrophilic and van der Waals interactions and diameter of the nanotube. Heat capacity, diffusion coefficient, free energy and contact coefficient change with the temperature and urea. Tretinoin molecule locates inside the nanotube due to the partial ππ interactions between oxygen atom of Tretinoin and the conjugated aromatic rings of nanotube. Finally, high concentration of urea causes the striking phenomenon of inducing the drying of nanotube that result in urea wires and instability of encapsulation.

A new strategy was introduced for ssDNA immobilization on a modified glassy carbon electrode. The electrode surface was modified using polyaniline and chemically reduced graphene oxide decorated cerium oxide nanoparticles (CeO2NPs-RGO). A single-stranded DNA (ssDNA) probe was immobilized on the modified electrode surface. Fast Fourier transform square wave voltammetry (FFT-SWV) was applied as detection technique and [Ru(bpy)3]2+/3+ redox signal was used as electrochemical marker. The hybridization of ssDNA with its complementary target caused a dramatic decrease in [Ru(bpy)3]2+/3+ FFT-SW signal. The proposed electrochemical biosensor was able to detect Aeromonas hydrophila DNA oligonucleotide sequence encoding aerolysin protein. Under optimal conditions, the biosensor showed excellent selectivity toward complementary sequence in comparison with noncomplementary and two-base mismatch sequences. The dynamic linear range of this electrochemical DNA biosensor for detecting 20-mer oligonucleotide sequence of A. hydrophila was from 1 × 10-15 to 1 × 10-8 mol L-1. The proposed biosensor was successfully applied for the detection of DNA extracted from A. hydrophila in fish pond water up to 0.01 μg mL-1 with RSD of 5%. Besides, molecular docking was applied to consider the [Ru(bpy)3]2+/3+ interaction with ssDNA before and after hybridization. © 2015 Elsevier B.V.

Co(II)-tetrasulfonated phthalocyanine (CoTSP) is known to be aggregated to dimer at high concentration levels in water. A study on the aggregation of CoTSP using multivariate curve resolution analysis of the visible absorbance spectra over a concentration range of 30, 40 and 50 μM in the presence of dimethyl sulfoxide (DMSO), dimethyl formamide (DMF), acetonitrile (AN) and ethanol (EtOH) in the concentration range of 0 to 3.57 M is conducted. A hard modeling-based multivariate curve resolution method was applied to determine the dissociation constants of the CoTSP aggregates at various temperatures ranging from 25, 45 and 65 °C and in the presence of various co-solvents. Dissociation constant for aggregation was increased and then decrease by temperature and concentration of phthalocyanine, respectively. Utilizing the vant Hoff relation, the enthalpy and entropy of the dissociation equilibriums were calculated. For the dissociation of both aggregates, the enthalpy and entropy changes were positive and negative, respectively. Molecular dynamics simulation of cosolvent effect on CoTSP aggregation was done to confirm spectroscopy results. Results of radial distribution function (RDF), root mean square deviation (RMSD) and distance curves confirmed more effect of polar solvent to decrease monomer formation.

The molecular structure, vibrational frequencies, corresponding vibrational assignments of 4-((9,10-dioxo-9,10-dihydroanthracen-1-yl)oxy)benzaldehyde in "trans" and "ana" forms have been investigated by UV-Vis, FT-IR and NMR spectroscopy as well as density functional theory (DFT) B3LYP method with 6-311++G(d,p) basis set. The vibrational analysis of the two forms of cited compound was performed by means of infrared absorption spectroscopy in combination with theoretical simulations. The obtained geometrical parameters and wavenumbers of vibrational normal modes from the DFT method were in good consistency with the experimental values. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. Computed molecular orbital and time dependent DFT oscillator renderings agree closely with experimental observations. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. In order to predict the reactive sites, a molecular electrostatic potential map (MEP) for the title compound was obtained. Transition structures were calculated by QST3 and IRC methods which yielded the potential energy surface and activation energy. © 2014 Elsevier B.V. All rights reserved.

Quantitative structure-activity relationship (QSAR) study on a series of HIV-1 reverse transcriptase inhibitors (diaryltriazines, DATAs) was carried out using suitable molecular descriptors calculated by Hyperchem and Dragon softwares. Chemometrics methods including multiple linear regression, principal component analysis, and principal component regression analysis, were used to set up QSAR models to predict anti-HIV-1 activity of DATAs derivatives. Correlation coefficient obtained by different methods were compared with each other. Cross-validation was applied to verify the validity of models. The results showed that aromatic, nonpolar, and planar molecules have higher anti-HIV activity, and the substituent at C(4) of triazine ring is important in DATAs against HIV-1 RT wild-type. Docking study was performed using AutoDock program on all the compounds. Using docking study, it has shown that all the studied DATAs derivatives bind to the HIV-1 RT and have a common binding modes. The most active inhibitors had higher hydrogen bond and π-π stacking with receptor. These computational studies can offer useful references for understanding the action mechanism and molecular design or modification of this series of the anti-HIV agents. © 2013 Springer Science+Business Media New York.

Kinetic study of the reaction of flavonoid naringenin with the stable free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) was performed in different percentage compositions of aqueous ethanol (50-90% v/v) using spectrophotometric method. The reaction, which follows the mixed second-order rate law, was investigated under pseudo first-order conditions with respect to the DPPH radical, at (25.0 ± 0.1) °C and an ionic strength of 0.1 mol dm - 3. The rate of reaction was found to decrease with increasing organic solvent content in binary mixture. The reaction mechanism was inferred from the stoichiometry, kinetics, and product identification. Furthermore, the effects of solvent composition on the reaction rate in the mixed solvents were analyzed in terms of Reichardt parameter (ETN), and Kamlet, Abboud and Taft (KAT) solvatochromic parameters (α, β, and π*). To further investigate the solvent effects we theoretically studied the three antioxidant action mechanisms of naringenin using density functional theory (DFT) method. Reaction enthalpies related to these mechanisms were calculated in gas-phase, water, ethanol and 50-90% (by v/v) ethanol-water. It was found that theoretical findings are in good agreement with experimental results. © 2014 Elsevier B.V.

Studies on the interactions between metallodrugs and human serum albumin (HSA), as carrier for drugs and biological molecules, are extremely important to design and discover new drugs. The interaction of three novel synthesized complexes of [Pd(phen)(R-gly)]NO3, where R-gly is methyl-, propyl-, and amyl-glycine and phen is 1,10-phenanthroline, with HSA were investigated using spectroscopic studies in combination with a molecular dynamic simulation. These water soluble complexes can denature HSA at ∼50 μM. According to the results obtained for the isothermal titration at 27 and 37°C, it was found that there are 10, 8, and 6 binding sites (g) for methyl-, propyl-, and amyl-glycine complexes on the HSA with positive cooperativity in binding, respectively. Also, the binding and thermodynamic parameters were analyzed. We found a good consistency between secondary structure and simulation data with spectroscopic studies, and the experimental data are confirmed by molecular simulation results. In addition, the results related to helix, beta sheets, and coil percentages revealed that all complexes decrease the helix structure and increase the beta structure;; and that the amyl derivative is more effective in denaturing the HSA structure. © 2014 Bentham Science Publishers.

A di-copper(II) complex of the formula [(dien)Cu(μ-1,6-DAH)Cu(dien) (NO3)2](NO3)2, where μ-1,6-DAH = 1,6-diaminohexane, has been synthesized and characterized by X-ray crystallography, X-ray powder diffraction, thermal gravimetric (TG) and differential thermal analyses, cyclic voltammetry, infrared, ultraviolet visible spectroscopies and elemental analysis methods. It was crystallized in a monoclinic system, space group P21/n, with a = 8.0297(8) Å, b = 12.4937(14) Å, c = 15.3786(15) Å, β = 102.739(8) Å and z = 2. Each copper(II) has a square-based pyramidal coordination geometry with four N atoms building the basal plane (three from dien and one from μ-1,6-DAH). TGA study of the complex revealed the compound to be stable up to 245 °C. Electrochemical behavior of complex and enzyme-like catalytic activity of this complex, as a potential functional model for the active site of tyrosinase, was studied extensively. Kinetic studies show that the complex has the maximum enzymatic activity at pH 8, temperature of 40 °C and ionic strength of 50 mM. © 2014 Iranian Chemical Society.

The interaction of gold(III) trichlorophenanthridine complex, [Au(phend)Cl3], with calf thymus DNA was investigated by UV-Vis absorption, circular dichroism, and fluorescence spectrophotometery as well as viscometry, cyclic voltammetry (CV), and molecular docking. The values of binding constants K b (obtained by UV-Vis) and K f (obtained by fluorescence) are 3 × 104 and 7.68 × 10 5 M-1, respectively. Evidence for intercalation comprised a hyperchromic effect at 210 nm and a hypochromic effect at 250 nm caused by the ligand, increasing the T m of DNA, increasing of viscosity, increasing the intensity of the positive peak, decreasing the intensity of the negative peak, and the positive shift of the cathodic peak potential in CV. © 2013 Springer-Verlag Wien.

This paper compares the inhibition effect of porphyrin aggregation in the presence of urea, guanidinium chloride (Gdn) and sorbitol by molecular dynamics simulation. It demonstrates that porphyrin aggregation increases in sorbitol, but decreases towards addition of urea and Gdn. It shows that urea, Gdn and sorbitol can have a large effect - positive or negative, depending on the concentration - on the aggregation of the porphyrin. The effect of urea, Gdn and sorbitol on porphyrin aggregation has been inferred from the effect of these solutes on the hydration layer of porphyrin. It appears that the Gdn is more suitable than urea for decreasing the hydration layer of porphyrin while several osmolites like sorbitol are known to increase hydration layer and thus might stabilize the porphyrin aggregation. Results of radial distribution function (RDF), distributed atoms or molecules around target species, indicated that the increase and exclusion of solvent around porphyrin by osmolytes and Gdn would affect significantly on porphyrin aggregation. There was a sizeable difference in potency between the Gdn and urea, with the urea being less potent to decrease hydration layer and porphyrin aggregation. [Figure not available: see fulltext.] © 2013 Indian Academy of Sciences.

The effect of two ionic liquids, 1-allyl 3-methyl-imidazolium (IL1) and 1-octhyl 3-methyl-imidozolium chlorides (IL2), on the structure and activity of adenosine deaminase (ADA) were described by UV-vis and fluorescence spectrophotometry in phosphate buffer and results were compared with docking and molecular dynamics (MD) simulation studies. All results showed that inhibition of activity and reduction of enzyme tertiary structure are more for octhyl than allyl derivative due to the more hydrophobic property of it. Finally structure parameters obtained from MD simulation showed that ionic liquid reduces intermolecular hydrogen bond and unfold enzyme structure. Calculation results are in good agreement with spectrophotometric studies. © 2013 Elsevier B.V.

Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work, all-atom molecular dynamic simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chloride (GdmCl) at 273-395 K by molecular dynamics simulation. Analysis of surface area, radial distribution function, radius of gyration, heat capacity, hydrogen bond, helix, coil and beta contents showed that an intermediate appears on the way of helix to coil transition. GdmCl at low concentration increases the midpoint of transition temperature (Tm), number of solvent molecules in the hydration layer and interapeptide hydrogen bond as well as decreases in rate of helix to coil transition. Thus, the role of guanidine at low concentration is as the same as osmolytes which decreases the beta form and, increases hydration layer and the polypeptide thermal stability.

A water-soluble Cu (II) complex [(dien)Cu (l-1,6-DAH)Cu(dien) (NO 3)2](NO3)2 has been synthesized and its effect on the carrier model DNA structure and cancer cell line proliferation was investigated. In this regard, calf thymus DNA (CT-DNA) and human breast cancer cell line, T47D, were the targets. The effect of the complex on DNA structure was investigated by means of UV/vis, fluorescence and circular dichroism (CD) spectroscopic techniques as well as dynamic light scattering (DLS), zeta potential analysis and docking assay for more analysis. The UV-vis absorption spectra of complex withDNAshowed a slight red shift and hypochromic effect, which indicated the intercalation and electrostatic effect of complex with CT-DNA. Using ethidium bromide (EB) as a probe in fluorescence studies revealed that complex can quench the EB-DNA fluorescence emission at different temperatures. Besides, the far UV-CD studies displayed that the complex induces changes in the secondary structure of CT-DNA and can increase the melting temperature of DNA up to 14 °C. The DLS and zeta potential measurements confirmed the electrostatic interaction of complex with the negatively charged DNA and subsequent DNA condensation. Besides, computational studies reflect that major and minor groove binding are two modes of interaction between complex andDNA. On the other hand, growth inhibition of the complex toward T47D cell line was measured using 3-(4,5-dimethylthiazol- 2-yl)-2,5-diphenyltetrazolium bromide assay, which showed no cytotoxic properties. © Iranian Chemical Society 2012.

Due to increasing of population of diabetic patients, identifying factors for disease control has received much attention, α-glucosidase (EC 3.2.1.20) is an essential enzyme that helps to digestion of carbohydrates such as starch and sugar. Carbohydrates are normally converted into simple sugars, which can be absorbed through the intestine. Therefore, α-glucosidase inhibitors can be used to decrease the blood sugar level. We have studied the effect of inhibition of N-(phe-noxydecyl) phthalimide derivatives by a computer drug-design protocol involving homology modeling, docking simulation and Quantitative Structure Activity Relationship. The homology modeling of a-glucosidase showed a structure very similar to the crystal structure of oligo-l,6-glucosidase from Saccharomyces cerevisiae. Docking results showed the position of inhibitors binding site is close to active site and the carboxyl oxygen in phthalimide is an effective functional group for binding inhibitors to protein. The equation obtained by QS AR showed that, logIC 50 decreases and so inhibition property increases when the size, polarity, geometry and number of halogen factors increase.

Aggregation kinetics of a porphyrin derivative in the absence and presence of different concentrations, below and above the critical micelle concentration (CMC) of three ionic liquids (ILs); 1-octyl-3-methylimidazolium, 1-dodecyl-3-methyl imidazolium and 1-octadecyl-3-methylimidazolium chloride was studied using molecular dynamics simulation. Effect of IL, with different chain lengths on the aggregation of a porphyrin derivative, 5,10,15,20-tetrakis(2,5- dihydroxyphenyl)porphyrin, was investigated. The low amount of each ionic liquid (below CMC) observed to favors the formation of aggregates; further increasing ionic liquid concentration leads to the destabilization of aggregates. The compared calculated rate constants also support these results. Aggregation of imidazolium ILs proved to take place with longer alkyl chains that favors aggregation. © 2012 World Scientific Publishing Company.

Kinetic and structural studies have been carried out on the effects of meso-tetrakis(4-sulfonatophenyl)- porphyrin (H2TPPS4) as an anionic and meso-tetrakis(3-N-methyl-pyridyl)porphyrin (H2TMPYP) as a cationic porphyrin with adenosine deaminase (ADA) in 25 mM citrate/phosphate buffer, pH = 4-8, at 37 °C using UVvis spectrophotometry, circular dichroism (CD), fluorescence spectrophotometry as well as molecular dynamics (MD) and molecular docking. Kinetic results showed that the two porphyrins are non-competitive inhibitors. Increasing pH, increases KI and cationic porphyrin has a higher KI and lower binding constant (Kb) at all pH ranges. Analyzing the secondary structure revealed that both ligands decrease the secondary structure and that the anionic porphyrin is more effective.

The aggregation of 85 porphyrin derivatives and a report on a kinetic and thermodynamic study of such aggregation behavior on varying the derivatives of porphyrin was carried out using molecular dynamics simulation and Docking. Distance diagrams of simulated compounds were obtained and decrease of curves is a clear evidence of the aggregation. Aggregation rates were studied by origin software. In order to calculate interaction energies of derivatives, compounds were docked and the equilibrium constant of porphyrin-porphyrin interaction were obtained. Quantitative Structure-Property Relationship (QSPR) studies were performed for the sets of 85 Porphyrin derivatives. Multiple Linear Regression method (MLR) and Principal Component Analysis (PCA) were used and resulted in useful models with good prediction ability. This models were able to predict the kinetic and equilibrium constant for all sets of our compounds. The correlation coefficients for prediction of rate and logarithm of equilibrium constants were 0.67 and 0.97 by MLR method respectively and 0.90 for prediction of equilibrium constant by PCA analyses. In order to have a better prediction, compounds were divided into two groups, oxygenated and non-oxygenated group and correlation coefficient for prediction of rate constants of them were obtained 0.89 and 0.94 by MLR model respectively. Results of structure-property relationship showed that, larger, more hydrophobe and more planner derivatives have higher aggregation rate. © 2011 World Scientific Publishing Company.

The pharmacokinetics and pharmacodynamics of any drug will depend, largely, on the interaction that has with human serum albumin (HSA), the most abundant plasma protein. The interaction between newly synthesized Pd(II) complexe, 2, 2′-bipyridin Butylglycinato Pd(II) nitrate, an anti-tumor component, with HSA was studied at different temperatures by fluorescence, far UV circular dichroism (CD), UV-visible spectrophotometry and theoretical approaches. The Pd(II) complex has a strong ability to quench the intrinsic fluorescence of HSA through a dynamic quenching procedure. The binding parameters and thermodynamic parameters, including ΔH°, ΔS° and ΔG° were calculated by fluorescence quenching method, indicated that hydrophobic forces play a major role in the interaction of Pd(II) complex with HSA. Based on Autodock, FRET (fluorescence resonance energy transfer) and fluorescence quenching data, it may be concluded that one of the binding sites in the complex of HSA is near the only one Trp of HSA (Trp214) in sub domain IIA of the protein. Far-UV-CD results indicated that Pd(II)-complex induced increase in the α-helical content of the protein. The anti-tumor property of the synthesized Pd(II) complex was studied by testing it on human tumor cell line K562. The 50% cytotoxic concentration (Cc50) of complex was determined using MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl tetrazolium bromide) assay. Also, fluorescence staining with DAPI (4, 6-diamidino-2-phenylindole) revealed some typical nuclear changes that are characteristic of apoptosis which is induced at Cc50 concentration of Pd(II) complex in K562 cell line after 24 h incubation. Our results suggest that Pd(II) complex is a promising anti-proliferative agent and should execute its biological effects by inducing apoptosis. © 2011 Taylor & Francis Group, LLC.

Electrochemical behavior of some anthraquinone (Aq) derivatives were investigated in acetonitrile (AN), N,N-dimethyl formamide (DMF) and dimethylsulfoxide (DMSO) by cyclic voltammetry (CV), quantum mechanics and statistical methods. A reasonable correlation between the computational and experimental standard reduction potential (E°) for electron transfer was obtained. It was concluded that the first step reduction potential, E°1 in acetonitrile, increases with hydrogen bonding, aromaticity and HOMO energy and decreases with size and polarity of anthraquinone. Trend of average values for E°1 in three solvents is AN < DMSO < DMF, while the trend of E°₂ is inversely. The E°₁values increase with polarity, dielectric constant, molecular size and hydrogen bonding of solvent and this trend is reverse in the case of E°₂values. Difference in trend of reduction potential is related to solutesolvent and solvent interactions. Solvent effect in the explicit model presents better correlation with experimental E°. © 2010 by ESG.

Le Chatelier's principle states that when a system is disturbed, it will shift its equilibrium to counteract the disturbance. However for a chemical reaction in a small, confined system, the probability of observing it proceed in the opposite direction to that predicted by Le Chatelier's principle, can be significant. This work gives a molecular level proof of Le Chatelier's principle for the case of a temperature change. Moreover, a new, exact mathematical expression is derived that is valid for arbitrary system sizes and gives the relative probability that a single experiment will proceed in the endothermic or exothermic direction, in terms of a microscopic phase function. We show that the average of the time integral of this function is the maximum possible value of the purely irreversible entropy production for the thermal relaxation process. Our result is tested against computer simulations of the unfolding of a polypeptide. We prove that any equilibrium reaction mixture on average responds to a temperature increase by shifting its point of equilibrium in the endothermic direction. © 2009 American Institute of Physics.

Effects of some diacid, diamine and dinitro aromatic compounds on the structure and activity of adenosine deaminase (ADA) were investigated by UV-Vis spectrophotometry in 50 mM phosphate buffer at pH = 7.5 and 27°C and molecular docking studies. The results showed that all tested ligands are showing inhibition; five ligands are uncompetitive and other two ligands are mixed of competitive and noncompetetive inhibitors with majority of competitive behavior. For the later case analysis was done based on competitive inhibition. Diacids have larger size and higher inhibition constant (KI) relative to others. A logical correlation between calculated free energy of binding and experimental values was obtained for un-competitive. Experimental and calculated data showed that competitive inhibitors are distributed near the active site of enzyme and form several cluster of ranks, whereas uncompetitive inhibitors bind to the enzyme-substrate complex and distributed far from the active site. Results of structure-activity relationship showed that, larger, more hydrophobe, less spherical and more aromatic ligands have higher inhibition constants.

The relationship between thermal decomposition temperature and structure of a new data set of eighty monomers of different polymers were studied by multiple linear regression (MLR). The stepwise method was used in order to variable selection. The best descriptors were selected from over 1400 descriptors including; topological, geometrical, electronic and hybrid descriptors. The effect of number of descriptors on the correlation coefficient (R) and F-ratio were considered. Two models were suggested, one model having four descriptors (R2 = 0.894, Q2 cv = 0.900, F = 172.1) and other model involving 13 descriptors (R2 = 0.956, Q 2 cv = 0.956, F = 125.4).

Effects of sodium dodecyl sulfate, dodecyltrimethylammonium bromide, sodium chloride, sodium sulfate, methanol and ethanol, on the structure and activity of adenosine deaminase (ADA) were investigated by UV-Vis, circular dichroism spectrophotometry and molecular dynamics (MDs) studies. Relative activity, experimental and computational helix content, total accessible surface area (ASA) and exposed charged surface area (ECSA) were obtained. The relative activity of ADA in the absence and the presence of denaturants were compared with structural results. It was shown that an increase in the surface area and a decrease in the amount of helicity are associated with a decrease in the activity of ADA. © 2008 Elsevier B.V. All rights reserved.

The kinetic and thermodynamic effects of aspirin and diclofenac on the activity of adenosine deaminase (ADA) were studied in 50 mM phosphate buffer pH = 7.5 at 27 and 37°C, using UV-Vis spectrophotometry and isothermal titration calorimetry (ITC). Aspirin exhibits competitive inhibition at 27 and 37°C and the inhibition constants are 42.8 and 96.8μM respectively, using spectrophotometry. Diclofenac shows competitive behavior at 27°C and uncompetitive at 37°C with inhibition constants of 56.4 and 30.0 μM, at respectively. The binding constant and enthalpy of binding, at 27°C are 45 μM, -64.5kJ/mol and 61 μM, - 34.5 kJ/mol for aspirin and diclofenac. Thermodynamic data revealed that the binding process for these ADA inhibitors is enthalpy driven. QSAR studies by principal component analysis implemented in SPSS show that the large, polar, planar, and aromatic nucleoside and small, aromatic and polar non-nucleoside molecules have lower inhibition constants.

The interaction of a polyoxometal (POM), K6SiW 11Co(H2O)O39.10H2O (K6) as a Keggin, with human serum albumin (HSA) was studied by different methods and techniques. Binding studies show two sets of binding sites for interaction of POM to HSA. Binding analysis and isothermal calorimetery revealed that, the first set of binding site has lower number of bound ligand per mole of protein ( ν), lower Hill constant (n), higher binding constant (K), more negative entropy (ΔS) and more electrostatic interaction in comparison to the second set of binding site. In addition, differential scanning calorimetery (DSC) and spectrophotometery data showed that, there are two energetic domains. The first domain is less stable (lower Tm and Cp) which corresponds to the tail segment of HSA and another with more stability is related to the head segment of HSA. Polyoxometal also decreases the stability of protein as Tm, secondary and tertiary structure as well as quenching of the fluorescence decrease. On other hand, perturbations in tertiary structure are more than secondary structure.

The kinetic parameters of adenosine deaminase such as Km and Ki were determined in the absence and presence of adenine derivatives (R1- R24) in sodium phosphate buffer (50 mM; pH 7.5) solution at 27°C. These kinetic parameters were used for QSAR analysis. As such, we found some theoretical descriptors to which the binding affinity of adenosine deaminase (ADA) towards several adenine nucleosides as inhibitors is correlated. QSAR analysis has revealed that binding affinity of the adenine nucleosides upon interaction with ADA depends on the molecular volume, dipole moment of the molecule, electric charge around the N1 atom, and the highest of positive charge for the related molecules.

The stability of four hemoglobins (Hb) in dimer forms (low concentration) were investigated by the kinetics of denaturation. The rate constants of denaturation were obtained by variation of 280 nm absorption versus time in 10 mM Tris-HCl, 10 mM EDTA, pH 8.0 at 45°C in the absence and presence of 0.5 M ethanol, dimethyl sulfoxide (DMSO), formamide, and glycerol. The results show the trend of rate constants in different co-solvents in the following order: chicken hemolysate < human hemolysate and chicken Hb D < chicken Hb A. The buried surface area was calculated for Hb samples in the absence of co-solvents. Accordingly, the trend points out that: chicken Hb D > chicken Hb A > human Hb A. These results suggest that both chicken hemolysate and chicken Hb D are relatively more stable than human and chicken Hb A, respectively. However, the denaturation rate constants of Hb in different co-solvents have designated the following order: ethanol > DMSO > formamide > glycerol. As a matter of fact, this phenomenon is an indication of an increase in the denaturation capacity (DC) and hydrophobicity, and a decrease in the surface tension of the solution in the preceding co-solvents.