Journal of Molecular Modeling

Following our previous work, where we described the interaction of calcium with the Cx26 hemichannel, we further explore the same system by atomistic molecular dynamics simulations considering a different di-cation, magnesium. Specifically, the interaction of magnesium di-cation with the previously reported calcium binding sites (ASP2, ASP117, ASP159, GLU114, GLU119, GLU120, and VAL226) was investigated to identify similarities and differences between them. In order to do so, four extensive simulations were carried out. Two of them considered a Cx26 hemichannel embedded on a POPC bilayer with one of the di-cations and a sodium-chlorine solution. For the remaining two, no di-cations were included and a sodium-chlorine or potassium-chlorine solution was considered. Potassium has a similar atomic mass to calcium, and sodium to magnesium, but they both differ in charge (1e and 2e respectively). Magnesium and calcium, even having the same charge, showed different affinity for the explored protein. From the calcium binding sites referred above, we found that the magnesium di-cations only binds strongly to the GLU114 site of one connexin. For the sodium and potassium simulations, no specific interactions with the protein were found. Altogether, these results suggest that mass and steric effects play an important role in determining cation binding to Cx26 hemichannels.

The paper aims to investigative the cacuses and impacts of In- and Vacancy-doped to 6H-SiC, expecting that improving optical properties of materials. Design-Using the first-principles calculations, we discuss the electronic structure and optical properties of different doped 6H-SiC systems. The results show that In-doped 6H-SiC becomes a direct bandgap p-type semiconductor and the energy bandgap is reduced from the intrinsic 2.059 to 1.515 eV. We demonstrate the stability of the systems through the formation energy analysis, meanwhile identify their physical origins and discuss applications of all structures in electronic devices within optical analysis. Find the energy beginning values of the VSi-doped and VC-doped systems’ optical absorption spectrums and extend to 0.4 2 eV and 0.11 eV respectively compared with the original 3.23 eV. In the visible light region, the reflectivity images of the VC/VSi and (In, VSi)-codoped systems rise obviously. The optical properties of all doping systems were analyzed to be improved compared with the intrinsic, all above mentioned provide a theoretical basis for the fabrication of spintronic and optical devices.

The biological toxicity of uranyl ion (UO 2 2+ ) lies in interacting with proteins and disrupting their native functions. The structural and functional consequences of UO 2 2+ interacting with cytochrome b 5 (cyt b 5), a small membrane heme protein, and its heme axial ligand His39Ser variant, cyt b 5 H39S, were investigated both experimentally and theoretically. In experiments, although cyt b 5 was only slightly affected, UO 2 2+ binding to cyt b 5 H39S with a K D of 2.5 μM resulted in obvious alteration of the heme active site, and led to a decrease in peroxidase activity. Theoretically, molecular simulation proposed a uranyl ion binding site for cyt b 5 at surface residues of Glu37 and Glu43, revealing both coordination and hydrogen bonding interactions. The information gained in this study provides insights into the mechanism of uranyl toxicity toward membrane protein at an atomic level.

We present quantum chemical theoretical estimations of the anti-corrosive properties of THAM (tris(hydroxymethyl)aminomethane) and three derivatives that differ in the number of benzene rings: THAM-1 (2-amino-3-hydroxy-2-(hydroxymethyl) propylobenzoate), THAM-2 (2-amino-2-(hydroxymetyl)prapan-1,3-diyldibenzoate) and THAM-3 (2-amino-propan-1,2,3-triyltribenzoate). Fourteen exchange-correlation functionals based on the density functional theory (DFT) were chosen for quantum chemical study of THAM derivatives. The objective was to examine the effect of benzene rings on potential anti-corrosive properties of THAM compounds. The results indicate that the addition of benzene rings in THAM derivatives is likely to significantly enhance electrostatic bonding of a THAM-based coating to a presented metal surface and, thus, its adhesion and long-term effect in corrosion inhibition. Whereas it is clear that all three derivatives appear to be superior in their bonding characteristics to pure THAM, the potential order of merit between the three is less clear, although THAM-3 presents as possibly superior.

Việc vận chuyển điện tích qua các dây phân tử dựa trên thiophen-dithiol được gắn vào các điện cực vàng với ba loại hướng tinh thể khác nhau (<1,1,1>, <1,1,0> và <1,0,1>) đã được nghiên cứu. Sự vận chuyển electron trong các hệ thống được xem xét đã được đánh giá một cách có hệ thống bằng cách phân tích giá trị dòng điện, phổ truyền dẫn, mật độ trạng thái thiết bị dự kiến và phân tích quỹ đạo không thiên lệch sử dụng lý thuyết chức năng mật độ kết hợp với hàm Green không cân bằng. Các cuộc điều tra đã chứng minh rằng việc điều chỉnh độ dẫn trong các khớp phân tử nano là khả thi thông qua các hướng điện cực khác nhau. Do khoảng cách HOMO–LUMO trong khớp thiophen dithiol có hướng <1,1,0> thấp hơn đáng kể so với các cấu hình khác đang được xem xét, cấu hình <1,1,0> thể hiện độ dẫn xây dựng vượt trội so với các hướng khớp khác. Điều này đã cung cấp cho chúng tôi ý tưởng để thiết kế các thiết bị điện tử nano quy mô nhỏ có cấu trúc dị vòng tiên phong. Ngoài ra, <1,1,0> đã được phát hiện có hành vi độ dẫn vi phân âm trên +2,6 V và dưới −2,6 V, do đó có tiềm năng ứng dụng trong các mạch dao động và công tắc.

The single crystal architecture of the high-symmetry octathio[8]circulene and sym-tetraselenatetrathio[8]circulene is studied at the density functional theory (DFT) level with the quantum theory of atoms in molecules (QTAIMs) approach to the electron density distribution analysis. The presence of stabilizing intermolecular C---C, C---S and C---Se contacts in the longitudinal and transversal projections of the single crystals is postulated on the grounds of the previous high-resolution X-ray data for octathio[8]circulene; it is supported by the present QTAIM calculations and also predicted in some new details for both circulenes. We suggest that the appearance of the observed red color for the monocrystalline octathio[8]circulene is caused by strong intermolecular interactions between the molecules in the single crystal. However, the intermolecular interactions for the sym-tetraselenatetrathio[8]circulene crystal fragment are weaker and molecular layers are more friable in comparison to octathio[8]circulene crystal structure. These lead to the absence of visible absorption for the sym-tetraselenatetrathio[8]circulene crystal.

Hydrogenases are redox metalloenzymes in bacteria that catalyze the uptake or production of molecular hydrogen. Two homologous nickel–iron hydrogenases, HupSL and HydSL from the photosynthetic purple sulfur bacterium Thiocapsa roseopersicina, differ substantially in their thermal stabilities despite the high sequence similarity between them. The optimum temperature of HydSL activity is estimated to be at least 50 °C higher than that of HupSL. In this work, homology models of both proteins were constructed and analyzed for a number of structural properties. The comparison of the models reveals that the higher stability of HydSL can be attributed to increased inter-subunit electrostatic interactions: the homology models reliably predict that HydSL contains at least five more inter-subunit ion pairs than HupSL. The subunit interface of HydSL is more polar than that of HupSL, and it contains a few extra inter-subunit hydrogen bonds. A more optimized cavity system and amino acid replacements resulting in increased conformational rigidity may also contribute to the higher stability of HydSL. The results are in accord with the general observation that with increasing temperature, the role of electrostatic interactions in protein stability increases. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00894-001-0071-8.

S-adenosyl-L-homocysteine hydrolase (SAHase) is an important regulator in the methylation reactions in many organisms and thus is crucial for numerous cellular functions. In recent years, SAHase has become one of the popular targets for drug design, and SAHase inhibitors have exhibited potent antiviral activity. In this study, we established the complex-based pharmacophore models based on the known crystal complex of SAHase (PDB ID: 1A7A) to screen the drug-likeness compounds of ChEMBL database. Then, three molecular docking programs were used to validate the reliability of compounds, involving Libdock, CDOCKER, and AutoDock Vina programs. The four promising hit compounds (CHEMBL420751, CHEMBL346387, CHEMBL1569958, and CHEMBL4206648) were performed molecular dynamics simulations and MM-PBSA calculations to evaluate their stability and binding-free energy in the binding site of SAHase. After screening and analyzing, the hit compounds CHEMBL420751 and CHEMBL346387 were suggested to further research to obtain novel potential SAHase inhibitors. A series of computer-aided drug design methods, including pharmacophore, molecular docking, molecular dynamics simulation and MM-PBSA calculations, were employed in this study to identity novel inhibitors of S-adenosyl-L-homocysteine hydrolase (SAHase). Some compounds from virtual screening could form various interactions with key residues of SAHase. Among them, compounds CHEMBL346387 and CHEMBL420751 exhibited potent binding affinity from molecular docking and MM-PBSA, and maintained good stability at the binding site during molecular dynamics simulations as well. All these results indicated that the selected compounds might have the potential to be novel SAHase inhibitors.