Davood Ajloo

Professor of Physical Chemistry

  • TEL: +98-23-3522-0095
  • Google Scholar
  • Education

    • Ph.D. 2001

      Physical Chemistry

      Tarbiat Modarres University,Tehran, Iran

    • M.Sc. 1997

      Physical Chemistry

      Tarbiat Modares University, Tehran, Iran

    • B.Sc.1994

      Pure Chemistry

      University of Mazandaran, Babolsar, Iran


    Courses taught in the past and present

    • Physical Chemistry
    • Biophysical chemistry
    • Mathematics for physical chemistry
    • Quantum chemistry
    • Computational chemistry
    • Statistical thermodynamics

    Selected Publications

    Amiri, M., Ajloo, D., Fazli, M., Mokhtarieh, A., Grivani, G., Saboury, A.A. Spectroscopic, electrochemical, docking and molecular dynamics studies on the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin and their cytotoxicity against cancer (2018) Journal of Biomolecular Structure and Dynamics, 36 (14), pp. 3753-3772.

    DOI: 10.1080/07391102.2017.1400467

    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.

    AUTHOR KEYWORDS: bovine serum albumin; cytotoxicity assay; molecular dynamics simulation; Schiff base complex; spectroscopy

    PUBLISHER: Taylor and Francis Ltd.

    Isfahani, F., Ajloo, D., Kanaani, A., Saboury, A.A. Photoconversion of an anthraquinone derivative in the presence of human serum albumin (2018) 205, pp. 298-311.

    DOI: 10.1016/j.saa.2018.07.044

    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

    AUTHOR KEYWORDS: Anthraquinones; Cyclic voltammetry; Molecular docking; Molecular dynamics; Photochromic compounds; Spectroscopy
    INDEX KEYWORDS: Aromatic compounds; Body fluids; Calculations; Dichroism; Electron transport properties; Hydrogen bonds; Ketones; Molecular dynamics; Photochromism; Spectroscopy, Accessible surface areas; Anthraquinone derivatives; Anthraquinones; Electron delocalization; Molecular docking; Non-equilibrium Green's function; Photochromic compound; Structural parameter, Cyclic voltammetry
    PUBLISHER: Elsevier B.V.

    Shams Abyaneh, F.S., Eslami Moghadam, M., Divsalar, A., Ajloo, D., Hosaini Sadr, M. Improving of Anticancer Activity and Solubility of Cisplatin by Methylglycine and Methyl Amine Ligands Against Human Breast Adenocarcinoma Cell Line (2018) 186 (2), pp. 271-291.

    DOI: 10.1007/s12010-018-2715-5

    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.

    AUTHOR KEYWORDS: Anticancer drug; Cisplatin analog; Cytotoxicity; DNA interaction; Methylglycine; Molecular docking; Thermodynamic parameters
    INDEX KEYWORDS: Cell culture; Circular dichroism spectroscopy; Cytotoxicity; Dichroism; DNA; Drug delivery; Drug interactions; Fluorescence quenching; Ligands; Metal complexes; Platinum metals; Spectroscopic analysis; Synthesis (chemical); Thymus, Anticancer drug; Cis-platin; DNA interaction; Methylglycine; Molecular docking; Thermodynamic parameter, Platinum compounds, cisplatin; DNA; ethidium bromide; methylamine; sarcosine; antineoplastic agent; calf thymus DNA; cisplatin; DNA; ethidium; ligand; methylamine; sarcosine, absorption spectroscopy; antineoplastic activity; Article; breast adenocarcinoma cell line; circular dichroism; drug solubility; fluorescence; human; human cell; incubation time; MCF-7 cell line; MTT assay; adenocarcinoma; breast tumor; chemistry; conformation; drug effect; female; molecular dynamics; pathology; solubility; spectrofluorometry; thermodynamics; ultraviolet spectrophotometry, Adenocarcinoma; Antineoplastic Agents; Breast Neoplasms; Circular Dichroism; Cisplatin; DNA; Ethidium; Female; Humans; Ligands; MCF-7 Cells; Methylamines; Molecular Dynamics Simulation; Nucleic Acid Conformation; Sarcosine; Solubility; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet; Thermodynamics
    PUBLISHER: Humana Press Inc.

    Feizabadi, M., Ajloo, D., Soleymanpour, A., Faridnouri, H. Study of electron transport in the functionalized nanotubes and their impact on the electron transfer in the active site of horseradish peroxidase (2018) 116, pp. 313-323.

    DOI: 10.1016/j.jpcs.2018.01.050

    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

    AUTHOR KEYWORDS: Carbon nanotube; Density functional theory; Differential pulse voltammetry; Horseradish peroxidase; Non-equilibrium Green's function; Transmission
    INDEX KEYWORDS: Carbon; Carbon nanotubes; Electrodes; Electron transport properties; Food products; Nanotubes; Transmissions; Transport properties; Voltammetry; Yarn, Differential pulse voltammetry; Electrochemical characterizations; Electronic transmission coefficient; Functionalized carbon nanotubes (f-CNT); Functionalized nanotubes; Horse-radish peroxidase; Non-equilibrium Green's function; Transmission coefficients, Density functional theory
    PUBLISHER: Elsevier Ltd

    Kanaani, A., Vakili, M., Ajloo, D., Nekoei, M. Current-Voltage Characteristics of the Aziridine-Based Nano-Molecular Wires: A Light-Driven Molecular Switch (2018) 35 (4), art. no. 048501, .

    DOI: 10.1088/0256-307X/35/4/048501

    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.

    PUBLISHER: Institute of Physics Publishing

    Pourmousavi, S.A., Fattahi, H.R., Ghorbani, F., Kanaani, A., Ajloo, D. A green and efficient synthesis of isoxazol-5(4H)-one derivatives in water and a DFT study (2018) 15 (2), pp. 455-469.

    DOI: 10.1007/s13738-017-1246-2

    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.

    AUTHOR KEYWORDS: Antimony trichloride; DFT calculations; Isoxazol-5(4H)-ones; Spectroscopy; Three-component process
    PUBLISHER: Springer Verlag

    Kanaani, A., Ajloo, D., Kiyani, H., Amri, S.A.N. First-principles study of the electronic transport properties of a 1,3-diazabicyclo[3.1.0]hex-3-ene molecular optical switch (2018) 153, pp. 135-143.

    DOI: 10.1016/j.ijleo.2017.09.125

    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

    AUTHOR KEYWORDS: Electronic transport; Non-equilibrium green's function; Optical molecular switch
    INDEX KEYWORDS: Calculations; Irradiation; Molecular orbitals; Optical switches; Transport properties, Electronic transmission coefficient; Electronic transport; Electronic transport properties; First-principles calculation; Frontier molecular orbitals; Molecular optical switch; Non-equilibrium Green's function; Optical molecular switches, Electric switches
    PUBLISHER: Elsevier GmbH

    Amiri, M., Fazli, M., Ajloo, D. QSAR, docking and molecular dynamics studies on the piperidone-grafted monoand bis-spiro-oxindole-hexahydropyrrolizines as potent butyrylcholinesterase inhibitors (2018) 6 (4), pp. 685-711.

    DOI: 10.22036/pcr.2018.109597.1438

    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.

    AUTHOR KEYWORDS: Alzheimer; Butyrylcholinesterase inhibitors; Docking; Molecular dynamics; QSAR
    PUBLISHER: Iranian Chemical Society

    Amiri, M., Ajloo, D., Fazli, M., Mokhtarieh, A., Grivani, G., Saboury, A.A. Spectroscopic, electrochemical, docking and molecular dynamics studies on the interaction of three oxovanadium (IV) Schiff base complexes with bovine serum albumin and their cytotoxicity against cancer (2017) pp. 1-20. Article in Press.

    DOI: 10.1080/07391102.2017.1400467

    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

    AUTHOR KEYWORDS: bovine serum albumin; cytotoxicity assay; molecular dynamics simulation; Schiff base complex; spectroscopy
    PUBLISHER: Taylor and Francis Ltd.

    Hadian Rasanani, S., Eslami Moghadam, M., Soleimani, E., Divsalar, A., Ajloo, D., Tarlani, A., Amiri, M. Anticancer activity of new imidazole derivative of 1R,2R-diaminocyclohexane palladium and platinum complexes as DNA fluorescent probes (2017) pp. 1-19. Article in Press.

    DOI: 10.1080/07391102.2017.1385538

    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

    AUTHOR KEYWORDS: DNA binding; Fluorescent complex; Imidazole derivative; Molecular dynamics and docking; Platinum and palladium complexes
    PUBLISHER: Taylor and Francis Ltd.

    Hosseini, M., Khaki, F., Shokri, E., Khabbaz, H., Dadmehr, M., Ganjali, M.R., Feizabadi, M., Ajloo, D. Study on the Interaction of the CpG Alternating DNA with CdTe Quantum Dots (2017) 27 (6), pp. 2059-2068.

    DOI: 10.1007/s10895-017-2145-8

    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.

    AUTHOR KEYWORDS: CdTe quantum dots; CpG islands; DNA methylation; Fluorescence
    INDEX KEYWORDS: Alkylation; Cadmium telluride; DNA; DNA sequences; Electrophoresis; Fluorescence; Fluorescence spectroscopy; Genes; Methylation; Nanocrystals; Probes, Adenomatous polyposis coli; CdTe quantum dots; Cdte quantum dots (QDs); CpG islands; DNA Methylation; Fluorescence intensities; Fluorescence probes; Tumor suppressor genes, Semiconductor quantum dots, APC protein; APC protein, human; cadmium derivative; cadmium telluride; DNA; fluorescent dye; quantum dot; tellurium, chemistry; CpG island; fluorescence; human; limit of detection; metabolism; spectrofluorometry, Adenomatous Polyposis Coli Protein; Cadmium Compounds; CpG Islands; DNA; Fluorescence; Fluorescent Dyes; Humans; Limit of Detection; Quantum Dots; Spectrometry, Fluorescence; Tellurium
    PUBLISHER: Springer New York LLC

    Vakili, M., Sobhkhizi, A., Darugar, V., Kanaani, A., Ajloo, D. A first-principles study of aryloxyanthraquinone-based optical molecular switch (2017) 686, pp. 140-147.

    DOI: 10.1016/j.cplett.2017.08.045

    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.

    AUTHOR KEYWORDS: Aryloxyanthraquinone; Electronic transport; Nano-electronic device; Non-equilibrium Green's function
    PUBLISHER: Elsevier B.V.

    Pourmousavi, S.A., Kanaani, A., Fatahi, H.R., Ghorbani, F., Ajloo, D. SbCl3 as effective catalyst for the preparation of 2,3-Dihydroquinazolin-4(1H)-ones, spectroscopic investigation and DFT study (2017) 106, pp. 82-93.

    DOI: 10.1016/j.jpcs.2017.03.008

    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

    AUTHOR KEYWORDS: 2,3-Dihydroquinazolin-4(1H)-ones; 2-Aminobenzamide; Catalyst; DFT
    INDEX KEYWORDS: Catalysis; Catalysts; Chemical bonds; Gravimetric analysis; Hydrogen bonds; Nitrogen compounds; Thermodynamic stability; Thermogravimetric analysis, 2,3-Dihydroquinazolin-4(1H)-ones; 2-Aminobenzamide; Intramolecular hydrogen bonding; Molecular device; Quinazolines; Short reaction time; Spectroscopic investigations; Theoretical calculations, Density functional theory
    PUBLISHER: Elsevier Ltd

    Fahid, F., Kanaani, A., Pourmousavi, S.A., Ajloo, D. Synthesis, tautomeric stability, spectroscopy and computational study of a potential molecular switch of (Z)-4-(phenylamino)pent-3-en-2-one (2017) 115 (7), pp. 795-808.

    DOI: 10.1080/00268976.2017.1287439

    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.

    AUTHOR KEYWORDS: DFT; molecular switch; Schiff base; spectroscopic investigation; tautomerism
    INDEX KEYWORDS: Carbon; Hydrogen bonds; Isomers; Molecular physics; Optical properties; Quantum chemistry, Intramolecular hydrogen bonding; Intramolecular proton transfer; Molecular electrostatic potentials; Molecular switches; Non-linear optical properties; Schiff-base; Spectroscopic investigations; tautomerism, Potential energy
    PUBLISHER: Taylor and Francis Ltd.

    Jabbari, M., Khosravi, N., Feizabadi, M., Ajloo, D. Solubility temperature and solvent dependence and preferential solvation of citrus flavonoid naringin in aqueous DMSO mixtures: an experimental and molecular dynamics simulation study (2017) 7 (24), pp. 14776-14789.

    DOI: 10.1039/c7ra00038c

    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.

    INDEX KEYWORDS: Atmospheric pressure; Dimethyl sulfoxide; Dissolution; Flavonoids; Mixtures; Molecular dynamics; Molecules; Organic solvents; Solubility; Solutions; Solvation; Solvents; Temperature; Temperature distribution; Thermodynamics, Aqueous solutions of dimethyl sulfoxides; Experimental solubility datum; Hildebrand's solubility parameters; Kirkwood-Buff integrals; Molecular dynamics simulations; Preferential solvation; Solvatochromic parameters; Thermodynamic parameter, Atmospheric temperature
    PUBLISHER: Royal Society of Chemistry

    Rasouli, N., Sohrabi, N., Ajloo, D., Rezvani, N. Spectroscopic, thermodynamic and molecular docking studies on interaction of Toxic Azo Dye with bovine serum albumin (2017) 5 (3), pp. 541-554.

    DOI: 10.22036/pcr.2017.72343.1343

    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.

    AUTHOR KEYWORDS: Bovine serum albumin; Fluorescence quenching; Molecular docking; Thermodynamic; Toxic Azo dye
    PUBLISHER: Iranian Chemical Society

    Mahmoodabadi, N., Ajloo, D. QSAR, docking, and Molecular dynamic studies on the polyphenolic as inhibitors of β-amyloid aggregation (2016) 25 (10), pp. 2104-2118.

    DOI: 10.1007/s00044-016-1620-0

    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.

    AUTHOR KEYWORDS: Amyloid-β peptide; MD simulation; Molecular docking; Principal component analysis; QSAR
    INDEX KEYWORDS: amyloid beta protein; apigeninidin chloride; citreorosein; epicatechin; isoliquiritigenin; luteolin; maritimetin; morin; naringenin; polyphenol derivative; quercetin; quercetin 3 methyl ether; robinetin; solvent; taxifolin; transilitin; unclassified drug, Article; drug mechanism; drug potency; enzyme inhibition; molecular docking; molecular dynamics; multiple linear regression analysis; principal component analysis; protein aggregation; protein interaction; quantitative structure activity relation; surface area
    PUBLISHER: Birkhauser Boston

    Kanaani, A., Ajloo, D., Kiyani, H., Shaheri, F., Amiri, M. Synthesis, molecular structure, spectroscopic investigations and computational study of a potential molecular switch of 2-([1,1’-biphenyl]-4-yl)-2-methyl-6-(4-nitrophenyl)-4-phenyl-1,3 diazabicyclo [3.1.0]hex-3-ene (2016) 128 (8), pp. 1211-1221.

    DOI: 10.1007/s12039-016-1118-9

    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.

    AUTHOR KEYWORDS: DFT; molecular switch; Photochromism; spectroscopy
    INDEX KEYWORDS: Computation theory; Computational chemistry; Isomers; Molecular orbitals; Molecular structure; Photochromism; Spectroscopy, Density-functional methods; Frontier molecular orbitals; Light-sensitive molecular switches; Molecular electrostatic potentials; Molecular switches; Reactivity descriptors; Spectroscopic investigations; Time dependent density functional theory, Density functional theory
    PUBLISHER: Springer India

    Kanaani, A., Ajloo, D., Kiyani, H., Vakili, M., Farahani, M., Amiri, M. Synthesis, spectroscopic investigations, and computational study of 4-((9,10-dioxo-9,10-dihydroanthracen-1-yl)oxy)-3-methoxybenzaldehyde (2016) 121 (2), pp. 246-252.

    DOI: 10.1134/S0030400X16080038

    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.

    INDEX KEYWORDS: Electronic properties; Energy gap; Nonlinear optics; Optical properties; Photochromism; Potential energy; Quantum chemistry; Urea, Computational studies; Methoxybenzaldehyde; Non-linear optical properties; Photochromic compound; Spectroscopic investigations; Time-dependent DFT; Transition structures; UV-Visible spectra, Activation energy
    PUBLISHER: Maik Nauka-Interperiodica Publishing

    Ajloo, D., Mahmoodabadi, N., Ghadamgahi, M., Saboury, A.A. Spectroscopy and computational studies on the interaction of octyl, dodecyl, and hexadecyl derivatives of anionic and cationic surfactants with adenosine deaminase (2016) 34 (7), pp. 1495-1511.

    DOI: 10.1080/07391102.2015.1081571

    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.

    AUTHOR KEYWORDS: docking; fluorescence; molecular dynamics; secondary structure; surfactant
    INDEX KEYWORDS: adenosine deaminase; anionic surfactant; cationic surfactant; dodecyl derivative; hexadecyl derivative; octyl derivative; unclassified drug; adenosine deaminase; anion; cation; protein binding; surfactant, Article; chemical interaction; chemical reaction; circular dichroism; comparative study; concentration (parameters); enzyme active site; enzyme denaturation; enzyme structure; fluorescence analysis; gyration; mathematical computing; molecular docking; molecular dynamics; priority journal; protein stability; spectroscopy; surface area; binding site; chemistry; conformation; metabolism; molecular model, Adenosine Deaminase; Anions; Binding Sites; Catalytic Domain; Cations; Models, Molecular; Molecular Conformation; Molecular Docking Simulation; Molecular Dynamics Simulation; Protein Binding; Spectrum Analysis; Surface-Active Agents
    PUBLISHER: Taylor and Francis Ltd.

    Kanaani, A., Ajloo, D., Kiyani, H., Ghasemian, H., Vakili, M., Feizabadi, M. Molecular structure, spectroscopic investigations and computational study on the potential molecular switch of (E)-1-(4-(2-hydroxybenzylideneamino)phenyl)ethanone (2016) 114 (13), pp. 2081-2097.

    DOI: 10.1080/00268976.2016.1178822

    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.

    AUTHOR KEYWORDS: molecular switch; Schiff base; spectroscopic investigation; tautomerism
    INDEX KEYWORDS: Computational chemistry; Cyclic voltammetry; Hydrogen bonds; Molecular orbitals; Urea, Frontier molecular orbitals; Molecular electrostatic potentials; Molecular switches; Nonlinear optical properties; Reactivity descriptors; Schiff-base; Spectroscopic investigations; tautomerism, Spectroscopic analysis
    PUBLISHER: Taylor and Francis Ltd.

    Kanaani, A., Ajloo, D., Grivani, G., Ghavami, A., Vakili, M. Tautomeric stability, molecular structure, NBO, electronic and NMR analyses of salicylideneimino-ethylimino-pentan-2-one (2016) 1112, pp. 87-96.

    DOI: 10.1016/j.molstruc.2016.02.024

    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.

    AUTHOR KEYWORDS: 1H NMR and UV spectra; DFT; Schiff base; Tautomerism
    INDEX KEYWORDS: Chemical bonds; Complexation; Hydrogen bonds; Nuclear magnetic resonance spectroscopy; Phase equilibria; Solvents; Ultraviolet spectroscopy, Different solvents; Intramolecular hydrogen bonding; Nmr and uv spectrum; Reactivity parameters; Schiff-base; Tautomeric equilibria; Tautomerism; Theoretical calculations, Density functional theory
    PUBLISHER: Elsevier

    Pourmousavi, S.A., Kanaani, A., Ghorbani, F., Damghani, K.K., Ajloo, D., Vakili, M. Synthesis, spectroscopic investigations and computational study of monomeric and dimeric structures of 2-methyl-4-quinolinol (2016) 42 (2), pp. 1237-1274.

    DOI: 10.1007/s11164-015-2084-4

    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.

    AUTHOR KEYWORDS: 2-Methyl-4-quinolinol; 1H NMR and UV spectra; DFT; FT-IR; Hydrogen bonded dimer; NBO analysis
    INDEX KEYWORDS: Chemical bonds; Conformations; Electronic properties; Hydrogen; Hydrogen bonds; Molecules; Nuclear magnetic resonance; Potential energy; Quantum theory; Ultraviolet spectroscopy, 2-Methyl-4-quinolinol; DFT; Hydrogen-bonded dimers; NBO analysis; Nmr and uv spectrum, Dimers
    PUBLISHER: Springer Netherlands

    Ghadamgahi, M., Ajloo, D., Alipour, Y. How do palladium complexes affect on coil structure of human serum albumin in the presence of carbon nanotube? A molecular dynamics study (2016) 4 (1), pp. 47-60.

    DOI: 10.22036/pcr.2016.11742

    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.

    AUTHOR KEYWORDS: Carbon nanotube (CNT); Denaturation; Helix; Human serum albumin (HSA); Molecular dynamics simulation
    PUBLISHER: Iranian Chemical Society

    Ghadamgahi, M., Ajloo, D. Molecular dynamics simulation of the water transportation through a carbon nanotube. the effect of electric field (2015) 89 (11), pp. 2120-2125.

    DOI: 10.1134/S0036024415110059

    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.

    AUTHOR KEYWORDS: carbon nanotube; flow of water; free energy; molecular dynamics simulation; orthogonal and axial electric field
    INDEX KEYWORDS: Electric fields; Flow of water; Free energy; Hydraulics; Molecular dynamics; Molecules; Nanotubes; Yarn, Electric field strength; Electric-field directions; Molecular dynamics simulations; Orthogonal electric fields; Reverse behavior; Water molecule; Water permeation; Water transportation, Carbon nanotubes
    PUBLISHER: Maik Nauka-Interperiodica Publishing

    Kiyani, H., Kanaani, A., Ajloo, D., Ghorbani, F., Vakili, M. N-bromosuccinimide (NBS)-promoted, three-component synthesis of α,β-unsaturated isoxazol-5(4H)-ones, and spectroscopic investigation and computational study of 3-methyl-4-(thiophen-2-ylmethylene)isoxazol-5(4H)-one (2015) 41 (10), pp. 7739-7773.

    DOI: 10.1007/s11164-014-1857-5

    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.

    AUTHOR KEYWORDS: 3-Methyl-4-(thiophen-2-ylmethylene)isoxazol-5(4H)-one; DFT; Fukui function; Isoxazol-5(4H)-ones; NBO analysis; NMR and UV spectra
    INDEX KEYWORDS: Computation theory; Density functional theory; Electronic properties; Molecular orbitals; Synthesis (chemical); Thermodynamic stability; Ultraviolet spectroscopy; Unsaturated compounds, 3-Methyl-4-(thiophen-2-ylmethylene)isoxazol-5(4H)-one; DFT; Fukui functions; Isoxazol-5(4H)-ones; NBO analysis; Nmr and uv spectrum, Thermogravimetric analysis
    PUBLISHER: Kluwer Academic Publishers

    Kanaani, A., Ajloo, D., Ghasemian, H., Kiyani, H., Vakili, M., Mosallanezhad, A. Synthesis, molecular structure, spectroscopic investigations and computational studies of (E)-1-(4-(4-(diethylamino)-2-hydroxybenzylideneamino)phenyl)ethanone (2015) 26 (4), art. no. 571, pp. 1095-1113.

    DOI: 10.1007/s11224-015-0571-2

    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.

    AUTHOR KEYWORDS: DFT; Intramolecular proton transfer; Schiff base; Spectroscopy
    PUBLISHER: Springer New York LLC

    Zahra Bathaie, S., Ajloo, D., Daraie, M., Ghadamgahi, M. Comparative study of the interaction of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP) in its free base and Fe derivative form with oligo(dA.dT) 15 and oligo(dG.dC) 15 (2015) 33 (7), pp. 1598-1611.

    DOI: 10.1080/07391102.2014.963674

    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.

    AUTHOR KEYWORDS: binding; DNA; docking; molecular dynamics simulation; porphyrin; resonance light scattering
    INDEX KEYWORDS: iron; oligodeoxyribonucleotide; porphyrin, chemical structure; chemistry; circular dichroism; conformation; molecular docking; molecular dynamics; osmolarity, Circular Dichroism; Iron; Models, Molecular; Molecular Conformation; Molecular Docking Simulation; Molecular Dynamics Simulation; Oligodeoxyribonucleotides; Osmolar Concentration; Porphyrins
    PUBLISHER: Taylor and Francis Ltd.

    Ajloo, D., Shabanpanah, S., Shafaatian, B., Ghadamgahi, M., Alipour, Y., Lashgarbolouki, T., Saboury, A.A. Interaction of three new tetradentates Schiff bases containing N2O2 donor atoms with calf thymus DNA (2015) 77, pp. 193-202.

    DOI: 10.1016/j.ijbiomac.2015.03.016

    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.

    AUTHOR KEYWORDS: Calf-thymus DNA; Schiff-base; Spectroscopy
    INDEX KEYWORDS: 1,3 bis(2 hydroxy 3 methoxybenzylidene)urea; 1,3 bis(2 hydroxy 3 methoxybenzylidene)urea nickel; 1,3 bis(2 hydroxybenzylidene)urea; calf thymus DNA; DNA; DNA; DNA fragment; nitrogen oxide; Schiff base; Schiff base; unclassified drug, absorption spectroscopy; animal; Article; atom; binding affinity; binding site; bovine; chemistry; circular dichroism; conformation; cyclic potentiometry; DNA binding; DNA structure; electrochemical analysis; electrochemistry; fluorescence; hydrogen bond; interactions with DNA; metabolism; molecular docking; molecular docking; molecular dynamics; molecular dynamics; nonhuman; Scatchard plot; temperature; thermostability; viscometry; viscosity, Animals; Cattle; chemistry; chemistry; chemistry; DNA; Electrochemistry; metabolism; metabolism; Molecular Docking Simulation; Molecular Dynamics Simulation; Nitrogen Oxides; Nucleic Acid Conformation; Schiff Bases; Temperature
    PUBLISHER: Elsevier B.V.

    Ajloo, D., Eslami Moghadam, M., Ghadimi, K., Ghadamgahi, M., Saboury, A.A., Divsalar, A., Sheikhmohammadi, M., Yousefi, K. Synthesis, characterization, spectroscopy, cytotoxic activity and molecular dynamic study on the interaction of three palladium complexes of phenanthroline and glycine derivatives with calf thymus DNA (2015) 430, pp. 144-160.

    DOI: 10.1016/j.ica.2015.03.006

    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.

    AUTHOR KEYWORDS: ct-DNA; Ligand binding; Molecular dynamic simulation; Palladium complexes; Spectroscopy
    PUBLISHER: Elsevier S.A.

    Ghadamgahi, M., Ajloo, D. Correlation of drug and carbon nanotube size in encapsulation and free energy calculation: A molecular insight (2015) 36 (1), pp. 168-179.

    DOI: 10.1002/bkcs.10039

    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.

    AUTHOR KEYWORDS: Drug delivery; Encapsulation; Molecular dynamics simulation; Multiple linear regressions; Radius of gyration
    INDEX KEYWORDS: Aromatic compounds; Carbon; Drug delivery; Drug interactions; Encapsulation; Free energy; Molecular dynamics; Molecules; Regression analysis; Yarn, Free energy of interactions; Free-energy calculations; Molecular dynamics simulations; Multiple linear regressions; Potential of mean force; Quantitative structure property relationships; Radius of gyration; Regression parameters, Carbon nanotubes
    PUBLISHER: Korean Chemical Society

    Ghadamgahi, M., Ajloo, D. Molecular dynamics insight into the urea effect on Tretinoin encapsulation into carbon nanotube (2015) 26 (1), pp. 185-195.

    DOI: 10.5935/0103-5053.20140242

    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.

    AUTHOR KEYWORDS: Carbon nanotube; Linear interaction energy; Molecular dynamics simulation; Tretinoin
    PUBLISHER: Sociedade Brasileira de Quimica

    Jafari, S., Faridbod, F., Norouzi, P., Dezfuli, A.S., Ajloo, D., Mohammadipanah, F., Ganjali, M.R. Detection of Aeromonas hydrophila DNA oligonucleotide sequence using a biosensor design based on Ceria nanoparticles decorated reduced graphene oxide and Fast Fourier transform square wave voltammetry (2015) 895, pp. 80-88.

    DOI: 10.1016/j.aca.2015.05.055

    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.

    AUTHOR KEYWORDS: Aeromonas hydrophila; Biosensor; Cerium oxide; Fast Fourier transforms; Graphene oxide; Square wave voltammetry
    INDEX KEYWORDS: Biosensors; Carbon; Cerium; Cerium compounds; DNA; Electrodes; Fish ponds; Glass membrane electrodes; Graphene; Nanoparticles; Oligonucleotides; Oxides; Polyaniline; Signal detection; Signal receivers; Voltammetry, Aeromonas hydrophila; Cerium oxides; Chemically reduced graphene oxides; Electrochemical DNA biosensors; Graphene oxides; Modified electrode surfaces; Modified glassy carbon electrode; Square wave voltammetry, Fast Fourier transforms, aerolysin; bacterial DNA; carbon; cerium oxide; graphene oxide; nanoparticle; polyaniline; ruthenium derivative; single stranded DNA; bacterial DNA; ceric oxide; cerium; graphite; nanoparticle; oxide, Aeromonas hydrophila; Article; bacterium detection; base mispairing; biosensor; DNA extraction; DNA hybridization; DNA sequence; electrochemistry; electrode; equipment design; fast Fourier transform square wave voltammetry; Fourier analysis; immobilization; molecular docking; nonhuman; nucleotide sequence; oxidation reduction state; potentiometry; priority journal; Aeromonas hydrophila; chemistry; electrochemical analysis; genetic procedures; nucleotide sequence; oxidation reduction reaction; surface property, Aeromonas hydrophila; Base Sequence; Biosensing Techniques; Cerium; DNA, Bacterial; Electrochemical Techniques; Electrodes; Fourier Analysis; Graphite; Molecular Docking Simulation; Nanoparticles; Oxidation-Reduction; Oxides; Surface Properties
    PUBLISHER: Elsevier

    Ajloo, D., Ghadamgahi, M., Shaheri, F., Zarei, K. Absorbtion spectroscopy, molecular dynamics calculations, and multivariate curve resolution on the phthalocyanine aggregation (2014) 35 (5), pp. 1440-1448.

    DOI: 10.5012/bkcs.2014.35.5.1440

    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.

    AUTHOR KEYWORDS: Molecular dynamics simulation; Multivariate curve resolution; Phthalocyanine; Solvent effect; Spectroscopy
    INDEX KEYWORDS: Dimers; Dimethyl sulfoxide; Dissociation; Enthalpy; Entropy; Molecular dynamics; Nitrogen compounds; Organic solvents; Phase equilibria; Solvents; Spectroscopy, Molecular dynamics calculation; Molecular dynamics simulations; Multivariate curve resolution; Multivariate curve resolution analysis; Phthalocyanine; Radial distribution functions; Root mean square deviations; Solvent effects, Aggregates
    PUBLISHER: Korean Chemical Society

    Kanaani, A., Ajloo, D., Kiyani, H., Farahani, M. Synthesis, spectroscopic investigations and computational study of 4-((9,10-dioxo-9,10-dihydroanthracen-1-yl)oxy)benzaldehyde (2014) 1063 (1), pp. 30-44.

    DOI: 10.1016/j.molstruc.2014.01.040

    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.

    AUTHOR KEYWORDS: Density functional theory; NBO; Photochromism; QST3; Spectroscopy

    Amiri, M., Ajloo, D. QSAR and docking studies on the diaryltriazine analogs as HIV-1 reverse transcriptase inhibitors (2014) 23 (2), pp. 969-979.

    DOI: 10.1007/s00044-013-0701-6

    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.

    AUTHOR KEYWORDS: Molecular docking; Principal component analysis; QSAR; Reverse transcriptase
    INDEX KEYWORDS: anti human immunodeficiency virus agent; diaryltriazine derivative; RNA directed DNA polymerase; RNA directed DNA polymerase inhibitor; triazine; triazine derivative; unclassified drug, antiviral activity; article; binding kinetics; chemometrics; drug protein binding; enzyme substrate complex; Human immunodeficiency virus 1; hydrogen bond; molecular docking; multiple linear regression analysis; principal component analysis; principal component regression analysis; quantitative structure activity relation; regression analysis

    Jabbari, M., Mir, H., Kanaani, A., Ajloo, D. Kinetic solvent effects on the reaction between flavonoid naringenin and 2,2-diphenyl-1-picrylhydrazyl radical in different aqueous solutions of ethanol: An experimental and theoretical study (2014) 196, pp. 381-391.

    DOI: 10.1016/j.molliq.2014.04.015

    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.

    AUTHOR KEYWORDS: DFT calculations; DPPH radical; Ethanol-water mixtures; Kinetic solvent effect; Naringenin; Reichardt and KAT parameters
    PUBLISHER: Elsevier

    Moghadam, M.E., Saidifar, M., Rostami-Charati, F., Ajloo, D., Ghadamgahi, M. Molecular dynamic simulation and spectroscopic investigation of some cytotoxic palladium(II) complexes interaction with human serum albumin (2014) 17 (9), pp. 781-789.

    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.

    AUTHOR KEYWORDS: Glycine derivatives; HSA denaturation; Molecular dynamics simulation; Pd(II) complex
    INDEX KEYWORDS: human serum albumin; palladium complex; organometallic compound; palladium; serum albumin, absorption spectroscopy; Article; beta sheet; conformational transition; drug binding site; drug protein binding; drug synthesis; enthalpy; equilibrium constant; fluorescence; fluorescence spectroscopy; Hill coefficient; hydrogen bond; macromolecule; molecular dynamics; molecular interaction; pH; priority journal; protein denaturation; protein interaction; protein secondary structure; protein unfolding; surface area; temperature; chemical structure; chemistry; human; spectrofluorometry; synthesis; thermodynamics; ultraviolet spectrophotometry, Humans; Molecular Dynamics Simulation; Molecular Structure; Organometallic Compounds; Palladium; Serum Albumin; Spectrometry, Fluorescence; Spectrophotometry, Ultraviolet; Thermodynamics
    PUBLISHER: Bentham Science Publishers B.V.

    Derakhshankhah, H., Saboury, A.A., Divsalar, A., Mansouri-Torshizi, H., Bamery, I., Ajloo, D., Moosavi-Movahedi, A.A., Hosseinzadeh, R., Ganjali, M.R., Ilkhani, H., Khavasi, H.R. Synthesis and characterization of a newly designed di-copper(II)-based complex and study of its artificial enzyme catalytic activity (2014) 11 (5), pp. 1381-1390.

    DOI: 10.1007/s13738-014-0407-9

    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.

    AUTHOR KEYWORDS: Artificial tyrosinase; Bi-copper(II) complex; Dopamine; Enzyme kinetic; Voltammetiric study
    PUBLISHER: Springer Verlag

    Moradi, S., Ajloo, D., Lashkarbolouki, T., Alizadeh, R., Saboury, A.A. Physicochemical studies on the interaction of gold(III) trichlorophenanthridine complex with calf thymus DNA (2013) 144 (10), pp. 1499-1505.

    DOI: 10.1007/s00706-013-1032-5

    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.

    AUTHOR KEYWORDS: DNA; Fluorescence spectroscopy; Gold complex; Intercalation compounds; Ligand docking

    Ghadamgahi, M., Ajloo, D. The effects of urea, guanidinium chloride and sorbitol on porphyrin aggregation: Molecular dynamics simulation (2013) 125 (3), pp. 627-641.

    DOI: 10.1007/s12039-013-0411-0

    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.

    AUTHOR KEYWORDS: aggregation; molecular dynamics simulation; Porphyrin; radial distribution function; sorbitol; urea
    INDEX KEYWORDS: Guanidinium chlorides; Hydration layers; Inhibition effect; Molecular dynamics simulations; Osmolytes; Radial distribution functions; sorbitol; Target species, Agglomeration; Alcohols; Chlorine compounds; Hydration; Metabolism; Molecular dynamics; Urea, Porphyrins

    Ajloo, D., Sangian, M., Ghadamgahi, M., Evini, M., Saboury, A.A. Effect of two imidazolium derivatives of ionic liquids on the structure and activity of adenosine deaminase (2013) 55, pp. 47-61.

    DOI: 10.1016/j.ijbiomac.2012.12.042

    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.

    AUTHOR KEYWORDS: Adenosine deaminase; Docking; Hydrogen bond; Ionic liquid; Molecular dynamics simulation; Tertiary structure
    INDEX KEYWORDS: 1 allyl 3 methyl imidazolium; 1 octhyl 3 methyl imidazolium; adenosine deaminase; imidazole derivative; ionic liquid; phosphate buffered saline; unclassified drug, article; controlled study; drug effect; drug structure; enzyme activity; enzyme conformation; fluorescence analysis; hydrogen bond; hydrophilicity; hydrophobicity; molecular docking; molecular dynamics; protein interaction; simulation; structure activity relation; ultraviolet spectrophotometry, Adenosine Deaminase; Allyl Compounds; Binding Sites; Borates; Catalytic Domain; Enzyme Activation; Imidazoles; Ionic Liquids; Kinetics; Ligands; Molecular Conformation; Molecular Docking Simulation; Molecular Dynamics Simulation; Protein Binding; Protein Conformation

    Ajloo, D., Ghalehaghababaie, S., Mahmoodabadi, N. Molecular dynamics studies on the denaturation of polyalanine in the presence of guanidinium chloride at low concentration (2013) 1 (2), pp. 152-165.

    DOI: 10.22036/pcr.2013.3319

    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.

    AUTHOR KEYWORDS: Heat capacity; Intermediate; Phase transition; Polyalanine; Thermal stability
    PUBLISHER: Iranian Chemical Society

    Derakhshankhah, H., Saboury, A.A., Bazl, R., Tajmir-Riahi, H.A., Falahati, M., Ajloo, D., Mansoori-Torshizi, H., Divsalar, A., Hekmat, A., Moosavi-Movahedi, A.A. Synthesis, cytotoxicity and spectroscopy studies of a new copper (II) complex: Calf thymus DNA and T47D as targets (2012) 9 (5), pp. 737-746.

    DOI: 10.1007/s13738-012-0086-3

    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.

    AUTHOR KEYWORDS: DNA-complex; Electrostatic interaction; Fluorescence; Intercalation

    Pooyafar, M., Ajloo, D. Tertiary structure prediction of α-glucosidase and inhibition properties of n-(phenoxydecyl) phthalimide derivatives (2012) 59 (2), pp. 221-232.

    Due to increasing of population of diabetic patients, identifying factors for disease control has received much attention, α-glucosidase (EC 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.

    AUTHOR KEYWORDS: α-glucosidase; Docking; Homology modeling; Inhibition; Molecular dynamics simulation; QSAR

    Ghadamghahi, M., Ajloo, D., Moalem, M. Kinetic studies on the self-aggregation of a non ionic porphyrin in the presence and absence of ionic liquid by molecular dynamics simulation (2012) 16 (10), pp. 1082-1093.

    DOI: 10.1142/S1088424612500915

    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.

    AUTHOR KEYWORDS: aggregation; CMC; ionic liquid; molecular dynamics simulation; porphyrin; rate constant
    PUBLISHER: World Scientific Publishing Co. Pte Ltd

    Ajloo, D., Hajipour, S., Saboury, A.A., Zakavi, S. Effect of cationic and anionic porphyrins on the structure and activity of adenosine deaminase (2011) 32 (9), pp. 3411-3420.

    DOI: 10.5012/bkcs.2011.32.9.3411

    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.

    AUTHOR KEYWORDS: Binding constant; Circular dichroism; Fluorescence; Inhibition constant; Porphyrin
    INDEX KEYWORDS: Adenosine deaminases; Binding constant; Cationic porphyrin; Fluorescence spectrophotometry; Inhibition constant; Molecular docking; pH range; Secondary structures; Structural studies; UV-vis spectrophotometry, Dichroism; Fluorescence; Molecular dynamics; pH effects; Potassium iodide; Spectrophotometry, Porphyrins

    Ghadamgahi, M., Ajloo, D. Calculation and prediction of rate and equilibrium constants for aggregation of porphyrin by molecular dynamics, Docking and QSPR methods (2011) 15 (4), pp. 240-256.

    DOI: 10.1142/S1088424611003215

    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.

    AUTHOR KEYWORDS: equilibrium constant; molecular dynamics simulation; porphyrin aggregation; QSPR; rate constant
    PUBLISHER: World Scientific Publishing Co. Pte Ltd

    Divsalar, A., Saboury, A.A., Ahadi, L., Zemanatiyar, E., Mansouri-Torshizi, H., Ajloo, D., Sarma, R.H. Biological evaluation and interaction of a newly designed anti-cancer pd(ii) complex and human serum albumin (2011) 29 (2), pp. 283-296.

    DOI: 10.1080/07391102.2011.10507385

    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.

    AUTHOR KEYWORDS: Apoptosis; Cytotoxic; HAS; Pd(II) complex; Quenching; Thermodynamic parameters
    INDEX KEYWORDS: 2,2' bipyridin butylglycinato palladium nitrate; antineoplastic metal complex; human serum albumin; palladium complex; tryptophan; unclassified drug, albumin blood level; alpha helix; antineoplastic activity; apoptosis; article; binding site; cancer inhibition; cell strain K 562; circular dichroism; concentration response; controlled study; drug cytotoxicity; drug determination; drug protein binding; drug structure; fluorescence analysis; fluorescence resonance energy transfer; human; human cell; hydrophobicity; in vitro study; photochemical quenching; priority journal; thermodynamics; ultraviolet spectrophotometry

    Ajloo, D., Yoonesi, B., Soleymanpour, A. Solvent effect on the reduction potential of anthraquinones derivatives. The experimental and computational studies (2010) 5 (4), pp. 459-477.

    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.

    AUTHOR KEYWORDS: Anthraquinones; Cyclic voltammetry; Quantitative structure-property relationship (QSPR); Self consistent reaction field; Solvent effect
    PUBLISHER: Electrochemical Science Group

    Dasmeh, P., Searles, D.J., Ajloo, D., Evans, D.J., Williams, S.R. On violations of le Chatelier's principle for a temperature change in small systems observed for short times (2009) 131 (21), art. no. 214503, .

    DOI: 10.1063/1.3261849

    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.

    INDEX KEYWORDS: Arbitrary systems; Confined systems; Entropy production; Equilibrium reactions; Le chatelier's principles; Mathematical expressions; Molecular levels; Phase functions; Relative probability; Small systems; Temperature changes; Temperature increase; Thermal relaxation process; Time integrals, Chemical reactions; Computer simulation; Thermal effects, Functions, polyglutamic acid, article; chemical model; chemistry; computer simulation; probability; protein conformation; protein folding; temperature; thermodynamics, Computer Simulation; Models, Chemical; Polyglutamic Acid; Probability; Protein Conformation; Protein Folding; Temperature; Thermodynamics

    Ajloo, D., Najafi, L., Saboury, A.A. Effects of dimaine, diacid and dintitro derivatives on the inhibition of adenosine deaminase; experimental, molecular docking and QSAR studies (2009) 30 (11), pp. 2523-2531.

    DOI: 10.5012/bkcs.2009.30.11.2523

    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.

    AUTHOR KEYWORDS: Binding constant; Enzyme inhibition; Principal component analysis; QSAR
    INDEX KEYWORDS: Active site; Adenosine deaminases; Aromatic ligands; Binding constant; Case analysis; Competitive behavior; Competitive inhibition; Dinitro aromatic compounds; Enzyme-substrate complexes; Experimental values; Free energy of binding; Inhibition constants; Molecular docking; Phosphate buffers; QSAR studies; Structure activity relationships; UV-vis spectrophotometry, Aromatic compounds; Binding energy; Docking; Enzymes; Financial data processing; Ligands; Molecular modeling; pH effects; Principal component analysis; Sulfur compounds, Enzyme inhibition

    Ajloo, D., Sharifian, A., Behniafar, H. Prediction of thermal decomposition temperature of polymers using QSPR methods (2008) 29 (10), pp. 2009-2016.

    DOI: 10.5012/bkcs.2008.29.10.2009

    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).

    AUTHOR KEYWORDS: Cross validation; Geometrical descriptors; Polymer; Semi-empirical; Thermal decomposition temperature
    INDEX KEYWORDS: Decomposition; Linear regression; Thermolysis, Correlation coefficient; Cross validation; Descriptors; Multiple linear regressions; Semi-empirical; Stepwise methods; Thermal decomposition temperature; Variable selection, Polymers
    PUBLISHER: Korean Chemical Society

    Ajloo, D., Taghizadeh, E., Saboury, Ali.A., Bazyari, E., Mahnam, K. Effects of surfactant, salt and solvent on the structure and activity of adenosine deaminase: Molecular dynamic and spectrophotometric studies (2008) 43 (2), pp. 151-158.

    DOI: 10.1016/j.ijbiomac.2008.04.007

    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.

    AUTHOR KEYWORDS: Enzyme activity; Molecular dynamics; Secondary structure
    INDEX KEYWORDS: adenosine deaminase; alcohol; dodecyl sulfate sodium; dodecyltrimethylammonium bromide; methanol; sodium chloride; sodium sulfate; solvent; surfactant, article; chemical interaction; circular dichroism; computer simulation; enzyme activity; enzyme structure; molecular dynamics; spectrophotometry; surface charge; ultraviolet radiation, Adenosine Deaminase; Circular Dichroism; Ethanol; Kinetics; Methanol; Quantitative Structure-Activity Relationship; Quaternary Ammonium Compounds; Sodium Chloride; Sodium Dodecyl Sulfate; Solvents; Spectrophotometry, Ultraviolet; Sulfates; Surface-Active Agents

    Ajloo, D., Saboury, A.A., Haghi-Asli, N., Ataei-Jafarai, G., Moosavi-Movahedi, A.A., Ahmadi, M., Mahnam, K., Namaki, S. Kinetic, thermodynamic and statistical studies on the inhibition of adenosine deaminase by aspirin and diclofenac (2007) 22 (4), pp. 395-406.

    DOI: 10.1080/14756360701229085

    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.

    AUTHOR KEYWORDS: Adenosine deaminase inhibitors; Aspirin; Diclofenac; Principal component analysis; QSAR; Quantitative structure-activity relationship
    INDEX KEYWORDS: acetylsalicylic acid; adenosine deaminase; diclofenac, animal cell; article; calorimetry; competitive inhibition; controlled study; drug protein binding; enthalpy; enzyme activity; enzyme inhibition; inhibition kinetics; nonhuman; principal component analysis; priority journal; quantitative structure activity relation; spectrophotometry; thermodynamics; ultraviolet radiation, Adenosine Deaminase; Anti-Inflammatory Agents, Non-Steroidal; Aspirin; Binding, Competitive; Diclofenac; Enzyme Inhibitors; Kinetics; Models, Chemical; Models, Statistical; Nucleotides; Principal Component Analysis; Spectrophotometry, Ultraviolet; Structure-Activity Relationship; Temperature; Thermodynamics

    Ajloo, D., Behnam, H., Saboury, A.A., Mohamadi-Zonoz, F., Ranjbar, B., Moosavi-Movahedi, A.A., Hasani, Z., Alizadeh, K., Gharanfoli, M., Amani, M. Thermodynamic and structural studies on the human serum albumin in the presence of a polyoxometalate (2007) 28 (5), pp. 730-736.

    DOI: 10.5012/bkcs.2007.28.5.730

    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.

    AUTHOR KEYWORDS: Circular dichroism; Fluorescence; Human serum albumin; Isothermal titration calorimetery; Polyoxometalate
    INDEX KEYWORDS: Blood; Coulomb interactions; Differential scanning calorimetry; Fluorescence; Molecular structure; Perturbation techniques; Thermodynamics, Circular dichroisms; Human serum albumin (HSA); Isothermal titration calorimetery; Polyoxometalate, Proteins
    PUBLISHER: Korean Chemical Society

    Moosavi-Movahedi, A.A., Safarian, S., Hakimelahi, G.H., Ataei, G., Ajloo, D., Panjehpour, S., Riahi, S., Mousavi, M.F., Mardanyan, S., Soltani, N., Khalafi-Nezhad, A., Sharghi, H., Moghadamnia, H., Saboury, A.A. QSAR Analysis for ADA upon Interaction with a Series of Adenine Derivatives as Inhibitors (2004) 23 (3), pp. 613-624.

    DOI: 10.1081/NCN-120030719

    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.

    AUTHOR KEYWORDS: Adenine nucleosides; Adenosine deaminase; Cyclic and acyclic adenosine derivatives; QSAR analysis
    INDEX KEYWORDS: adenine derivative; adenosine deaminase; buffer; nucleoside; sodium dihydrogen phosphate, article; binding affinity; cattle; chemical structure; dipole; electricity; kinetics; nonhuman; quantitative structure activity relation; quantum mechanics, Adenine; Adenosine Deaminase; Humans; Molecular Structure; Protein Binding; Quantitative Structure-Activity Relationship; Statistics, Ada; Bos taurus

    Ajloo, D., Moosavi-Movahedi, A.A. Kinetics of denaturation of human and chicken hemoglobins in the presence of co-solvents (2003) 36 (4), pp. 367-372.

    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.

    AUTHOR KEYWORDS: Denaturation capacity; Hemoglobin; Hydrophobicity; Rate constant; Solvent effect; Stability; Surface tension
    INDEX KEYWORDS: alcohol; dimer; dimethyl sulfoxide; edetic acid; formamide; glycerol; hemoglobin; hemoglobin A; hemoglobin d; hydrochloric acid; solvent; unclassified drug, absorption; article; calculation; chicken; comparative study; concentration (parameters); controlled study; hemolysate; human; hydrophobicity; kinetics; nonhuman; pH; protein denaturation; protein stability; sample; surface tension; temperature; time, Animals; Chickens; Dimerization; Dimethyl Sulfoxide; Ethanol; Formamides; Glycerol; Hemoglobin A; Hemoglobins, Abnormal; Humans; Kinetics; Protein Denaturation; Solvents; Surface Properties; Thermodynamics, Gallus gallus