Analysis Of Surface Electrostatic Potentials Research Articles

Mechanism of Dihydromyricetin-Induced Reduction of Furfural Derived from the Amadori Compound: Formation of Adducts between Dihydromyricetin and Furfural or Its Precursors.

Dihydromyricetin (DMY) was employed to reduce the yield of furfural derived from the Amadori rearrangement product of l-threonine and d-xylose (Thr-ARP) by trapping Thr-ARP, 3-deoxyxyosone (3-DX), and furfural to form adducts. The effect of different concentrations of DMY at different pH values and temperatures on the reduction of furfural production was studied, and the results showed that DMY could significantly reduce furfural production at higher pH (pH 5-7) and lower temperature (110 °C). Through the surface electrostatic potential analysis by Gaussian, a significant enhancement of the C6 nucleophilic ability at higher pH (pH ≥ 5) was observed on DMY with hydrogen-dissociated phenol hydroxyl. The nucleophilic ability of DMY led to its trapping of Thr-ARP, 3-DX, and furfural with the generation of the adducts DMY-Thr-ARP, DMY-3-DX, and DMY-furfural. The formation of the DMY-Thr-ARP adduct slowed the degradation of Thr-ARP, caused the decrease of the 3-DX yield, and thereby inhibited the conversion of 3-DX to furfural. Therefore, DMY-Thr-ARP was purified, and the structure was identified by nuclear magnetic resonance (NMR). The results confirmed that C6 or C8 of DMY and carbonyl carbon in Thr-ARP underwent a nucleophilic addition reaction to form the DMY-Thr-ARP adduct. In combination with the analysis results of Gaussian, most of the DMY-Thr-ARP adducts were calculated to be C6-DMY-Thr-ARP. Furthermore, the formation of DMY-furfural caused furfural consumption. The formation of the adducts also shunted the pathway of both Thr-ARP and 3-DX conversion to furfural, resulting in a decrease in the level of furfural production.

Theoretical exploration and experimental regulation of the degradation of Δ9-tetrahydrocannabinol in hemp seed oil by density functional theory

Δ9-tetrahydrocannabinol (Δ9-THC) in hemp seed oil is a psychoactive cannabinoid, and the content of Δ9-THC can be reduced. Density functional theory (DFT) was used to simulate the degradation path of Δ9-THC, and the ultrasonic treatment was used to degrade the Δ9-THC in hemp seed oil. Results found that the reaction of Δ9-THC degradation to cannabinol (CBN) was a spontaneous exothermic reaction, which required a certain amount of external energy to initiate reaction process. Through the surface electrostatic potential analysis, the minimum value of electrostatic potential of Δ9-THC was −37.68 kcal/mol, and the maximum value was 40.98 kcal/mol. The frontier molecular orbitals analysis found that the energy level difference of Δ9-THC was lower than that of CBN, indicating that the reactivity of Δ9-THC was stronger. The degradation process of Δ9-THC could be divided into two stages, which needed to cross the reaction energy barriers of 3197.40 and 3087.24 kJ/mol, respectively. Ultrasonic treatment was used to degrade Δ9-THC standard solution, it was found that Δ9-THC can be effectively degraded into CBN through intermediate. Subsequently, ultrasonic technology was applied to hemp seed oil, under the conditions of ultrasonic power 150 W and ultrasonic time 21 min, the Δ9-THC was degraded to 10.00 mg/kg.

Theoretical study into effects of different substituents on the structure and properties of Keto-RDX compounds

Forty kinds of keto-RDX based derivatives containing different substituents (for instance –NHNH2, -C(NO2)3, –NHNO2, –NO2 and –ONO2) were designed and have been optimized at the B3LYP-D3/6-311G** level. The effects of single and multiple substituents on the properties of these energetic materials were analyzed. The electronic structure, energy gap, heat of formation, detonation performance, thermal stability, thermodynamic parameters and surface electrostatic potential of the compounds were systematically studied. Compared with the traditional energetic compounds HMX (D = 9.10 km s−1, P = 39.0 GPa) and RDX (D = 8.75 km s−1, P = 34.0 GPa), most of the derivatives designed in this paper have higher detonation velocity and detonation pressure. Among them, the largest density, detonation velocity, and detonation pressure are 2.14 g cm−3 (B6), 10.95 km s−1 (D2), and 57.81 GPa (E7), respectively. Combined with surface electrostatic potential analysis, seven keto-RDX based derivatives of C1, C4, C5, E3, E4, E5, and E7 that can be selected as promising high energy density materials were finally picked out.

Atomically dispersed nano Au clusters stabilized by Zr on the TS-1 surface: Significant enhancement of catalytic oxidation ability using H2 and O2

Au and Zr are uniformly loaded on the surface of TS-1 by coprecipitation method to obtain atomically dispersed Au-Zr binary clusters. The interaction between Au clusters, Zr and TS-1 is analyzed by Independent Gradient Model based on Hirshfeld partition (IGMH), adsorption energy of Au cluster, Mayer bond order. It is found that the existence of Zr is conducive to the stability of nano Au on TS-1 surface. The catalyst is applied to the gas phase epoxidation of C3H6 to obtain 14.06 % initial conversion, 93.93 % initial selectivity and 479.52 gPO·kgcat-1·h-1 initial productivity. It shows good stability in the continuous test for more than 50 h. Density functional theory (DFT) is used to calculate the possible catalytic reaction mechanism on the surface of atomically dispersed Au clusters. The whole process from C3H6 epoxidation reaction to catalyst regeneration is completely described. In the analysis of H2O desorption, the concept of “relay desorption” is proposed. Combined with charge and surface electrostatic potential analysis, the different attack directions of C3H6 on the catalyst surface are discussed in detail. This will provide guidance and help for the synthesis and catalytic application of nano Au catalysts.

Identification and structural analysis of a carbohydrate-binding module specific to alginate, a representative of a new family, CBM96

Carbohydrate-binding modules (CBMs) are the noncatalytic modules that assist functions of the catalytic modules in carbohydrate-active enzymes, and they are usually discrete structural domains in larger multimodular enzymes. CBMs often occur in tandem in different alginate lyases belonging to the CBM families 13, 16, and 32. However, none of the currently known CBMs in alginate lyases specifically bind to an internal alginate chain. In our investigation of the multidomain alginate lyase Dp0100 carrying several ancillary domains, we identified an alginate-binding domain denoted TM6-N4 using protein truncation analysis. The structure of this CBM domain was determined at 1.35Å resolution. TM6-N4 exhibited an overall β-sandwich fold architecture with two antiparallel β-sheets. We identified an extended binding groove in the CBM using site-directed mutagenesis, docking, and surface electrostatic potential analysis. Affinity analysis revealed that residues of Lys10, Lys22, Lys25, Lys27, Lys31, Arg36, and Tyr159 located on the bottom or the wall of the shallow groove are responsible for alginate binding, and isothermal titration calorimetry analyses indicated that the binding cleft consists of six subsites for sugar recognition. This substrate binding pattern is typical for type B CBM, and it represents the first CBM domain that specifically binds internal alginate chain. Phylogenetic analysis supports that TM6-N4 constitutes the founding member of a new CBM family denoted as CBM96. Our reported structure not only facilitates the investigation of the CBM-alginate ligand recognition mechanism but also inspires the utilization of the CBM domain in biotechnical applications.

Effect of formic-acid-to-acetic-acid ratio on the structure and spinnability of aqueous aluminium sol of alumina fibre

The structure and spinnability of sol are essential for obtaining high-performance continuous alumina-based fibres. Herein, the surface electrostatic potential analysis and conventional experimental methods (X-ray diffraction, Fourier-transform infrared spectroscopy, 27Al nuclear magnetic resonance solution spectra and rheological methods) were combined to investigate and discuss the relationship between the structure and spinnability of aluminium carboxylate sols with different formic-acid-to-acetic-acid molar ratios. The results showed that the aluminium carboxylate sol structure changed with the formic-acid-to-acetic-acid molar ratio and greatly affected the sol's spinnability. The tetramer (AlO6 oligomer) products comprising two effective active carboxylate groups in the sol increased with the formic acid content, which helped form linear long-chain polymers. However, excess formic acid content led to a large increase of AlO6 monomer products that were unable to form linear long-chain polymers, which decreased the sol's spinnability. When the formic-acid-to-acetic-acid molar ratio was 1.15:0.85, the sol containing more AlO6 oligomer products had the best spinnability. Furthermore, α-Al2O3 ceramic fibres with good morphology, small grains and uniform diameter distribution were obtained after calcination at 1200 °C.

Molecular Dynamics Simulation of Transmembrane Transport of Chloride Ions in Mutants of Channelrhodopsin.

Channelrhodopsins (ChRs) are light-gated transmembrane cation channels which are widely used for optogenetic technology. Replacing glutamate located at the central gate of the ion channel with positively charged amino acid residues will reverse ion selectivity and allow anion conduction. The structures and properties of the ion channel, the transport of chloride, and potential of mean force (PMF) of the chimera protein (C1C2) and its mutants, EK-TC, ER-TC and iChloC, were investigated by molecular dynamics simulation. The results show that the five-fold mutation in E122Q-E129R-E140S-D195N-T198C (iChloC) increases the flexibility of the transmembrane channel protein better than the double mutations in EK-TC and ER-TC, and results in an expanded ion channel pore size and decreased steric resistance. The iChloC mutant was also found to have a higher affinity for chloride ions and, based on surface electrostatic potential analysis, provides a favorable electrostatic environment for anion conduction. The PMF free energy curves revealed that high affinity Cl− binding sites are generated near the central gate of the three mutant proteins. The energy barriers for the EK-TC and ER-TC were found to be much higher than that of iChloC. The results suggest that the transmembrane ion channel of iChloC protein is better at facilitating the capture and transport of chloride ions.

On the strength and nature of intermolecular X···O interactions in CF2ClBr−O3complexes (X = F, Cl, Br): an ab initio investigation

Ab initio calculations were realized to analyze the existence of intermolecular X···O interactions in bromochlorodifluoromethane (CF2ClBr) complexes with ozone, where X = F, Cl, and Br. These calculations have been carried out using MP2 and CCSD(T) methods, through analysis of surface electrostatic potentials V(r), intermolecular interaction energies, and electron density analysis. Coupled cluster (CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ) calculations indicate that the stabilization energies for the CF2ClBr−O3complexes lie in the range between –3.9 and –7.7 kJ/mol. The characteristic of X···O interactions has been identified in terms of the electron density analysis within the quantum theory of atoms in molecules. Energy decomposition analysis shows that the attractive nature of the X···O interactions within the title complexes is chiefly due to dispersion effects, but electrostatic contribution also plays an important role.

Membrane association of peroxiredoxin-2 in red cells is mediated by the N-terminal cytoplasmic domain of band 3

Band 3 (B3), the anion transporter, is an integral membrane protein that plays a key structural role by anchoring the plasma membrane to the spectrin-based membrane skeleton in the red cell. In addition, it also plays a critical role in the assembly of glycolytic enzymes to regulate red cell metabolism. However, its ability to recruit proteins that can prevent membrane oxidation has not been previously explored. In this study, using a variety of experimental approaches including cross-linking studies, fluorescence and dichroic measurements, surface plasmon resonance analysis, and proteolytic digestion assays, we document that the antioxidant protein peroxiredoxin-2 (PRDX2), the third most abundant cytoplasmic protein in RBCs, interacts with the cytoplasmic domain of B3. The surface electrostatic potential analysis and stoichiometry measurements revealed that the N-terminal peptide of B3 is involved in the interaction. PRDX2 underwent a conformational change upon its binding to B3 without losing its peroxidase activity. Hemichrome formation induced by phenylhydrazine of RBCs prevented membrane association of PRDX2, implying overlapping binding sites. Documentation of the absence of binding of PRDX2 to B3 Neapolis red cell membranes, in which the initial N-terminal 11 amino acids are deleted, enabled us to conclude that PRDX2 binds to the N-terminal cytoplasmic domain of B3 and that the first 11 amino acids of this domain are crucial for PRDX2 membrane association in intact RBCs. These findings imply yet another important role for B3 in regulating red cell membrane function.

Comparative analysis of surface electrostatic potentials of carbon, boron/nitrogen and carbon/boron/nitrogen model nanotubes

We have extended an earlier study, in which we characterized in detail the electrostatic potentials on the inner and outer surfaces of a group of carbon and B(x)N(x) model nanotubes, to include several additional ones with smaller diameters plus a new category, C(2x)B(x)N(x). The statistical features of the surface potentials are presented and analyzed for a total of 19 tubes as well as fullerene and a small model graphene. The potentials on the surfaces of the carbon systems are relatively weak and rather bland; they are much stronger and more variable for the B(x)N(x) and C(2x)B(x)N(x). A qualitative correlation with free energies of solvation indicates that the latter two categories should have considerably greater water solubilities. The inner surfaces are generally more positive than the corresponding outer ones, while both positive and negative potentials are strengthened by increasing curvature. The outsides of B(x)N(x) tubes have characteristic patterns of alternating positive and negative regions, while the insides are strongly positive. In the closed C(2x)B(x)N(x) systems, half of the C-C bonds are double-bond-like and have negative potentials above them; the adjacent rows of boron and nitrogens show the usual B(x)N(x) pattern. When the C(2x)B(x)N(x) tubes are open, with hydrogens at the ends, the surface potentials are dominated by the B+-H- and N(-)-H+ linkages.

Crystal structure reveals basis for the inhibitor resistance of human brain trypsin

Severe neurodegradative brain diseases, like Alzheimer, are tightly linked with proteolytic activity in the human brain. Proteinases expressed in the brain, such as human trypsin IV, are likely to be involved in the pathomechanism of these diseases. The observation of amyloid formed in the brain of transgenic mice expressing human trypsin IV supports this hypothesis. Human trypsin IV is also resistant towards all studied naturally occurring polypeptide inhibitors. It has been postulated that the substitution of Gly193 to arginine is responsible for this inhibitor resistance. Here we report the X-ray structure of human trypsin IV in complex with the inhibitor benzamidine at 1.7 Å resolution. The overall fold of human trypsin IV is similar to human trypsin I, with a root-mean square deviation of only 0.5 Å for all C α positions. The crystal structure reveals the orientation of the side-chain of Arg193, which occupies an extended conformation and fills the S2′ subsite. An analysis of surface electrostatic potentials shows an unusually strong clustering of positive charges around the primary specificity pocket, to which the side-chain of Arg193 also contributes. These unique features of the crystal structure provide a structural basis for the enhanced inhibitor resistance, and enhanced substrate restriction, of human trypsin IV.

Prediction on the binding domain between human interleukin-6 and its receptor

Based on the spatial conformations of human interleukin-6 (hIL-6) derived from nuclear magnetic resonance analysis and human interleukin-6 receptor (hIL-6R) modeled with homology modeling method using human growth hormone receptor as template, the interaction between hIL-6 and its receptor (hIL-6R) is studied with docking program according to the surface electrostatic potential analysis and spatial conformation complement. The stable region structure composed of hIL-6 and hIL-6R is obtained on the basis of molecular mechanism optimization and molecular dynamics simulation. The binding domain between hIL-6 and hIL-6R is predicted theoretically. Furthermore, the especial binding sites that influence the interaction between hIL-6 and hIL-6R are confirmed. The results lay a theoretical foundation for confirming the active regions of hIL-6 and designing novel antagonist with computer-guided techniques.