@article { author = {Moradi, Mahmood and Rostami, Mohammad}, title = {First Principle Study of MC (M= Al, Ga, and In) at Equilibrium and under Negative Stress}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {99-103}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.2850}, abstract = {The electronic and magnetic properties of the hypothetical compounds of MC (M=Al, Ga and In) are investigated by using first-principle calculations and pseudopotential plane wave self-consistent field method based on density functional theory. In order to find the most stable phase of MC (M=Al, Ga and In), we study them in zinc-blende (ZB), rocksalt (RS), wurtzite and NiAs crystal structures. We find that the most stable crystal structure is the RS structure by comparing the total energies of these compounds in different structures. Our calculations show that these compounds are metals in all of these structures. However, many of the nanospintronic devices are the heterojunctions of half-metals and semiconductors where the crystal structures of the layers that are grown on the semiconductors are the same as that of the semiconductors. Because most of the semiconductors have ZB structure, we investigate the electronic and magnetic properties of these compounds in this structure. It is shown that although MC (M=Al, Ga and In) compounds are metals in ZB structure, they become half-metal when relatively high negative stresses are applied over them. Therefore these compounds could be used in spintronic devices.}, keywords = {Electronic band structure,Magnetic property,Density functional theory:Half-metals}, url = {https://www.physchemres.org/article_2850.html}, eprint = {https://www.physchemres.org/article_2850_f1cddf0cf437c70890910b9244914e49.pdf} } @article { author = {Alipour, Mojtaba}, title = {Does One-third Scheme of PBE0 Functional Dominate Over PBE0 for Electronic Properties of Transition Metal Compounds?}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {104-110}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.2870}, abstract = {The one-third paradigm of PBE0 density functional, PBE0-1/3, has shown to be a successful method for various properties. In this paper, the applicability of PBE0-1/3 is put into broader perspective for transition metals chemistry. As a comparative study, the performance of PBE0 and PBE0-1/3 has been assessed for geometries and vibrational frequencies of some transition metal hydrides and transition metal containing molecules, and static dipole polarizabilities and dipole moments for transition metal halides. The numerical results show that although PBE0-1/3 performs better than the parent PBE0 for response properties of small molecules, it does not approach the quality of PBE0 for structural parameters. Overall, the results of this investigation suggest that there is no real incentive to use PBE0-1/3 in place of PBE0 for calculations involving transition metals. However, it remains challenging to develop a generally density functional resolving all the qualitative failures of previous approximations at a reasonable computational cost.}, keywords = {DFT,PBE0,PBE0-1/3,transition-metal,Polarizability}, url = {https://www.physchemres.org/article_2870.html}, eprint = {https://www.physchemres.org/article_2870_dfe8b5e31e660c8b0404652bdd24c3c9.pdf} } @article { author = {Keshavarz, Fatemeh and Alavianmehr, Mohammad Mehdi and Yousefi, Reza}, title = {Molecular Interaction of Benzalkonium Ibuprofenate and its Discrete Ingredients with Human Serum Albumin}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {111-116}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3039}, abstract = {Studying the interaction of pharmaceutical ionic liquids with human serum albumin (HSA) can help investigating whether or not ionic liquid formation can enhance pharmacological profile of the discrete ingredients. In this respect, in the present work, the interactions of Benzalkonium Ibuprofenate, as a well-known active pharmaceutical ionic liquid, Benzalkonium Chloride, and also Sodium Ibuprofenate with HSA were studied by molecular dynamics (MD) and docking simulations. First, molecular dynamics simulation using the GROMACS 4.5.0 package was employed to obtain the equilibrium HSA structure at pressure 1 bar and temperature of 310 K. Then, molecular docking approach by AutoDock Vina using a genetic algorithm was employed to find the binding sites of the three ligands on HSA. It was revealed that the three ligands can bind to the same residues at Sudlow site II. It was also found out that steric and electrostatic interactions played major roles in the interaction of aforementioned three ligands with HSA but the contribution of these interactions in HSA binding has been altered by ionic liquid formulation.}, keywords = {Ionic Liquid,Human Serum Albumin,Benzalkonium Ibuprofenate,Molecular Dynamics Simulation,Docking}, url = {https://www.physchemres.org/article_3039.html}, eprint = {https://www.physchemres.org/article_3039_34bfe27356783fdec16ac0c2eb7d0502.pdf} } @article { author = {Mirzaei, Masoud and Kazemi, Seyed Hasan and Eshtiagh-Hosseini, Hossein and Izadyar, Mohammad}, title = {Computational study of the intramolecular proton transfer between 6-hydroxypicolinic acid tautomeric forms and intermolecular hydrogen bonding in their dimers}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {117-125}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3102}, abstract = {This paper is a density functional theory (DFT) calculation of intramolecular proton transfer (IPT) in 6-hydroxypicolinic acid (6HPA, 6-hydroxypyridine-2-carboxylic acid) tautomeric forms. The transition state for the enol-to-keto transition is reported in the gas phase and in four different solvents. The planar and non-planar dimer forms of 6HPA keto and enol, respectively, were also studied in the gas phase The IPT reactions and dimerization processes were studied at the B3LYP/6-31++G(d) level of the theory. The influence of the solvent on the tautomerization reaction of 6HPA was examined using the conductor-polarizable continuum model (CPCM). The IPT reaction in the gas phase is almost the same as in solution. The calculated dimerization energies show that the stability of 6HPA tautomer dimer structures is directly affected by the distance of intermolecular hydrogen bonding and electrostatic potential (ESP) value in the tautomer dimer.  }, keywords = {Intramolecular proton transfer (IPT),Intermolecular hydrogen bonding,6-Hydroxypicolinic acid (6HPA),Electrostatic potential (ESP),Tautomerization}, url = {https://www.physchemres.org/article_3102.html}, eprint = {https://www.physchemres.org/article_3102_b75e59d47652a38c0ca8e05d9d533d8d.pdf} } @article { author = {kimiagar, salimeh}, title = {Hydrophilicity and antibacterial properties of Ag / TiO2 nanoparticle}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {126-133}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3223}, abstract = {TiO2 thin films and Ag/TiO2 nanoparticles were prepared by CVD and plasma bombardment method. XRD results showed the presence of Ag nanoparticles in TiO2 matrix. SEM image confirmed formation of Ag nanoparticles. XPS analysis was utilized to study the chemical state of the Ag/TiO2 nanostructure. Statistical surface analysis revealed that since there is a linear relation between logarithmic diagram of Cq(r) and r < Rc ~ 4 µm for all q, both surfaces have self-affine structure. Formation of Ag/TiO2 nanoparticles led to the reduction of  roughness of the samples from 0.72 nm to 0.61 nm. Ag/TiO2 nanoparticles represented greater hydrophilicity under UV illumination and visible light compared with TiO2. TiO2 thin films and Ag/TiO2 nanoparticles showed an inhibition for proliferation of the bacteria on their surfaces. Antibacterial activity of the samples contributed to the growth inhibition of the bacteria on their surfaces.}, keywords = {Ag Nanoparticles,Hydrophilicity,antibacterial,Roughness,Self-affine}, url = {https://www.physchemres.org/article_3223.html}, eprint = {https://www.physchemres.org/article_3223_5a3eda885aace4336d7fe8803b9e27e0.pdf} } @article { author = {Shoarinejad, Saeedeh and Shahzamanian, Mohammad Ali}, title = {Director Structures in a Chiral Nematic Slab: Threshold Field and Pitch Variations}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {134-141}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3289}, abstract = {Abstract The liquid crystal director distribution is determined for a confined chiral nematic slab. The molecular director distribution of the field-controlled chiral nematic slab is directly calculated. The director profiles for the tilt and the twist angles, under different applied fields, are calculated in the slab with weak boundary conditions. Then, the dependence of the threshold field on a dimensionless parameter containing the anchoring and thickness variations is obtained. The variation of the threshold field is found as a function of anchoring strengths for different ratios of the slab-thickness to the pitch, d/P. It confirms that for a constant ratio of d/P, the field decreasing rate in strong anchoring conditions is high and that by decreasing the strength of anchoring, the threshold field becomes approximately constant. This study is based on a stable and simple numerical method that gives accurate results in a short time, compared to the existing methods. The excellent agreement of the solutions with the previously reported solutions shows the usefulness of the method.}, keywords = {Threshold field,Chiral Twisted Nematic,Anchoring,Pitch variations}, url = {https://www.physchemres.org/article_3289.html}, eprint = {https://www.physchemres.org/article_3289_b9c9b3202f076c8268b29edf596f5073.pdf} } @article { author = {Esrafili, Mehdi and Solimannejad, Mohammad}, title = {A theoretical survey on strength and characteristics of F•••F, Br•••O and Br•••Br interactions in solid phase}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {142-151}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3298}, abstract = {A quantum chemical investigation was carried out to study the properties of intermolecular F•••F, Br•••Br and Br•••O interactions in crystalline 1-bromo-2,3,5,6-tetrafluoro-nitrobenzene (BFNB). This system was selected to mimic the halogen-halogen as well as halogen bonding interactions found within crystal structures as well as within biological systems. We found that fluorine atoms have weak positive electrostatic potentials (VS,max≈+1 kcal/mol) and these could be responsible for their weak electrophilic behavior. According to quantum theory of atoms in molecules, the values of electron density at the F•••F critical points are calculated to be in a range of 0.004−0.006 au, whereas the values of ∇2ρBCP are all positive, ranging from 0.023−0.031 au. This indicates that all F•••F interactions in crystalline BFNB, are weak and basically electrostatic in nature. The nature of intermolecular interactions is analyzed using energy decomposition analysis (EDA). Our results indicate that, for those nuclei participating in intermolecular interactions, nuclear magnetic resonance parameters exhibit considerable changes on going from the isolated gas phase molecule model to crystalline BFNB. Of course, the magnitude of these changes at each nucleus depends directly on its amount of contribution to the interactions.}, keywords = {Halogen bonds,Electrostatic potential,DFT,NMR,QTAIM}, url = {https://www.physchemres.org/article_3298.html}, eprint = {https://www.physchemres.org/article_3298_9774a935a7ca6cd65280599361351da4.pdf} } @article { author = {Ajloo, Davood and Ghalehagababaie, Sharbanoo and Mahmoodabadi, Najmeh}, title = {Molecular dynamics studies on the denaturation of polyalanine in the presence of guanidinium chloride at low concentration}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {152-165}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3319}, abstract = {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 dynamics 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 same as osmolytes which decreases the beta form, increases hydration layer and the polypeptide thermal stability.}, keywords = {Phase transition,Polyalanine,Thermal stability,Heat Capacity,Intermediate}, url = {https://www.physchemres.org/article_3319.html}, eprint = {https://www.physchemres.org/article_3319_7776ae7bff555724db818036241aa3b2.pdf} } @article { author = {Entezari, Mohammad and Ghows, Narjes}, title = {Quantum dots of CdS synthesized by micro-emulsion under ultrasound: size distribution and growth kinetics}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {166-174}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3349}, abstract = {Quantum dots of CdS with hexagonal phase were prepared at relatively low temperature (60 oC) and short time by micro-emulsion (O/W) under ultrasound. This study was focused on the particle size distribution and the growth kinetics. The particle size distribution obtained from the optical absorption edge. It was relatively symmetrical with sonication time. In addition, an agreement was observed with the size distribution obtained from the TEM images of the sample under ultrasound. The growth kinetics was monitored by the red-shift in UV-Visible absorbance peaks. The cubed average particle radius showed an emergence of linear regions at longer times. This indicates that the increase of particle size at longer time can be attributed to the diffusion-limited coarsening process. The rate constant for the coarsening increases with increasing the temperature. The Arrhenius-type plot was created by using the slopes of Lifshitz-Slyozov-Wagner (LSW) curves. The activation energy was 71.72 kJ.mol-1 for the ripening process. In fact, the acoustic cavitation strongly increases the diffusion of surface atoms.}, keywords = {Quantum dots,Microemulsion,Ultrasound,Coarsening,Particle size distribution}, url = {https://www.physchemres.org/article_3349.html}, eprint = {https://www.physchemres.org/article_3349_c55b973625dde7bc2099e7abeee789a7.pdf} } @article { author = {hosseinnejad, tayebeh}, title = {Computational Study on the Energetic and Electronic Aspects of Tautomeric Equilibria in 5-methylthio-1,2,4-triazole}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {175-184}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3513}, abstract = {The main purpose of this research is to investigate computationally the tautomeric reaction pathway of 5-methyl-3-methylthio-1,2,4-triazole from the thermodynamical and mechanistical viewpoints. In this respect, density functional theory (DFT) in conjunction with the quantum theory of atoms in molecule (QTAIM) has been employed to model the energetic and electronic features of tautomeric mechanism in the gas phase. Moreover, the effect of two different solvents, dimethylformamide (DMF) and H2O, has been examined via the polarized continuum model (PCM) calculations. Then we have presented the potential energy profile for the two-step tautomeric reaction in the gas and solution phases and analyzed comparatively the energetic aspects of tautomers, intermediate and transition states. On the other hand, we have concentrated on the survey of tautomerism by means of topological electronic indices. Strictly speaking, QTAIM calculations have been performed to explore the variation of electronic density and its laplacian at some key bond critical points of tautomers, intermediate and transition states and also to interpret the proposed tautomeric mechanism.}, keywords = {Triazoles,Tautomeric reaction,Density functional theory,QTAIM analysis,Polarized continuum model}, url = {https://www.physchemres.org/article_3513.html}, eprint = {https://www.physchemres.org/article_3513_090c06bc596213a5c95275df86ca7c6f.pdf} } @article { author = {Saboury*, A.A. and Rahimi-Vaghar, R. and Divsalar, A. and Mansouri-Torshizi, H.}, title = {Heme Releasing from Human Hemoglobin upon Interaction with a New Synthesized Complex of 1,10-Phenanthroline-n-butyl Dithiocarbamato Pd(II) Nitrate}, journal = {Physical Chemistry Research}, volume = {1}, number = {2}, pages = {185-196}, year = {2013}, publisher = {Iranian Chemical Society}, issn = {2322-5521}, eissn = {2345-2625}, doi = {10.22036/pcr.2013.3588}, abstract = {In the present study, we investigated the effect of a new anticancer Pd(II) complex, 1,10-phenanthroline-n-butyl dithiocarbamato Pd(II) nitrate, on the heme releasing from human hemoglobin (Hb) as well as alterations in the structure and function of Hb using different spectroscopic methods of UV-Vis, fluorescence and circular dichroism (CD)at two temperatures of 25 and 37 °C. Fluorescence data revealed that the Pd (II) complex is able to quench the intrinsic fluorescence of Hb. The binding constant, number of binding sites and thermodynamic parameters at two temperatures were calculated. The values of ΔH°, ΔS°, and ΔG° indicated that the van der Waals force or hydrogen bond interactions might play a major role in the interaction of complex with Hb. The far-UV-CD studies displayed that the regular secondary structure of Hb had no significant changes. To evaluate the functional changes of Hb via destruction of the heme structure, fluorescence studies were performed at excitation wavelengths of 321 nm and 460 nm with emission wavelengths of 465 nm and 525 nm, respectively. The results demonstrated that two fluorescent heme degradation products are found during the interaction of Pd(II) complex with Hb. The results of thermal behavior of Hb studied at 415 nm confirmed the heme degradation, which referred to decrease in the hemoglobin stability in the presence of Pd(II) complex. Also, the cytotoxic effects and anti-tumor activity of the complex against human breast cell line, T47D were carried out using MTT assay. The Cc50value obtained after different incubation times of 24 and 48 h. The finding related to structural and functional changes of Hb induced by Pd(II) complex may be important to improve understanding of side effects of new designed metal anti-cancer drugs undergoing.}, keywords = {Hemoglobin,Palladium(II) complex,Heme degradation,Fluorescence,Cytotoxicity}, url = {https://www.physchemres.org/article_3588.html}, eprint = {https://www.physchemres.org/article_3588_fdd3dc15666dd7cfaf3a7aafc32daee3.pdf} }