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Thermodynamics of binding of divalent metal ions including Ca(2+) , Mg(2+) , Ba(2+) , and Cd(2+) to Ca-free horseradish peroxidase (HRP) enzyme was investigated using UV/VIS spectrophotometry and molecular-mechanic (MM) calculations. According to the obtained binding and thermodynamic parameters, trend of the relative binding affinities of these divalent metal cations was found to be: Ca(2+) >Cd(2+) >Mg(2+) >Ba(2+) . Binding analysis based on Scatchard and Hill models showed positive cooperativity effect between the two distal and proximal binding sites. Furthermore, kinetics of binding and reconstitution process was examined (using relaxation-time method) for binding of Ca(2+) (as the typical metal ion) to Ca-free HRP, which was found a second-order type having a two-step mechanism involving fast formation of Ca-free HRP/1?Ca(2+) as the kinetic intermediate in step 1. Finally, by means of MM calculations, the comparative stability energies were evaluated for binding of M(2+) metal cations to Ca-free HRP. Based on MM calculations, preferential binding of Ca(2+) ion was occurred on distal and proximal binding sites of Ca-free HRP associated with higher stability energies (E(total) ). Indeed, among the divalent metal ions, Ca(2+) with the highest binding affinity (maximum value of K(bin) and minimum value of ΔG$\rm{{_{bin}^{0}}}$), maximum value of exothermic binding enthalpy, and stability energies stabilizes the HRP structure along with an optimized catalytic activity. 相似文献
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The structural and electronic properties of a three-state molecular switch—an active device in a nano-electronic circuit—were
studied using the B3LYP/6-31G* method. Due to its chemical stability, high conductivity upon doping, and non-linear optical
properties, polythiophene is among the most widely studied conjugated organic polymers, both experimentally and theoretically.
The aim of the present work was to theoretically study a very complex case: a three-state switch synthesized and experimentally
investigated by Nishida et al. (Org Lett 6:2523–2526, 2004). An initial set of test calculations showed B3LYP level of theory
and 6-31G* basis set to be the most appropriate for our purpose, i.e., the study of the structure, charge and spin distributions,
as well as electrical characteristics such as electric polarizability, HOMO-LUMO gap (HLG) and electric dipole moment, for
one of the 1,2-dithienylcyclopentene derivatives. Also, natural bond orbital analyses were performed to calculate local charges
and charge transfers in order to study the capability of the molecule as a molecular switch. The results reported here are
of general significance, and demonstrate that it is possible to use certain structural and electrical properties to understand
and design electro-photochromic compounds showing a switching function in cases where stable forms can be exchanged by light
or electron transfer.
Figure Model of a thiophene wire incorporating a redox active unit 相似文献
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Zabiollah Bolboli Nojini Amir Abbas Rafati Seyed Majid Hashemianzadeh Sepideh Samiee 《Journal of molecular modeling》2011,17(4):785-794
The adsorption of helium and neon mixtures on single-walled carbon nanotubes (SWCNTs) was investigated at various temperatures
(subcritical and supercritical) and pressures using canonical Monte Carlo (CMC) simulation. Adsorption isotherms were obtained
at different temperatures (4, 40, 77 and 130 K) and pressures ranging from 1 to 16 MPa. Separation factors and isosteric enthalpies
of adsorption were also calculated. Moreover, the adsorption isotherms were obtained at constant specific temperatures (4
and 40 K) and pressures (0.2 and 1.0 MPa) as a function of the amount adsorbed. All of the adsorption isotherms for an equimolar
mixture of helium and neon have a Langmuir shape, indicating that no capillary condensation occurs. Both the helium and the
neon adsorption isotherms exhibit similar behavior, and slightly more of the helium and neon mixture is adsorbed on the inner
surfaces of the SWCNTs than on their outer surfaces. More neon is adsorbed than helium within the specified pressure range.
The data obtained show that the isosteric enthalpies for the adsorption of neon are higher than those for helium under the
same conditions, which means that adsorption of neon preferentially occurs by (15, 15) SWCNTs. Furthermore, the isosteric
enthalpies of adsorption of both gases decrease with increasing temperature. 相似文献
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Razavi Seyedeh Saleheh Hashemianzadeh Seyed Majid Karimi Hedayat 《Journal of molecular modeling》2011,17(5):1163-1172
Canonical Monte Carlo (CMC) simulations were carried out to investigate the behavior of CO2 and N2 mixtures upon adsorption on single walled carbon nanotubes (CNTs). In the simulation, all the particle–particle interactions
between CO2, N and C were modeled using Lennard-Jones (LJ) potential. To provide deep insight into the effect of pore width, temperature,
pressure and bulk composition on the adsorption behavior of CO2 /N2 mixtures, five different CNTs [(6,6), (7,7), (8,8) (9,9) and (10,10) CNT] with diameters ranging from 0.807 to 1.35 nm, three
temperatures (300 323 and 343 K), six pressures (0.15, 2, 4, 6, 8 and 10 MPa), and three bulk mole compositions of carbon
dioxide (0.3 0.5 and 0.7) were tested. The results from all the simulation conditions investigated in this work show that
CNTs preferentially adsorb carbon dioxide relative to nitrogen in a binary mixture. The results are consistent with the hypothesis
that stronger interaction of one component with the nanotube surface results in a higher adsorption capacity compared to the
other component. An optimized pore size of D = 8.07 nm corresponding to (6, 6) CNT, at T = 300 K and P = 0.15 MPa at a bulk
mole composition of yCO2 =0.3 was identified in which carbon nanotubes demonstrate the greatest selectivity for separation of carbon dioxide relative
to nitrogen. In addition, it is worth pointing out that, under similar simulation conditions, CNTs exhibit higher selectivity
compared to other carbon-based materials [carbon membrane polyimide (PI) and PI/multi-wall carbon nanotubes (MWCNTs)] for
CO2 adsorption. As a prototype, the selectivity of an equimolar mixture of CO2 /N2 for adsorption on (6, 6) CNTs at 300 K and 0.15 MPa reaches 9.68, which is considerably larger than that reported in carbon
membrane. Therefore, it can be concluded that carbon nanotubes can act as a capable adsorbent for adsorption/desorption of
CO2 in comparison with other carbon-based materials in the literature. 相似文献
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Nanotubes are believed to open the road toward different modern fields, either technological or biological. However, the applications of nanotubes have been badly impeded for the poor solubility in water which is especially essential for studies in the presence of living cells. Therefore, water soluble samples are in demand. Herein, the outcomes of Monte Carlo simulations of different sets of multiwall nanotubes immersed in water are reported. A number of multi wall nanotube samples, comprised of pure carbon, pure silicon and several mixtures of carbon and silicon are the subjects of study. The simulations are carried out in an (N,V,T) ensemble. The purpose of this report is to look at the effects of nanotube size (diameter) and nanotube type (pure carbon, pure silicon or a mixture of carbon and silicon) variation on solubility of multiwall nanotubes in terms of number of water molecules in shell volume. It is found that the solubility of the multi wall carbon nanotube samples is size independent, whereas multi wall silicon nanotube samples solubility varies with diameter of the inner tube. The higher solubility of samples containing silicon can be attributed to the larger atomic size of silicon atom which provides more direct contact with the water molecules. The other affecting factor is the bigger inter space (the space between inner and outer tube) in the case of silicon samples. Carbon type multi wall nanotubes appeared as better candidates for transporting water molecules through a multi wall nanotube structure, while in the case of water adsorption problems it is better to use multi wall silicon nanotubes or a mixture of multi wall carbon/ silicon nanotubes. 相似文献
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Ketabi Sepideh Haeri Haleh Hashemi Hashemianzadeh Seyed Majid 《Journal of molecular modeling》2011,17(4):889-898
Most biological ion channels demonstrate a high degree of selectivity for one type of ion more than others, and in many cases,
how they control attaining this is still not clear. So we have studied on some metal ion compounds of glutamate. The Glutamate
and its meal ion compounds (Ca2+, Na+, K+ and Li+) were first modeled by ab initio calculations and then Monte Carlo simulation was used to calculate solvation free energies
and also the complexes free energies for the related structures. The results indicated that Glutamate-Ca2+ have more stability in water than other metal ion. Also, it was found out that the more movement in ions; less stability
of the structure would result. This trend can be seen both in gas and liquid phase. 相似文献
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Sepideh Ketabi Seyed Majid Hashemianzadeh Morteza MoghimiWaskasi 《Journal of molecular modeling》2013,19(4):1605-1615
Due to the importance of soluble nanotubes in biological systems, computational research on DNA base functionalized nanotubes is of interest. This study presents the quantitative results of Monte Carlo simulations of Li-doped silicon carbide nanotubes and its nucleic acid base complexes in water. Each species was first modeled by quantum mechanical calculations and then Monte Carlo simulations were applied to study their properties in aqueous solution. Solvation free energies were computed to indicate the solvation behavior of these compounds. The computations show that solvation free energies of the complexes of DNA bases with Li-doped SiC nanotubes are in the order: thymine > cytosine > adenine > guanine. The results of complexation free energies were also used to study the stability of related structures, which indicate that thymine-Li-doped SiC nanotubes produce the most stable compound among the four DNA base complexes. 相似文献
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