Origin of Enantioselectivity in Engineered Cytochrome -Catalyzed Carbon-Radical FePP Hydrolysis Revealed Using QM/MM (ABEEM Polarizable Force Field) and MD Simulations.

The origin of highly efficient asymmetric aminohydroxylation of styrene catalyzed by engineered cytochrome is investigated by the developed Atom-Bond Electronegativity Equalization Method polarizable force field (ABEEM PFF), which is a combined outcome of electronic and steric effects. Model molecules were used to establish the charge parameters of the ABEEM PFF, for which the bond-stretching and angle-bending parameters were obtained by using a combination of modified Seminario and scan methods. The interactions between carbon-radical Fe-porphyrin (FePP) and waters are simulated by molecular dynamics, which shows a clear preference for the pre- over the pre-.

Development of a QM/MM(ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX(8-oxo-G) tetrad.

The rapid deprotonation of G˙ in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G˙ in the G-tetrad makes it a more suitable carrier for hole conduction. The QM/MM(ABEEM) combined method, which involves the integration of QM and the ABEEM polarizable force field (ABEEM PFF), was developed to investigate the deprotonation of neutral and cation free radicals in the G-tetrad and GGX(8-oxo-G) tetrad (xanthine and 8-oxoguanine dual substituted G-tetrad). By incorporating valence-state electronegativity piecewise functions *() and implementing charge local conservation conditions, QM/MM(ABEEM) possesses the advantage of accurately simulating charge transfer and polarization effect during deprotonation.

A simple, rapid method for simultaneous determination of multiple elements in serum by using an ICP-MS equipped with collision cell.

We developed an inductively coupled plasma mass spectrometry method for testing 23 elements, namely, Mg, Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Mo, Cd, Sn, Sb, Ba, W, Tl, Pb, and U, in human serum. The serum samples were analyzed after diluting 1/25 with 0.5% nitric acid, 0.

Atomic charges in molecules defined by molecular real space partition into atomic subspaces.

Atomic charge (AC), which is the charge distribution of a molecule, is an important property that is closely associated with structures, reactivities, and intra- and inter-molecular interactions among molecules. Several theoretical models or methods can be used to obtain the magnitudes of AC with different characteristics. These models can be classified into fuzzy-atoms models and models partitioning a molecule into individual atoms with sharp boundaries.

Development of a QM/MM(ABEEM) method combined with a polarizable force field to investigate the excision reaction mechanism of damaged thymine.

This paper focuses on the development of a quantum mechanics/molecular mechanics method using the ABEEM polarizable force field (QM/MM(ABEEM) method) to investigate the excision reaction mechanism of damaged thymine. This method does not simply combine the QM method with the polarizable force field. A valence electronegativity piecewise function with the distance between atoms as a variable is introduced to describe the atomic partial charges, and changes greatly during the reaction process.

Development of QM/MM (ABEEM polarizable force field) method to simulate the excision reaction mechanism of damaged cytosine.

DNA damages are regarded as having harmful effects on cell. The base excision repair mechanism combats these effects by removing damaged bases. The deglycosylation mechanism of excising damaged bases by DNA glycosylase and the state of the leaving base have been controversial.

A daily carbon emission prediction model combining two-stage feature selection and optimized extreme learning machine.

Global warming caused by increased carbon emissions is a common challenge for all mankind. Facing the unprecedented pressure of carbon emission reduction, it is particularly important to grasp the dynamics of carbon emission in time and accurately. This paper proposes a novel daily carbon emission forecasting model.

Conjunctional Relationship between Serum Uric Acid and Serum Nickel with Non-Alcoholic Fatty Liver Disease in Men: A Cross-Sectional Study.

Serum uric acid (SUA) and heavy metals are closely related to non-alcoholic fatty liver disease (NAFLD). Yet, the conjunctional relationship between SUA and serum nickel (Ni) concentrations with the risk of NAFLD in men has not yet been investigated. Therefore, we designed this cross-sectional study to investigate the association of SUA or serum Ni with NAFLD in men.

A novel short-term carbon emission prediction model based on secondary decomposition method and long short-term memory network.

Grasping the dynamics of carbon emission in time plays a key role in formulating carbon emission reduction policies. In order to provide more accurate carbon emission prediction results for planners, a novel short-term carbon emission prediction model is proposed. In this paper, the secondary decomposition technology combining ensemble empirical mode decomposition (EEMD) and variational mode decomposition (VMD) is used to process the original data, and the partial autocorrelation function (PACF) is applied to select the optimal model input.

Refined models of coordination between Al/Mg and enzyme in molecular dynamics simulation in terms of ABEEM polarizable force field.

MF (AlF, AlF and MgF) as transition state analogues of phosphoryl transfer enzymes (enzyme-MF-TSAs) is of great significance for study of the catalytic mechanism of phosphoryl transfer enzymes. Bonded model and non-bonded model based on the ABEEM polarizable force field (ABEEM PFF) are developed and applied to study the coordination of enzyme-MF-TSAs. The bond stretching of the bond containing metal is simulated by Morse potential energy function, because the change of chemical bond is described more accurately in a large range.

Energetics and -coupling constants for Ala, Gly, and Val peptides demonstrated using ABEEM polarizable force field and an aqueous solution.

The development of an atom-bond electronegativity equalisation method at the σπ-level (ABEEM) polarisable force field (PFF) for peptides is presented. ABEEM PFF utilises a fluctuating charge model to explicitly describe the polarisation effects in an extensive environment. The partial charge of any individual site changes in response to changes in its surroundings.

Water-Mediated Oxidation of Guanine by a Repair Enzyme: Simulation Using the ABEEM Polarizable Force Field.

The recognition mechanism of oxidative damage in organisms has long been a research hotspot. Water is an important medium in the recognition process, but its specific role remains unknown. There is a need to develop a suitable force field that can adequately describe the electrostatic, hydrogen bond, and other interactions among the molecules in the complex system of the repair enzyme and oxidized base.

Directional depolymerization of lignin into high added-value chemical with synergistic effect of binary solvents.

This work exploits a one-pot method for directional depolymerizing organosolv lignin into high added-value phenolic monomers with synergistic reaction system consisted of methanol-dimethoxymethane binary solvents and acid catalyst. The influence of solvent composition and reaction parameters such as different catalyst, binary solvents ratio, time, and temperature on the conversion of lignin and yield of products were investigated carefully, the optimum yield of liquid products and phenolic monomers were achieved at 67.39% and 27.

Lignin Based Activated Carbon Using HPO Activation.

Activated carbon (AC) with a very high surface area of over 2000 m/g was produced from low sulfur acid hydrotropic lignin (AHL) from poplar wood using HPO at a moderate temperature of 450 °C (AHL-AC6). ACs with similar surface areas were also obtained under the same activation condition from commercial hardwood alkali lignin and lignosulfonate. Initial evaluation of AC performance was carried out using nitrogen adsorption-desorption and dye adsorption.

Dividing the Periodic Box into Subdivisions with Their Surroundings to Accelerate Molecular Dynamics Simulation with High Accuracy.

A major field of current research in chemistry and biology is the development of the tools that enable in situ analysis of complex systems. However, the long-time dynamics simulation for an extremely large system in solution is almost impossible by an all-atom force field combined with an explicit solvent model. The results show that the larger the periodic box is, the closer the properties of the system are to the experimental values.

Enhanced visible light photoelectrocatalytic degradation of tetracycline hydrochloride by I and P co-doped TiO photoelectrode.

Elimination of antibiotics such as tetracycline hydrochloride (TC) from wastewater is of great significance, but still faces challenges. Herein, for the first time, I and P co-doped TiO catalysts were prepared via a hydrolysis method. We also reported a simple method to prepare I and P co-doped TiO photoelectrodes, which exhibited preeminent photoelectrocatalytic (PEC) performance for the decomposition of TC.

Alterations of fatty acid composition and metabolism in APP/PS1 transgenic mice.

Accumulating evidence suggests that abnormal fatty acid composition is related to the development of Alzheimer's disease (AD). However, there is no consistency in the fatty acid profile and metabolism associated with AD pathogenesis. This study aims to define the characteristics of fatty acid composition and metabolism in AD.

Systematic Parameterization and Simulation of Boronic Acid-β-Lactamase Aqueous Solution in Developing the ABEEMσπ Polarizable Force Field.

Boronic acid, an inhibitor of β-lactamase, has begun to be applied to the treatment of biological infections and tumors. Scientists are working to develop new and more effective boronic acid. Molecular dynamics (MD) simulation provides a powerful auxiliary tool for drug design.

Directional and integrated conversion of whole components in biomass for levulinates and phenolics with biphasic system.

Integrated conversion and stepwise extraction of whole components in biomass with biphasic system are introduced for producing chemicals: levulinates and phenolics. When methanol/dimethoxymethane as biphasic solvent, 46.51% methyl levulinate and 18.

ABEEM/MM OH Models for OH(HO) Clusters and Aqueous OH: Structures, Charge Distributions, and Binding Energies.

Based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), two fluctuating charge models of OH-water system were proposed. The difference between these two models is whether there is charge transfer between OH and its first-shell water molecules. The structures, charge distributions, charge transfer, and binding energies of the OH(HO) ( = 1-8, 10, 15, 23) clusters were studied by these two ABEEM/MM models, the OPLS/AA force field, the OPLS-SMOOTH/AA force field, and the QM methods.

Partitioning a Molecule into the Atomic Basins and the Resultant Atomic Charges from Quantum Chemical Topology Analysis of the Kohn-Sham Potential.

Quantum chemical topology (QCT) solidifies the chemical basic concepts demonstrating how a molecular system is intrinsically partitioned into its components and what the interaction lines between them are. Here, QCT analysis using a Kohn-Sham one-electron potential (KSpot) in KS equation as a scalar function is initiated and explored, showing KSpot and its resultant electron force lines have novel spatial features which reveal that an atom in a molecule is a spatial basin governed by its nucleus as a 3D-attractor that terminates all the electron force lines defined by the negative gradient of KSpot and that a chemical bond line is just a minimum path of KSpot for the electron motion. Particularly, the atomic charges from this KSpot QCT analysis are moderate and good, having much lower dependence on basis sets chosen for computation.

Polarizable TIP7P Water Model with Perturbation Charges Evaluated from ABEEM.

A polarizable version of the rigid seven-site (TIP7P) water model with the atom-bond electronegativity equalization method (ABEEM) is proposed. The model uses direct polarization, where an isolated water monomer in the equilibrium geometry is assumed as a reference state and the polarization of the monomer arises from interacting with other molecules as a perturbation of the reference state. The charge on each site of the monomer splits into reference charge and perturbation charge.

Seven-Site Effective Pair Potential for Simulating Liquid Water.

Constant pressure simulations were carried out to construct a new rigid nonpolarizable seven-site water model (TIP7P), which is an effective and efficient version of flexible seven-fluctuating-charge water model. In this model, the positive charges are located on three nuclei and the negative charges disperse on two bond sites at the geometric center of each OH bond and two lone-pair sites along the tetrahedral direction away from the oxygen atom. Our new model performs better than other models in properties, such as radial distribution function, liquid density, thermal expansion coefficient, isothermal compressibility, vaporization enthalpy, isobaric heat capacity, static dielectric constant, self-diffusion coefficient, critical temperature, and density.

Reaction mechanism of NO with hydrolysates of NAMI-A: an MD simulation by combining the QM/MM(ABEEM) with the MD-FEP method.

Nitrosylation reaction mechanisms of the hydrolysates of NAMI-A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI-A occur in both the triplet and the singlet states.

Facile synthesis of bimetallic gold-palladium nanocrystals as effective and durable advanced catalysts for improved electrocatalytic performances of ethylene glycol and glycerol oxidation.

In this work, well-defined bimetallic AuPd alloyed nanocrystals (AuPd NCs) were facilely synthesized by a straightforward and controllable one-step wet-chemical strategy, using a biomolecule (L-hydroxyproline, L-Hyp) as the green stabilizer and the structure-directing agent. Their morphology, size, composition, crystal structures and growth mechanism were investigated by a series of techniques. The synthesized architectures exhibited enlarged electrochemically active surface area (ECSA), improved catalytic activity, enhanced durability and stability towards ethylene glycol oxidation reaction (EGOR) and glycerol oxidation reaction (GOR) in alkaline electrolytes in comparison with commercial Pd black catalyst.