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جستجوی مقالات مرتبط با کلیدواژه "binding energy" در نشریات گروه "شیمی"

تکرار جستجوی کلیدواژه «binding energy» در نشریات گروه «علوم پایه»
  • Nosrat Madadi Mahani *, Roya Yosefelahi, Reza Behjatmanesh-Ardekani

    Drug delivery based on nanocages is helpful in nanomedicine with the minimum side effects and targeting drugs in the cancer cell. Bendamustine, an anti-cancer drug, inhibits the activity of cancer cells in humans and is broadly used in the therapy of breast cancer. The interaction of single Bendamustine and Bendamustine @Al/B-N/P nanocages with P53 protein was studied. In this study, molecular docking and molecular dynamics simulations(MD) were conducted to investigate the interaction of some of the Bendamustine, Al/B-N/P nanocages with the P53 protein. The best pose of the configuration of Bendamustine and Bendamustine @Al/B-N/P nanocages in the active sites of the P53 protein results in negative binding energies. Complexes of Bendamustine@B12N12 and Bendamustine@B12P12 with P53 protein have the most binding energy. In addition, MD simulation was done on the stable complexes with high binding energy to recognize the structural changes in the complexes of Bendamustine, Bendamustine@B12N12, and bendamustine@B12P12 nanocages with P53 protein. Studies illustrated that B12N12 and B12P12 could serve as drug carriers for delivering the Bendamustine drug in a targeted procedure for inhibiting the P53 protein. In-silico studies are important parts of the structure-based drug design process that displayed that nanocages are suitable sensors of Bendamustine drug.

    Keywords: Binding energy, Drug Carriers, Root Mean Square Displacement, radius of gyration, Anti-cancer drug
  • معصومه شهرکی، پویا کریمی*، محمود سنچولی، مهدیه پورسرگل، حجت ثمره دلارامی
    باتری های قابل شارژ یون منیزیم  برای ذخیره ی انرژی الکتریکی مفید هستند زیرا فراوانی و چگالی انرژی منیزیم از لیتیم بیشتر است. در این تحقیق، با استفاده از محاسبات مکانیک کوانتومی ساختار اولیه ی نانولوله های کربنی تک دیواره دسته صندلی (4و4)، (5و5) و (6و6) با استفاده از روش M06-2X و مجموعه پایه ی (d,p) 6-31g توسط بسته نرم افزاری گوسین 09 بهینه شده است. سپس، برهمکنش یون منیزیم با این ساختارها مطالعه شد تا قابلیت آنها برای ساخت باتری های منیزیمی ارزیابی شود. نتایج نشان می دهد که کمپلکس های ایجاد شده از این ساختارها انرژی های اتصال خوبی دارند و هرچه قطر خارجی نانو لوله ها بیشتر باشد انرژی اتصال مطلوب تر است. در واقع، فاصله انرژی این نانو لوله ها با افزایش قطر نانولوله کاهش می یابد و بر قدرت اتصال آنها به یون منیزیم تاثیر می گذارد. از طرفی، نانو لوله های نیترید بور متناظر با نوع کربنی نیز با روش مشابهی بهینه شد و برهمکنش یون منیزیم با این ساختارها نیز بررسی شد. نتایج نشان می دهد که نانو لوله های نیترید بور با قطر خارجی کمتر کمپلکس های با انرژی اتصال بیشتر با یون منیزیم تشکیل می دهند. به طور کلی، هر دو نوع این نانو لوله ها گزینه های خوبی برای تهیه ی ماده ی آندی در باتری های یون منیزیم هستند. سرانجام، بیشتر شدن انرژی اتصال کمپلکس های آنها با یون منیزیم با افزایش ولتاژ باتری همراه است.
    کلید واژگان: نانولوله, نیتریدبور, باتری یون منیزیم, انرژی اتصال, مکانیک کوانتومی
    Masoumeh Shahraki, Pouya Karimi *, Mahmoud Sanchooli, Mahdieh Poorsargol, Hojat Samareh-Delarami
    Magnesium ion rechargeable batteries are useful for storing electrical energy because the abundance and energy density of magnesium is higher than lithium. In this research, the primary structures of the (4, 4), (5, 5) and (6, 6) single-walled carbon nanotubes were optimized using the M06-2X method and the 6-31g(d,p) basis set using Gaussian 09 program package. Then, the interaction of magnesium ion with these structures was studied to evaluate their ability to make magnesium batteries. The results show that the complexes created from these structures have good binding energies and the larger the outer diameter of the nanotubes, the more favorable the binding energy. In fact, the energy gap of these nanotubes decreases with the increase of the diameter of the nanotubes and affects their binding strength to magnesium ions. On the other hand, boron nitride nanotubes corresponding to carbon type were also optimized with a similar method and the interaction of magnesium ion with these structures was also investigated. The results show that boron nitride nanotubes with smaller outer diameters form complexes with higher binding energies with magnesium ions. In general, both types of these nanotubes are good options for preparing the anode material in magnesium ion batteries. Finally, increasing the binding energy of their complexes with magnesium ions is associated with increasing battery voltage.
    Keywords: Nanotube, Boron nitride, Magnesium-ion battery, Binding energy, Quantum Mechanics
  • Pouya Karimi *, Mahdiye Poorsargol, Mahmood Sanchooli
    Adsorption of phosgene on the surface of a graphene sheet was studied. The surface of this material was modified through a metamaterial approach using heteroatoms (N and B), the addition of hydrogen atom, and functionalized with four CHO groups at edges to survey the role of defects, Hydrogen Bonding (HB), and Intramolecular Hydrogen Bonding (IHB) interactions on adsorption. Generally, there is repulsion between the π-electron cloud of the graphene sheet and electrons of electronegative atoms on pollutants. However, the addition of hydrogen atoms to the surfaces of this material leads to the formation of attractive HB interactions with pollutants such as phosgene. Also, heteroatoms have helpful effects on the adsorption process. Therefore, the adsorption of phosgene on a modified graphene sheet is better than that of pristine graphene. Results of Molecular Dynamic (MD) simulations expose that van der Waals (vdW) and HB interactions have major contributions to the adsorption of phosgene on modified graphene.
    Keywords: Metamaterial, pollutants, Intramolecular hydrogen bonding, charge transfer, Binding energy
  • Fater Iorhuna *, Muhammad Ayuba, Abdulfatah Muhammad
    Quantum chemical parameters and molecular dynamic simulation studies were used to evaluate the corrosion inhibition of mild steel using pyrimidine derivatives (5-Phenoxy-6-phenyl-4-p-tolyl-1H-pyrimidin-2-one (PMO), 5-(7-Oxa-bicyclo[4.1.0]hepta-1(6),2,4-trien-2-yloxy)-pyrimidine-2,4-diamine (PMA), and 5-Phenoxy-6-phenyl-4-p-tolyl-1H-pyrimidine-2-thione (PMS)) as inhibitors. The pyrimidine derivatives were geometrically optimized using DFT with a restricted spin polarization, DNP basis set, and a local density function B3LYP. According to the local or global reactivity parameters investigated, including the energy gap (ΔE), dipole moment (μ), electronegativity (χ), global hardness (η), global electrophilicity index (ω), nucleophilicity (ε), energy of back donation (ΔEb-d), and fraction of electron transfer (ΔN) between the inhibitor molecule and the iron surface, PMS is relatively a better inhibitor on Fe(111) surface than other inhibitors studied. This is demonstrated by its higher nucleophilicity. According to the evaluated Fukui indices, the interaction point between molecules and Fe(111) surface involve heteroatoms of sulphur, oxygen, and nitrogen that donate electrons which are wholly nucleophilic in nature. The nature and strength of the compounds' adsorption on the Fe(111) surface was described by quenched molecular dynamics simulations in the following order: PMS>PMO>PMA. There is relatively a weak interaction for the studied molecules with the Fe(111) surface, according to the measured molecular bond lengths and angles before and after adsorption and as well as the calculated adsorption/binding energies. It is suggested that physical adsorption mechanism can be used to describe the nature of the interaction of the pyrimidine derivative molecules with the Fe (111) surface.
    Keywords: Fukui indices, Binding energy, geometric optimization, Quantum chemical parameters, physisorption
  • Fater Iorhuna *, Adulfatah Muhammad, Abdullahi Ayuba, Aondofa Nyijime
    Through the use of theoretical techniques, this study investigated the corrosion inhibition potentials of a few chosen nitrogen-based five membered ring heterocycles, such as 2-methyl-1H-imidazole (2MI), 2-methyl-oxazole (2MO), 2,4,5-trimethyl-thizole (2TT), and 3-methyl-4,5-dihydro-1H-pyrole (MPP), on the surface of mild steel. To determine the potentials of these compounds in corrosion inhibition and to suggest a mechanism for the process, quantum chemical parameters, Fukui indices, and quench molecular dynamic simulation approaches were used. The corrosion inhibition potentials of the examined compounds were discovered to be caused by the existence of numerous hetero atoms rich in n-electrons, pi-bonds, molecular shape, and charge distribution. The outcomes demonstrated that each molecule's adsorption or binding energy is negative and comparatively low, less than the +100kcal/mol threshold. It has also been discovered that, depending on the parameters examined, the 2TT molecule may be more efficient in preventing corrosion on the Fe(1 1 1) surface. This is owing to the sp3 sulfur heteroatom in its structure, which is probably less electronegative than other sp3 heteroatoms (oxygen and nitrogen) in the compounds, in addition to the sp2 nitrogen each of them contained. from the results, all of the investigated compounds have the capacity to prevent mild steel corrosion. The molecules adhere to the physical adsorption process, the mechanism, the expected adsorption/binding energies, and the molecule's examined properties all indicate that 2TT is substantially a stronger corrosion inhibitor on Fe(1 1 1), in the following order: 2TT >MDP > 2MI > 2MO.
    Keywords: physisorption, quantum-chemical parameters, Molecular Dynamic Simulation, Binding energy, Fukui indices
  • محمد اجمل خیشکی، محمد قاسم نژند، فرح مرصوصی*
    در این پژوهش، ویژگی های زیست حسگری گرافین های مولکولی از جمله کرونین، سیرکوم-کرونین و سیرکوم سیرکوم-کرونین از نظر اندازه، ساختار مولکولی و ویژگی های شیمیایی مورد بررسی قرار گرفته است. شبیه سازی ها با نرم افزار گوسین به روش نظریه ی تابعی چگالی تحت تابعی و توابع پایه ی B3LYP/6-31G(d,p) انجام شده است. نتایج محاسبات نشان می دهد که از ساختارهای مورد بررسی، دو ساختارهای کرونین و سیرکوم-کرونین به لحاظ ویژگی های فیزیکی همچون انرژی بستگی، و ویژگی های شیمیایی همچون سختی شیمیایی بالا، برای توالی یابی مولکول زیستی DNA پیشنهاد می شود و می توان از این ساختارها حسگرهایی ساخت که قابلیت تشخیص هر چهار نوکلیوبازهای مولکول DNA را داشته باشند.
    کلید واژگان: حسگرهای زیستی, کرونین, نوکلئوبازهای مولکول DNA, نظریه تابعی چگالی, انرژی بستگی
    Mohammad Ajmal Khishki, Mohammad Qasemnahznd, Farah Marsusi *
    Trying to discover the different characteristics of biosensor systems is the most important part of research development in various fields, especially in the field of biomolecular science. In this research, the biosensor properties of molecular graphene (Coronene, Circumcoronene and Circumcircumcoronene) have been investigated for their molecular size and chemical properties. Among the three mentioned structures, two of them (coronene and Circumcoronene) have been selected based on their properties for sequencing DNA molecules. Calculations were performed with the B3LYP hybrid function and 6-31G(d,p) basis set. After performing the necessary simulations and calculations, the results show that these graphene molecular structures can be used as biosensors.
    Keywords: Biosenso, Coronene, DNA, density functional theory, Binding energy
  • خاطره عبدی، علیرضا نوروزی، حسن منصوری ترشیزی، راضیه ملک محمدی

    یک کمپلکس Zn(II) با یک لیگاند باز شیف درشت حلقه که دارای چهار اتم نیتروژن دهنده است از واکنش بین اورتو-فنیلن دی آمین، استیل استن و ZnCl2 با نسبت استوکیومتری 1:2:1 تهیه شد. این واکنش به روش تمپلت تک ظرف انجام شد. این کمپلکس به روش های هدایت سنجی، آنالیز عنصری، دمای تجزیه و روش های طیف سنجی FT-IR، 1H NMR و UV-Vis شناسایی شد. برهمکنش بین کمپلکس تهیه شده (بیس(استیل استن-اورتو-فنیلن‌دی‌آمین) روی(II) کلرید) با دی اکسی ریبونوکلییک اسید استخراج شده از غده تیموس گوساله (CT-DNA) و آلبومین سرم گاوی (BSA) به کمک طیف سنجی جذب الکترونی فرابنفش-مریی بررسی شد. مقدار ثابت اتصال کمپلکس باCT-DNA بیش تر از BSA می باشد. غلظت کمپلکس Zn(II) در نقطه میانی انتقال CT-DNA از حالت طبیعی به حالت برهمکنش شده کمتر از BSA است. همچنین ثابت هیل (h) که مقدار آن 1/1 به دست آمد نشان دهنده غیرتعاونی بودن برهمکنش بین کمپلکس با BSA است. افزون بر این، به منظور بررسی برهمکنش کمپلکس Zn(II) با DNA و‌ BSA، از روش داکینگ مولکولی به کمک ساختار مینیمایز شده کمپلکس استفاده شد.

    کلید واژگان: لیگاند باز شیف, کمپلکس Zn(II), برهمکنش با DNA, برهمکنش با BSA, داکینگ مولکولی, انرژی اتصال
    Khatereh Abdi, Alireza Nowroozi, Hassan Mansouri-Torshizi, Raziyeh Malekmohammadi

    A tetraaza macrocyclic Schiff base complex of Zn(II) was synthesized by the reaction of ortho-phenylenediamine, acetylacetone, and anhydrous ZnCl2 in the ratio of 1:2:1, respectively. We adopted one pot template synthesis. The synthesized Zn(II) complex was characterized by repeating conductivity measurements, elemental analysis, decomposition point determinations, and spectroscopic methods such as FT-IR, 1H NMR, and UV-Vis studies. The interaction between the above Zn(II) complex (bis(acetylacetone-o-phenylenediamine)Zn(II) chloride) with calf thymus-deoxyribonucleic acid (CT-DNA) and bovine serum albumin (BSA) was studied by ultraviolet-visible absorption spectroscopy. The values of the binding constant suggest that the interaction affinity of the metal complex to CT-DNA is more as compared to BSA. The concentration of Zn(II) complex at the midpoint of the transition from native to interacted with CT-DNA is lower as compared to BSA. Moreover, the Hill coefficient, h, has a value of 1.1 which confirms the non-cooperativity in the binding of Zn(II) complex with BSA. Furthermore, in order to investigate the interaction between Zn(II) complex and DNA as well as BSA, the docking simulation was performed with the optimized structure of the complex.

    Keywords: Schiff base ligand, Zn(II) complex, DNA interaction, BSA interaction, Molecular docking, Binding energy
  • Nabieh Farhami *
    The effect of the adsorbed thiophene (T) on the surface of (8,0) zigzag single walled boron nitride nanotubes (BNNTs) was studied using density functional theory calculations in the gas phase. Geometry optimizations were also carried out at the B3LYP/6-31G (d) level of theory. The Gaussian 09 suites of programs were used. The geometric optimization of (8, 0) BNNT-T was performed using the minimum energy criterion in six different configurations of the adsorbed thiophene on the nanotube. Our computer simulations have found that the preferred adsorption site of the molecule is at the end of the nanotube for the T component and all cases have physical interactions. The results showed an increase in polarity due to the proper distribution of electrons. It was also found that the reduction in global hardness, energy gap and electronic chemical potential due to thiophene adsorption leads to an increase in the stability of the (8,0) zigzag BNNT-T complex. In this study, natural bond analysis, global softness, ionization potential and electrophilicity index for nanotubes were calculated.
    Keywords: Binding energy, Boron nitride nanotube, DFT theory, quantum molecular descriptors, thiophene
  • Mustapha Abdullahi *, Alhassan Usman, Ahmad Sani, Kamal Danazumi, Abdullahi Umar, Jaafar Yusuf
    Three expired antibiotic drugs namely, ampiclox, ciprofloxacin, and ampicillin were studied at low concentrations on the corrosion inhibition of mild steel (MS) in 0.1 M HCl medium using weight loss and scanning electron microscopy (SEM) techniques. Subsequently, the molecular structures of the antibiotic inhibitors were subjected to molecular dynamic (MD) simulation using Material Studio 8.0 software to have insight into their dynamic binding energy onto the Fe (110) surface in an acidic medium. The results showed that the weight loss and corrosion rate decrease with an increase in the inhibitor concentration, while the inhibition efficiency (%) and surface coverage increase with the increase in the inhibitor concentration respectively. The maximum inhibition efficiency of 97.72 % was attained at 0.009M concentration for ciprofloxacin followed by ampiclox and ampicillin. The SEM analysis of the MS with the expired ciprofloxacin (0.009 M) revealed a soother surface through the formation of a protective film that prevented the corrosion attack which confirms the highest inhibition efficiency. The MD simulation showed that the ciprofloxacin has the highest binding energy of -474.582 kcal/mol, followed by -248.448 kcal/mol for ampicillin and -234.955 kcal/mol for ampiclox respectively. Hence, the ciprofloxacin with the more negative magnitude of the binding energy was predicted to exhibit stronger chemisorption interaction onto the Fe (110) metal surface when compared with ampicillin and ampiclox. The findings in this research reveal good agreement between the experimental and theoretical results in studying the corrosion inhibition of the studied antibiotic drugs.
    Keywords: corrosion, Mild steel, Molecular Dynamics, Binding energy, Antibiotic drug
  • پویا کریمی*، محمود سنچولی
    در این پژوهش، نانو ساختارهای بر پایه ی گرافن با روش های شیمی کوانتمی محاسباتی شبیه سازی شده و برهم کن های جداگانه یون های ایزوالکترونیک سدیم و فلورید با وجه های درونی و بیرونی آن ها مطالعه شد. همچنین، برهمکنش های هم زمان این یون ها با وجه های درونی و بیرونی نانو ساختار ها با دو مدل بررسی شد. در مدل اول،یون فلورید با وجه بیرونی و یون سدیم با وجه درونی نانو ساختار ها به طور همزمان برهمکنش می دهد و در مدل دوم، موقعیت های یون ها تعویض شده تا اثر آن بر انرژی های اتصال کمپلکس های سه تایی مربوطه مطالعه شود. نتیجه ها مشخص نمود که انرژی های اتصال در مدل اول نسبت به مدل دوم به طور میانگین به میزان 90/1 کیلو کالری بر مول بیش تر است. همچنین، کاهش  استقرار نیافتگی الکترونی/ افزایش استقرار نیافتگی الکترونی در حلقه ی مرکزی نانو ساختارها برای برهمکنش یون ها با وجه بیرونی آن ها در مدل اول/مدل دوم دلخواه تر است. نتیجه ها پیشنهاد می کند که نانو ساختار های بر پایه ی گرافن به دلیل داشتن ویژگی های یگانه ساختاری و الکترونی بسترهای خوبی برای برهم کنش های یون ها هستند و می توانند به عنوان باتری های یون سدیم در نظر گرفته شوند. همچنین، افزایش انحنای نانو ساختار ها منجر به عامل دار شدن بهتر وجه های بیرونی آن ها با یون های با بار منفی می شود و می توان با تغییر دادن چگالی های ابر الکترونی دیواره آن ها عملکرد شان را به عنوان باتری های یونی بهینه نمود.
    کلید واژگان: نانو ساختار, گرافن, انتقال بار, انرژی اتصال, آروماتیسیته
    Pouya Karimi *, Mahmoud Sanchooli
    In this study, graphene-based nanostructures were simulated using computational quantum chemistry methods and individual interactions of isoelectronic ions sodium and fluoride with inner and outer faces of them have been studied. Also, simultaneous interactions of these ions with inner and outer faces of nanostructures have been investigated with two models.  In the first model, fluoride ion with outer face and sodium ion with the inner face of nanostructures interact simultaneously and in the second model, positions of ions were exchanged to study the effect of this on binding energies of the ternary complexes. Results indicate that binding energies in the first model are larger than the second one by an average 1.90 kcal mol-1. Indeed, a decrease of electron delocalization/increase of electron delocalization in the central ring of nanostructures is good for the interaction of ions with the outer face of them in the first model/second model. Results propose that graphene-based nanostructures due to unique structural and electronic properties are good beds for interactions of ions and can be considered as sodium-ion batteries. Also, the growth of curvature of nanostructures leads to better functionalization of their outer faces through ions with a negative charge and can optimize their performance as ion batteries using changing electronic cloud densities of their walls.
    Keywords: nanostructure, Graphene, charge transfer, Binding energy, aromaticity
  • Samuel Adawara *, Paul Mamza, Shallangwa Gideon, Abdulkadir Ibrahim
    Dengue infection is a major public health challenge in several parts of the world, especially the sub-tropical and tropical regions. The development of agents that are able to inhibit the dengue virus (DNV) replication are therefore of utmost significance. I. tinctoria is one of the most investigated Chinese herbs, which has been recognised to be effective in the treatment of dengue fever. However, the mechanisms through which it exhibits such biological activity of great importance are still unclear. A total number of about 27 compounds isolated from I. tinctoria leaves which have been identified and reported in the literature to be effective against dengue fever were investigated for their inhibitory potencies against dengue virus as novel drugs for treating early attacks of dengue fever. The compounds were optimized by employing a method of Density functional theory (DFT) and a basis set of B3LYP (6-31G**). The results of Molecular docking investigation between the compounds and the dengue viral protein (PDB: 6MO1) revealed that three of the compounds (GB-20, GB-19, and GB-6) possessing best binding energy in of -27.051, -26.193 and -24.664 kcal/mol respective were observed to inhibit the target through hydrogen bonds and hydrophobic interactions with amino acids residue of the protease binding site. The results of these studies would offer relevant insight into structural requirements for the development of effective and a specific therapeutic treatment against dengue virus infection.
    Keywords: Molecular docking, Binding energy, Hydrophobic interaction, Conventional hydrogen bond, Insatis tinctoria
  • Samah Abuzaid, Ayham Shaer, Mohammad Elsaid *
    In the present work, the exact diagonalization method had been implemented to calculate the ground state energy of shallow donor impurity located at finite distance along the growth axis in GaAs/AlGaAs heterostructure in the presence of a magnetic field taken to be along z direction. The impurity binding energy of the ground state had been calculated as a function of confining frequency and magnetic field strength. We  found that the ground state donor binding energy (BE)  calculated at =2  and  , decreases from BE=7.59822  to BE=2.85165 , as we change the impurity position from d=0.0  to d=0.5  ,respectively .In addition, the combined effects of pressure and temperature on the binding energy, as a function of magnetic field strength and impurity position, had been shown using the effective-mass approximation. The numerical results show that the donor impurity binding energy enhances with increasing the pressure while it decreases as the temperature decreases.
    Keywords: Binding Energy, Donor Impurity, Exact Diagonalization Method, Heterostructure, Magnetic Field
  • Arezoo Tahan *
    Density functional theory methods(DFT) and natural bond orbital (NBO) analysis were used to investigate the effects of isomerism and side chain mutation at a microscopic level on the stability, binding energy and NMR/NQR tensors of structural isomers, L- methionylasparagine (Met-Asn) and L- asparagylmethionine (Asn-Met) in the gas phase. The results represented that the isomerism and side chain mutation were caused to change the relative stability, binding energy and the thermodynamics parameters of peptide bond in the considered compounds. Therefore, Asn-Met had higher binding energy and relative stability than Met-Asn. On the other hand, NMR and NQR calculations at B3LYP/6-311+G (d, p) level of theory on the optimized structures of Met-Asn and Asn-Met indicated that the isotropic chemical shielding(σiso) values of oxygen and nitrogen nuclei in two structures with similar positions were different considerably and nitrogen nuclei were more shielded than oxygen nuclei in both dipeptides. In addition, amino nitrogens (N10 nuclei) had the highest values of chemical shielding (σiso) and the nuclear quadrupole coupling constant (χ) among nitrogen nuclei and the order of chemical shielding values of nitrogen nuclei in two structural isomers was amino nitrogen> amidic nitrogen> peptide nitrogen (N10>N9>N1). The mentioned order for chemical shielding values was exactly the opposite of the order of resonance energies values of nitrogen lone pair electrons in two dipeptides. In other words, by increasing contribution of nitrogen lone pair electrons in intra-molecular resonance interactions, NMR chemical shielding around nitrogen nuclei were decreased.
    Keywords: binding energy, L-Methionylasparagine, L-Asparagyl methionine, Isomerism, NBO analysis
  • حیدرعلی شفیعی گل، اعظم مرادی
    در این مطالعه، خواص ساختاری و الکترونی خوشه های GanNn (10-1=n) با استفاده از فرمول بندی تابعی چگالی(DFT) و به روش PAW در بسته ی نرم افزاری VASP مورد بررسی قرار می گیرند. نتایج حاصل ازمحاسبات نشان می دهد که در ساختارهای پایدارتر خوشه های کوچک، اتم های N تمایل بیشتری به تشکیل پیوند هایی بصورت واحدهای سازنده ی 2N و یون آزید دارند، در حالی که در خوشه بزرگتر، ساختارهای سه بعدی قفس مانند با پیوندهای Ga-N بیشتر ظاهر می شوند. یک افزایش سریع در انرژی بستگی بر اتم از 1n= به 2n= به دلیل گذار ساختار از حالت یک بعدی به دو بعدی و افزایش همپوشی های میان اوربیتال های N و Ga، جهت رسیدن به پایداری بیشتر است. این تغییرات برای ایزومرهای اول خوشه های 3 n> روندی تقریبا خطی را دنبال می کنند. پربند چگالی بار نشان می دهد که اگر چه پیوند Ga-N دارای خصلت یونی است ولی بطور خیلی جزئی نیز رفتار کووالانسی از خود نشان می دهد. همچنین پایین ترین ترازهای انرژی مربوط به اوربیتال های N-s، ترازهای میانی یک حالت هیبریدی از Ga-s و N-p و ترازهای نزدیک به تراز فرمی مربوط به Ga-p و N-p هستند.
    کلید واژگان: تابعی چگالی, خوشه, ایزومر اول, انرژی بستگی, ترازهای انرژی
    Ha Shafieygol, A. Moradi
    In this study, structural and electronic properties of GanNn clusters (n=1-10) are investigated using formalism of density functional theory (DFT) and projector augmented plane waves (PAW) within VASP software package. Results of calculations show that more tendency of N atoms in more stable structures of small clusters is the formation of building blocks N2 and AWT IMAGE azid, whereas the 3D structures are revealed as cage-like shape with Ga-N bonds. A sharp increase in binding energy per atom from n=1 to n=2 is due to structure transition from 1D to 2D and increase of overlapping between N and Ga orbitals in order to obtain more stability. These changes for clusters with n>3 follow approximately a linear trend. Charge density contour shows an ionic bond with partial covalent character for Ga-N. Also, the lowest energy levels devote to N-s orbitals, middle levels to a hybridized case of Ga-s and N-p orbitals and levels close to Fermi level to a hybridized case of Ga-p and N-p orbitals.
    Keywords: Density functional, cluster, first isomer, binding energy, energy levels
  • Fahimeh Shojaie *

    The effect of impurities on quantum chemical parameters of single-walled nanotubes (SWNTs) was studied using density functional theory (DFT). The density of states (DOS), Fermi energy and thermodynamic energies of (5,5) carbon nanotubes were calculated in the presence of nitrogen impurity. It was found that this nanotube remains metallic after being doped with one nitrogen atom. The partial density of states (PDOS) of spin up and spin down electrons shows that the SWNTs and nitrogen doped single-walled nanotubes (N-SWNTs) are anti-ferromagnetic. Comparing the results of SWNTs with N-SWNTs, it can be shown that there is a relationship between the energy gap and the DOS. The relationship between the thermodynamic properties and the binding energies of nanotubes is similar to the energy gap and the DOS relation.

    Keywords: Density of states, Binding energy, Single, walled nanotube, Fermi energy, Anti, ferromagnetic
  • F. R. Nikmaram *, M. Khan Ahmadi

    The binding energy and Thermodynamic Parameters of cis- Platinum Di Ammino Chlorine (cis-[Pt(NH3)2Cl]+) and trans- Platinum Di Ammino Chlorine (trans- [Pt(NH3)2Cl]+) complexes withGuanine has been studied by density functional theory (DFT) calculations in water. The bindingenergies (Ebin) of cis- and trans-[Pt(NH3)2ClG]+ are calculated to be 79.38 kcal/mol and 74.98kcal/mol, respectively. The binding energy (Ebin) of cis-[Pt(NH3)2ClG]+ turns out to be energeticallymore favorable by about 1.88 kcal/mol than the trans-[Pt(NH3)2Cl]+. At the point of thermodynamic,the formation of cis-[Pt(NH3)2ClG]+(aq)with G (Solv) equal to -10.36 kcal/mol is more favorablethan trans-[Pt(NH3)2ClG]+(aq) with 16.21 kcal/mol.

    Keywords: cis-Pt, trans-Pt, Guanine, binding energy, Thermodynamic Parameters
  • M. Oftadeh *, N. Madadi Mahani, R. Bahjatmanesh Ardakani
    Linear–dendrite copolymers containing hyper branched poly(citric acid) and linear poly(ethylene glycol) blocks PCA–PEG–PCA are promising nonmaterial to use in nanomedicine. To investigate their potential application in biological systems (especially for drug carries) ONIOM2 calculations were applied to study the nature of particular interactions between drug and the polymeric nanoparticles. Binding energy (BE) and interaction energy (IE) analysis of these complexes allowed the fundamental features of the drug- the Linear– dendritic copolymers interactions to be assessed based on ONIOM method. The results show that they have weak interaction and these complexes have relatively low stability and so PCA-PEG-PCA copolymers can use to as drug delivery.
    Keywords: Copolymeric nanoparticles, Drug carriers, ONIOM, Binding energy
  • P. Sadeghi, Alavijeh, M. Monemzadeh*, N. Tazimi
    In this paper, using Monte Carlo Fortran code, we have obtained the binding energies for three different systems of diquark–antidiquark in distances from 0.01 to 15 nm. In [0.1 - 15] nm interval, we made use of Coulomb potential because in this interval, strong interaction is negligible. We have compared the binding energies of the systems with one another. The results of these comparisons were close to our anticipations. We also obtained the binding energy of one of the systems in the interval below 1 fm, where diquark-antidiquark systems comprise a tetraquark and the potential is of strong interaction type. Because of weak Coulomb interaction, strong interaction has been used as the basis of the calculations. The binding energy resulted is consistent with the existing references.
    Keywords: Tetraquark System, Lippman, Schowinger, Equation, Binding Energy
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