2024-03-28T21:15:55Z
https://www.physchemres.org/?_action=export&rf=summon&issue=5065
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Chemical Kinetics for Reaction of 5-Nitro-1H-benzo[d]imidazole to Produce 6-Nitro-1H-benzo[d]imidazole and Calculation of Heat Capacity of Activation
Marzyeh
Mohammadi
Seyedeh Leila
Hashemi Dashtaki
Shapour
Ramazani
Bahador
Karami
The kinetics and mechanism of the reaction of 5-nitro-1H-benzo[d] imidazole to produce 6-nitro-1H-benzo[d] imidazole was studied by employing hybrid meta-density functional theory. MPWBlK/6-31+G** level calculations were carried out to obtain energies and optimize the geometries of all stationary points along the PES, and determine the harmonic vibrational frequencies. Two transition states (TS1 and TS2) and a chemically-energized intermediate (Int) are involved along the calculated potential energy surface. RRKM-TST was used to compute the temperature dependence of the rate constants, which were determined using nonlinear least-squares fitting at 273-1000 K. The Arrhenius plot for all reactions was shown positive temperature dependence. Thermodynamic parameters were also used to determine the stability and the extent of spontaneity of the reaction. The self-consistent reaction field (SCRF) was used with DFT energy, optimization, and frequency calculations to model systems in solution and compare them with the rate constants in the gas and solvent (water) phases. The variation of activation energy in the temperature range (273-1000 K) were determined in the gas and solvent phases. The heat capacity of activation of reactions ((∂E_a)/∂T) were also reported which is temperature dependent and is significant in low temperature.
Tautomerism
Rate constant
Tunneling effect
Heat capacity of activation
Kinetics
2017
09
01
409
424
https://www.physchemres.org/article_43477_6c9917bf7755f998e912569d49510545.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Selective Binding of Cyclic Nanopeptide with Halides and Ion Pairs; a DFT-D3 Study
Mohammad
Izadyar
Mohammad
Khavani
In this article, theoretical studies on the selective complexation of the halide ions (F¯, Cl¯ and Br¯) and ion pairs (Na+F¯, Na+Cl¯ and Na+Br¯) with the cyclic nano-hexapeptide (CP) composed of L-proline have been performed in the gas phase. In order to calculate the dispersion interaction energies of the CP and ions, DFT-D3 calculations at the M05-2X-D3/6-31G(d) level was employed. Based on the results, F¯ and Na+F¯ make the most stable complex with the CP. The dispersion interactions between the ions and the CP are small while the electrostatic interactions are the driving force of the complex formation. Finally, natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses indicate that F¯ makes the most stable complex with CP due to more charge transfer and stronger bond formation in comparison to other ions.
Cyclic nanopeptide
Dispersion interaction
Ion pair
Selective binding
Halide
2017
09
01
425
437
https://www.physchemres.org/article_43663_f1ff830a87e609857472f981faa98351.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Thermodynamics and Kinetics of Spiro-Heterocycle Formation Mechanism: Computational Study
Abdulfatai
Siaka
Adamu
Uzairu
Sulaiman
Idris
Hamza
Abba
Reaction mechanism among indoline-2,3-dione, pyrrolidine-2-carboxylic acid and (Z)-2-(1-(2-hydroxynaphthalen-1-yl)ethylidene)hydroxycarboxamide to form 1’-((((aminooxy)carbonyl)amino)methyl)-2’-(1-hydroxynaphthalen-2-yl)-2’-methyl-1’,2’,5’,6’,7’,7a’-hexahydrospiro[indoline-3,3’-pyrrolo[1,2-a]imidazole-2-one was investigated using density functional theory (DFT) at B3LYP basis theory. The three-step reaction occurred via five stationary points that include two van der Waals complexes (1 and 2), two intermediates and one transition state. The entropy change across the various steps indicated an appreciable interaction or overlap within the reacting molecules. This is evident in variations in the geometries of the optimized species as the reaction progressed from the intermediates through the transition state to the final product. The steps leading to the van der Waals complexes (1 and 2) formation were found to be thermodynamically feasible compare to the bimolecular transition step. From the equilibrium constant value, the transition step was found to be the rate-determining step. The study was able to provide information on the energy demand of the individual step of the reaction and the overall process in addition to change in geometry as the molecules undergo transformation to the final product.
Mechanism
Bimolecular
van der Waals complexes
Geometries and entropy
2017
09
01
439
446
https://www.physchemres.org/article_44488_276ee65ca0e9a32d2df596512a811144.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Hydrogen Adsorption on (5,0) and (3,3) Na-decorated BNNTs
Heydar Ali
Shafiei Gol
Mehdi
Noura
The storage capacity of hydrogen on Na-decorated born nitride nanotubes (BNNTs) is investigated by using density functional theory within Quantum Espresso and Gaussian 09. The results obtained predict that a single Na atom tends to occupy above the central region of the hexagonal rings in (5,0) and (3,3) BNNT structures with a binding energy of -2.67 and -4.28 eV/Na-atom respectively. When a single H2 molecule is absorbed by a Na decorated BNNT, electrostatic field around Na atom and consequently charge of the participating atoms in the interaction region also undergo change. According to Mulliken population and partial density of state (PDOS) analyses, it is observed that positive charge carried by Na atom decreases.Another result of this charge transfer is revealed as an increase in the magnitude of the dipole moment of BNNT-Na-1H2 with respect to BNNT-Na. The results of charge density, separation distance of atoms in adsorption region as well as the H2 binding energy show the hydrogen molecule adsorption is a physical adsorption (physisorption). In the adsorption process, a single sodium atom with losing about 0.4e of its net charge can adsorb up to six H2 molecules with the binding energy of -0.35 and -0.32 eV/ H2 molecule on (5,0) and (3,3) BNNTs respectively. A comparison of the H2 binding energy of two nanotubes implies that the (5,0) BNNT-Na is more favorable for the hydrogen molecule adsorption.
Density functional theory
BNNT
Partial charge density
Charge transfer
Dipole moment
Hydrogen storage
2017
09
01
447
463
https://www.physchemres.org/article_44489_e796fa0cb3b9d16140be3e4de93dd6d9.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
A Fugacity Approach for Prediction of Phase Equilibria of Methane Clathrate Hydrate in Structure H
Saeed
Sinehbaghizadeh
Jafar
Javanmardi
Aliakbar
Roosta
Amir
Mohammadi
In this communication, a thermodynamic model is presented to predict the dissociation conditions of structure H (sH) clathrate hydrates with methane as help gas. This approach is an extension of the Klauda and Sandler fugacity model (2000) for prediction of phase boundaries of sI and sII clathrate hydrates. The phase behavior of the water and hydrocarbon system is modeled using the Peng-Robinson equation of state (PR-EoS) with Wong-Sandler mixing rule, while the excess Gibbs free energy of the mixture is calculated using the UNIFAC activity model. The van der Waals-Platteeuw (vdWP) solid solution theory is used to model the hydrate phase. Results are compared with the results of the models proposed by Mehta and Sloan (1996) and Chen et al. (2003) for prediction of dissociation conditions of structure H hydrates. According to the results, the overall average absolute deviation of dissociation temperatures between experiments and predictions are 0.18 (K), depending on the promoter, and the accuracy of the model proposed in this study is found to be better than the accuracies of the aforementioned models.
Clathrate hydrate
Structure H
Promoter
Thermodynamic model
Gas Hydrate
2017
09
01
465
481
https://www.physchemres.org/article_44847_45520c2466c11d1a93b79739df9f6d81.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Molecular Dynamics Simulation and Free Energy Studies on the Interaction of Salicylic Acid with Human Serum Albumin (HSA)
Leila
Karami
Elham
Tazikeh-Lemeski
Ali Akbar
Saboury
Human serum albumin (HSA) is the most abundant protein in the blood plasma. Molecular dynamics simulations of subdomain IIA of HSA and its complex with salicylic acid (SAL) were performed to investigate structural changes induced by the ligand binding. To estimate the binding affinity of SAL molecule to subdomains IB and IIA in HSA protein, binding free energies were calculated using the Molecular Mechanics-Generalized Born Surface Area (MM-GBSA). It is found that the presence of SAL molecule resulted in the stability of HSA. Also, ligand binding decreases the α-helix content of HSA. Binding free energy calculations demonstrate that the binding affinity of the SAL molecule to subdomain IIA of HSA is more than that of subdomain IB of HSA and the contributions of van der Waals interactions are more than that of electrostatics interactions. The per-residue decomposition of binding free energy suggested that the favorable residues with the most contribution in the binding free energy are hydrophobic, contributing to van der Waals interactions. Our important finding is that the subdomain IIA of HSA is the main HSA-SAL binding site. The results obtained are in good agreement with the corresponding experimental data.
Molecular dynamics simulations
Binding free energy
Human Serum Albumin
Salicylic Acid
Molecular mechanics-generalized born surface area
2017
09
01
483
496
https://www.physchemres.org/article_44853_c8fc13520891d902dc304115ee630e4c.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
The Effect of Substrate on Structural and Electrical Properties of Cu3N Thin Film by DC Reactive Magnetron Sputtering
Alireza
Razeghizadeh
Maryam
Mahmoudi Ghalvandi
Farhang
Sohillian
Vahdat
Rafee
The aim of this paper is to study the effect of substrate on the Cu3N thin films. At first Cu3N thin films are prepared using DC magnetron sputtering system. Then structural properties, surface roughness, and electrical resistance are studied using X-ray diffraction (XRD), the atomic force microscope (AFM) and four-point probe techniques respectively. Finally, the results are investigated and compared for glass and Si substrate. The results show a phase transition in orientation from (111) and (100) planes to (200) plane when the substrate of the sample is changed from glass to Si. Also, the grain size of deposited particles on films increased, changing substrate from glass to Si. Then, AFM results show that surface roughness on Si substrate is more than the glass substrate. Finally, four-point probe techniques show that surface electrical resistivity is increased sharply, changing substrate from silicon to glass.
DC reactive magnetron sputtering
Thin films
Cu3N
X-ray diffraction
Atomic force microscopy
2017
09
01
497
504
https://www.physchemres.org/article_45112_eac6880b0b25b8d867cb83d5bbc773b3.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Modeling the Thermodynamic Properties of Solutions Containing Polymer and Electrolyte with New Local Composition Model
Ali
Mohammadian-Abriz
Roghayeh
Majdan-Cegincara
A new theory model based on the local composition concept (TNRF-modified NRTL (TNRF-mNRTL) model) was developed to express the short-range contribution of the excess Gibbs energy for the solutions containing polymer and electrolyte. An equation represented the activity coefficient of solvent was derived from the proposed excess Gibbs energy equation. The short-range contribution of interaction along with the long-range contribution of interaction and configurational entropy of mixing were used to correlate the activity coefficient of ternary polymer + electrolyte + water systems and also binary polymer + water and electrolyte + water systems. The long-range interaction and configurational entropy have been given by the Pitzer-Debye-Hückel equation and the Flory-Huggins relation, respectively. The performance of the proposed model in fitting the solvent activity of ternary polymer + electrolyte + water solutions has been compared with that obtained from the ternary NRTL, ternary Wilson, ternary modified NRTL and ternary modified Wilson models. Results comparison was demonstrated the validity of the proposed model for solvent activity of polymer + electrolyte + water solutions.
Mathematical Modeling
Aqueous solutions of polymer + electrolyte
Thermodynamic properties
TNRF-mNRTL model
Activity coefficient
2017
09
01
505
518
https://www.physchemres.org/article_45114_b5b3d83dc2fdd929000e53ffb29d00e3.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Adsorption Properties of Folic Acid onto Functionalized Carbon Nanotubes: Isotherms and Thermodynamics Studies
Shahla
Hamedani
Zahra
Felrgari
In the present research, we report the results of a systematic study on the adsorption properties of folic acid (FA) over functionalized single-walled carbon nanotubes (SWCNTs) using the various factors, such as adsorbent dose, contact time, temperature, and initial FA concentration. Our results reveal that SWCNT is an excellent adsorbent for folic acid, with an adsorption percentage of up to 76.2 % at initial folic acid concentration of 20 ppm and temperature of 298.15 K. Interpreting equilibrium isotherms on the basis of various adsorption models, including Freundlich and Langmuir, shows that the Langmuir model can describe the adsorption process better than the other one. To further examine the adsorption behavior, we perform thermodynamic calculations which indicate that the adsorption reaction of FA onto SWCNTs is an exothermic and spontaneous procedure in the temperature range of 298.15–313.15 K. Based on this experimental study, the functionalized SWCNTs are expected to be a potential efficient adsorbent and also can be used as a suitable drug delivery vehicle within biological systems.
Adsorbent
Adsorbate
Isotherm models
Thermodynamic functions
Equilibrium
2017
09
01
519
529
https://www.physchemres.org/article_45173_64017b2749c65d1a3fba7459ccb460bb.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Conductometric Study of the Thermodynamics of Micellization of Sodium dodecylsulfate (SDS) in the Presence of Some Aromatic Ammonium Salts
Olanrewaju
Owoyomi
Joseph
Funso Olorunyomi
Oluwasegun
Emmanuel Olaoye
The effect of three organic aromatic salts - Phenyltrimethylammonium (PhTMAB), benzyltrimethylammonium (BzTMAB) and benzyltrimethylammonium (BzTEAB) bromides - on the micellization of sodium dodecylsulfate has been investigated by conductometric method. The critical micelle concentration (CMC) values were found to decrease with increase in the concentration of the aromatic ammonium salts. Thermodynamic parameters of micellization were obtained from CMC measurement in the presence of 0.001 M of the three quaternary aromatic ammonium salts in the temperature range 293-313 K at 5 K intervals. The Gibbs free energy values were generally negative in the presence of the aromatic salts and slightly varied with temperature. The micellization process was both enthalpy and entropy driven. Enthalpy-entropy compensation was observed for all the system with a constant compensation temperature values around 302 K and negative intrinsic enthalpy of compensation.
Micellization
Aromatic ammonium salts
thermodynamic parameters
Enthalpy-entropy compensation
2017
09
01
531
540
https://www.physchemres.org/article_45367_695f80dfa33d84743ed351835536fd5d.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Spectroscopic, Thermodynamic and Molecular Docking Studies on Interaction of Toxic Azo Dye with Bovine Serum Albumin
Nahid
Rasouli
Nasrin
Sohrabi
Davood
Ajloo
Naficea
Rezvani
Investigation on interaction of azo dyes with bovine serum albumin as carrier protein will be important in the field of toxicology because of distribution and transportation of dyes in blood. 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 strength (NaCl) in 5 mM aqueous phosphate buffer of pH 7.0 at 25°C. Spectrophotometric studies of the interaction between Amaranth and BSA have shown that the binding constant was Kb = 7.1×104 M-1 at 298 K. Thermodynamic parameters (ΔH > 0 and ΔS > 0) indicated that hydrophobic forces play major roles in the interaction between Amaranth and BSA. Further, the fluorescent experiments revealed that the quenching mechanism of BSA by Amaranth was static. Also, no obvious increasing of BSA viscosity was observed by addition of Amaranth. The molecular docking method is also employed to understand the interaction of Amaranth with BSA. All these studies confirm that BSA has more affinity towards Amaranth and the groove binding must be predominant.
Toxic Azo dye
Bovine serum albumin
Thermodynamic
Fluorescence quenching
Molecular docking
2017
09
01
541
554
https://www.physchemres.org/article_45427_6675095942dc9d6eba6b0cd427925baa.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
The Effect of pH on the Liquid-liquid Equilibrium for a System Containing Polyethylene Glycol Di-methyl Ether and Tri-potassium Citrate and its Application for Acetaminophen Separation
Mohammed
Zafarani-Moattar
Hemayat
Shekaari
Parisa
Jafari
In this work liquid-liquid equilibrium for aqueous two phase system composed of polyethylene glycol di-methyl ether and tri-potassium citrate at different medium pH values (6.00, 7.00 and 8.00) and 298.15 K was studied. The obtained results show that two phase area expanded with an increasing of pH values. The performances of the Merchuk and semi-empirical equations were tested in correlating the obtained binodal data. The reliability of the experimental tie-lines was checked using the Hand and Bachman equations. Then, this two-phase system has been used to investigate partitioning of acetaminophen by determining the composition of coexisting phases in presence of acetaminophen. Experimental results show that 60-80% of the drug could be extracted into the polymer-rich phase in a single-step separation. The partitioning coefficient of acetaminophen was changed slightly with the increase of length tie-line (TLL) and also with the increase of pH values. Thermodynamic studies indicated that hydrophobic interactions were the main driving force, although electrostatic interactions and salting-out effects were also important for the transfer of the drug. Finally, the equation proposed by Diamond-Hsu was used to the correlating of the experimental partition coefficients of acetaminophen in the studied polymer- salt ATPS.
Aqueous two-phase system
Partitioning coefficient
Poly ethylene glycol di-methyl ether
Tri-potassium citrate
Acetaminophen
2017
09
01
555
567
https://www.physchemres.org/article_46045_8c90509aed6049d35047c24d5226673e.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Surface Tension Prediction of n-Alkanes by a Modified Peng-Robinson Equation of State Using the Density Functional Theory
Nahid
Farzi
Zakieh
Yazdanshenas
Through this study, the ability of a modified Peng-Robinson (MPR) equation of state in predicting the surface tension of n-alkanes based on the density functional theory approach was investigated and compared with other studies. The interfacial layer thickness and the density profile were calculated simultaneously at different temperatures from triple point to near critical point using the modified Peng-Robinson equation of state. It was shown that the calculated thickness of interfacial layer increases with decrease in the chain length of n-alkanes molecules and raising of temperature. The surface tension of n-alkanes was calculated using the calculated values of thin layers’ densities. It was shown that the calculated surface tension of n-alkanes decreases with temperature in accordance with the experiment. The average relative error in prediction of the surface tension by the MPR equation of state was in the range of 2.5-6% while it was 4.6-25.2% by the Peng-Robinson equation of state. The validity of the MPR equation of state in the surface tension prediction of n-alkanes containing C1-C10 has been proved by comparing the results of this work with other studies.
Surface tension
Density functional theory
n-Alkanes
Density profile
2017
09
01
569
583
https://www.physchemres.org/article_46260_2d17075faa66f6229c974450561475f0.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
The Application of Hybrid RSM/ANN Methodology of an Iron-based Catalyst Performance in Fischer-Tropsch Synthesis
Afshin
Razmjooie
Hossein
Atashi
Farhad
Shahraki
In this research, the performance and kinetics of an iron/manganese oxide catalyst in a fixed-bed reactor by Fischer-Tropsch Synthesis is studied. The range of operating conditions are; P = 1 – 12 bar, T = 513 - 553 K, H2/CO ratio = 1 - 2 and GHSV = 4200 – 7000 ((〖cm〗^3 (STP))/h/g_cat). The effect of these independent variables, on Fischer-Tropsch product were performed by using a statistical model based on experimental data. Two models, response surface methodology and artificial neural network, were applied for modeling and predicting of the experimental points for carbon monoxide conversion (CO% conversion) and catalytic kinetic for the consumption rate of CO (-rco). Some statistical parameters such as correlation coefficient and mean square error were calculated to capability and sensitivity analysis of two models. Results show that two models, have good agreement with experimental data but artificial neural network model was stronger and more accurate than the response surface method model. To achieve the optimum condition, optimization must be done. It was obtained that maximum amount of CO% conversion was achieved in P = 8 bar, T = 559.5 K, H2/CO = 2.5 and GHSV = 7325.2 ((〖cm〗^3 (STP))/h/g_cat) and maximum amount of consumption rate of CO was in P = 8 bar, T= 568 K, H2/CO = 2.5 and GHSV = 2800 ((〖cm〗^3 (STP))/h/g_cat). Finally, all of quadratic equations and optimum conditions for any variable and responses will be concluded.
Fischer-Tropsch synthesis
Catalytic kinetic modeling
Response Surface
Artificial Neural Network
optimization
2017
09
01
585
600
https://www.physchemres.org/article_46481_d8cd7d51f685d7762aca1cd9785866de.pdf
Physical Chemistry Research
PCR
2322-5521
2322-5521
2017
5
3
Geometric and Electronic Structures of Vanadium Sub-nano Clusters, Vn (n = 2-5), and their Adsorption Complexes with CO and O2 Ligands: A DFT-NBO Study
Ali Haidar
Pakiari
Fazlolah
Eshghi
In this study, electronic structures of ground state of pure vanadium sub-nano clusters, Vn (n=2-5), and their interactions with small ligands for example CO and triplet O2 molecules are investigated by using density functional theory (DFT) calibration at the mPWPW91/QZVP level of theory. The favorable orientations of these ligands in interaction with pure vanadium sub-nano clusters were determined. Multiplicities of these pure clusters are triple, doublet, singlet and doublet for dimer, trimer, tetramer and pentamer, respectively. While the CO molecule is associatively adsorbed on vanadium clusters, triplet O2 is dissociated over adsorption. Primary and secondary hyper-conjugation concepts have been employed to show stabilization of vanadium oxide complexes. Natural bond orbital (NBO) and natural resonance theory (NRT) analysis revealed that trimer, tetramer and pentamer clusters are relatively delocalized and have some resonance structures.
Transition metal clusters
Metal-metal multiple bond
Organometallic compounds
Catalytic activity
2017
09
01
601
615
https://www.physchemres.org/article_46570_427b90461045e46f447323967d6cfb70.pdf