A Computational Study of Microhydrated N-Acetyl-Phenylalaninylamide (NAPA): Kinetics and Thermodynamics

The formations of [NAPA-A(H2O)n (n = 1, 2, 3, 4)] complexes have been studied employing DFT/wB97XD/cc-pVTZ computational level to understand the kinetics and thermodynamics for the hydration reactions of N-acetyl-phenylalaninylamide (NAPA). Thermodynamic parameters such as reaction energy (E), enthalpy (H), Gibb’s free energy (G), specific heat capacity (Cv), entropy (S), and change of these parameters (ΔEr, ΔHr, ΔGr, ΔCr, and ΔSr) were studied using the explicit solvent model. The predicted values of H, G, C, and S increase with the sequential addition of water in NAPA-A due to the increase in the total number of vibrational modes. On the other hand, the value of ΔEr, ΔHr, and ΔGr increases (more negative to less negative) gradually for n = 1, 2, 3, and 4 that indicates an increase of hydration in NAPA-A makes exothermic to endothermic reactions. The barrier heights for the transition states (TS) of [NAPA-A(H2O)n (n = 1, 2, 3, 4)] complexes are predicted to lie at 4.41, 4.05, 3.72 and 2.26 kcal/mol respectively below the reactants. According to the calculations, the formations of [NAPA-A(H2O)1] and [NAPA-A(H2O)2] complexes are barrierless reactions because both water molecules are strongly bonded via two hydrogen bonds in the backbone of NAPA-A. On the contrary, the reactions of [NAPA-A(H2O)3] and [NAPA-A(H2O)4] complexation are endothermic and the barrier heights are predicted to stay at 6.30 and 10.54 kcal/mol respectively above the reactants. The free energy of activation (Δ‡G0) for the reaction of [NAPA-A(H2O)1], [NAPA-A(H2O)2], [NAPA-A(H2O)3], and [NAPA-A(H2O)4] complexation are 4.43, 4.28, 3.83 and 5.11 kcal/mol respectively which are very low. As well as the rates of reactions are 3.490 × 109 s-1, 4.514 × 109 s-1, 9.688 × 109 s-1, and 1.108 × 109 s-1 respectively which are very fast and spontaneous.

Durable poly(binaphthyl-co-p-terphenyl piperidinium)-based anion exchange membranes with dual side chains

Building well-developed ion-conductive highways is highly desirable for anion exchange membranes(AEMs).Grafting side chain is a highly effective approach for constructing a well-defined phaseseparated morphological structure and forming unblocked ion pathways in AEMs for fast ion transport.Fluorination of side chains can further enhance phase separation due to the superhydrophobic nature of fluorine groups.However,their electronic effect on the alkaline stability of side chains and membranes is rarely reported.Here,fluorine-containing and fluorine-free side chains are introduced into the polyaromatic backbone in proper configuration to investigate the impact of the fluorine terminal group on the stability of the side chains and membrane properties.The poly(binaphthyl-co-p-terphenyl piperidinium)AEM(QBNp TP)has the highest molecular weight and most dimensional stability due to its favorable backbone arrangement among ortho-and meta-terphenyl based AEMs.Importantly,by introducing both a fluorinated piperidinium side chain and a hexane chain into the p-terphenyl-based backbone,the prepared AEM(QBNp TP-QFC)presents an enhanced conductivity(150.6 m S cm^(-1))and a constrained swelling at 80℃.The electronic effect of fluorinated side chains is contemplated by experiments and simulations.The results demonstrate that the presence of strong electro-withdrawing fluorine groups weakens the electronic cloud of adjacent C atoms,increasing OH^(-)attack on the C atom and improving the stability of piperidinium cations.Hence QBNp TP-QFC possesses a robust alkaline stability at 80℃(95.3%conductivity retention after testing in 2 M Na OH for 2160 h).An excellent peak power density of 1.44 W cm^(-2)and a remarkable durability at 80℃(4.5%voltage loss after 100 h)can be observed.

Characterization of the dissociation pathways of dichloromethane and glutathione in dichloromethane dehalogenase

Dichloromethane(DCM)dehalogenase stands as a crucial enzyme implicated in the degradation of methylene chloride across diverse environmental and biological contexts.However,the unbinding pathways of ligands from DCM dehalogenase remain unexplored.In order to gain a deeper understanding of the binding sites and dissociation pathways of dichloromethane(DCM)and glutathione(GSH)from the DCM dehalogenase,random accelerated molecular dynamics(RAMD)simulations were performed,in which DCM and GSH were forced to leave the active site.The protein structure was predicted using Alphafold2,and the conformations of GSH and DCM in the binding pocket were predicted by docking.A long equilibrium simulation was conducted to validate the structure of the complex.The results show that GSH is most commonly observed in three main pathways,one of which is more important than the other two.In addition,DCM was observed to escape along a unique pathway.The key residues and protein helices of each pathway were identified.The results can provide a theoretical foundation for the subsequent dissociation mechanism of DCM dehalogenase.

Network pharmacology to decipher the mechanism of Danggui Longhui Wan against chronic myeloid leukemia

Chronic myeloid leukemia(CML)is a hematopoietic myeloproliferative disorder.The Chinese prescription Danggui Longhui Wan(DGLHW)has been utilized in CML treatment,but its underlying mechanisms remain unclear.In this study,we gathered 794 constituents,1249 drug targets,1654 disease genes and 129 intersection genes.GO and KEGG were used to analyze the function of these genes.Compatibility of prescription study showed that monarch drug,minister drug,assistant and guide drug played a synergistic role in the treatment of CML.In addition,we obtained 20 hub genes and 12 key components.Molecular docking indicated that the main compounds and core proteins had good binding ability.The results of this study also showed that DGLHW might play a role in the treatment of CML by affecting MAPK,PI3K/AKT,FoxO and p53 signaling pathways.

Probing Structure, Thermochemistry, Electron Affinity and Magnetic Moment of Dysprosium-doped Silicon Clusters DySi_n(n = 3～10) and Their Anions with Double-hybrid Density Functional Theory

The equilibrium geometries, electronic structures and electronic properties including adiabatic electron affinity（AEA）, vertical detachment energy（VDE）, simulated photoelectron spectroscopy, HOMO-LUMO gap, charge transfer, and magnetic moment for DySi_n（n = 3~10） clusters and their anions were systematically investigated by using the ABCluster global search technique combined with the B3 LYP and B2 PLYP density functional methods. The results showed that the lowest energy structure of neutral DySi_n（n = 3~10） can be regarded as substituting a Si atom of the ground state structure of Si_（n＋1） with a Dy atom. For anions, the extra electron effect on the structure is significant. Starting from n = 6, the lowest energy structures of DySi_n~？（n = 3~10） differ from those of neutral. The ground state is quintuplet electronic state for DySi_n（n = 3~10） excluding DySi_4 and DySi_9, which is a septet electronic state. For anions, the ground state is a sextuplet electronic state. The reliable AEA and VDE of DySi_n（n = 3~10） are reported. Analyses of HOMO-LUMO gaps indicated that doping Dy atom to silicon clusters can improve significantly their photochemical reactivity, especially for DySi_9. Analyses of NPA revealed that the 4 f electrons of Dy in DySi_4, DySi_9, and DySi_n~？ with n = 4 and 6~10 participate in bonding. That is, DySi_nbelongs to the AB type. The 4 f electrons of Dy atom provide substantially the total magnetic moments for DySi_n and their anions. The dissociation energies of Ln（Ln = Pr, Sm, Eu, Gd, Ho, and Dy） fromLn Sin and their anions were evaluated to examine the relative stabilities.

Adsorption and dissociation of H_2O on Cu_2O(100): A computational study

The adsorption and dissociation of water on Cu2O（100） have been investigated by the density functional theory-generalized gradient approximation （DFT-GGA） method. The corresponding reaction energies, the structures of the transition states and the activation energies were determined. Calculations with and without dipole correction were both studied to get an understanding of the effect of the dipole moment on the adsorption and reaction of water on dipole surface Cu2O（100）. When dipole correction was added, the adsorption energies of H2O on different sites generally decreased. The calculated activation barriers for HxO （x = 1, 2） dehydrogenation are 0.42 eV （1.01 eV without the dipole correction） and 1.86 eV, respectively, including the zero point energy correction. The first dehydrogenation outcome is energetically the most stable product.

Computational Analysis of Physicochemical, Pharmacokinetic and Toxicological Properties of Deoxyhypusine Synthase Inhibitors with Antimalarial Activity

Malaria is a parasitic disease which has as etiological agents protozoa of the genus Plasmodium prevalent in tropical countries. The appearance of Plasmodium strains resistant to artemisinin has become necessary the development of new drugs using computational tools to combat this epidemic. Diverse transporter proteins can act as antimalarials targets, thereby being the enzyme deoxyhypusine synthase a promising antimalarial target. The present study aimed to investigate 15 most active inhibitors of deoxyhypusine synthase target, deposited in databases Binding DB, in order to trace a pattern of physicochemical, pharmacokinetic and toxicological properties of the inhibitors for this enzyme and propose new inhibitors of deoxyhypusine synthase target. The physicochemical properties were obtained according to the Lipinski parameters to evaluate oral absorption. Based on the certain properties were proposed three new inhibitors (A, B and C). The ADME/Tox properties were calculated for new inhibitors compared with results of the selected compounds. The fifteen inhibitors for oral administration showed satisfactory results, because they have adapted to the Lipinski parameters. In relation to the penetration of the blood-brain barrier the inhibitors analyzed showed penetration values less than 1, and ranged from 0.0411815 to 0.481764, being that the compound 1 showed value of CBrain/CBlood = 0.135467. Compound B showed a higher strength in plasma protein binding in relation to the compound 1, having a variation be-tween them of ±1.489344. Therefore, the compound B would present a longer halflife compared with compound 1. The proposed compounds showed positive and satisfactory results, being able to reach less adverse effects related to the central nervous system depending of administered dose.

Computational Analysis for Residue-Specific CDK2-Inhibitor Bindings

Cyclin-dependent kinase 2 (CDK2) is a key macromolecule in cell cycle regulation. In cancer cells, CDK2 is often overexpressed and its inhibition is an effective therapy of many cancers including breast carcinomas, leukemia, and lymphomas. Quantitative characterization of the interactions between CDK2 and its inhibitors at atomic level may provide a deep understanding of protein-inhibitor interactions and clues for more effective drug discovery. In this study, we have used the computational alanine scanning approach in combination with an efficient interaction entropy method to study the microscopic mechanism of binding between CDK2 and its 13 inhibitors. The total binding free energy from the method shows a correlation of 0.76?0.83 with the experimental values. The free energy component reveals two binding mode in the 13 complexes, namely van der Waals dominant, and electrostatic dominant. Decomposition of the total energy to per-residue contribution allows us to identify five hydrophobic residues as hot spots during the binding. Residues that are responsible for determining the strength of the binding were also analyzed.

Computational Investigation on the Ethylene-induced Esterase from Citrus Sinensis

In order to understand the interaction between ethylene-induced esterase（EIE, EC 3.1.1.） from Citrus sinensis and α-naphthyl acetate, a3D model of EIE was generated based on the crystal structure of the tobacco salicylic acid binding protein 2（SABP2）. With the aid of the molecular mechanics and molecular dynamics methods, the final refined model was obtained and its reliability was further assessed. In this study, the docking results show that the main-chain amide of residue His85 and residue Vall8 can form hydrogen bonds to the carbonyl oxygen group of α-naphthyl acetate. MM-PBSA method was applied to calculating the binding free energy between EIE mutants and α-naphthyl acetate. Our calculated binding free energy of each of the two mutant complexes is increased compared with that of the one of the wild type, which is unfavorable to the reaction. It is well consistent with the experimental data. The above results clearly indicate that His85 and Vail8 in EIE function as the oxyanion role and take part in the catalytic reaction. The new structural insights obtained from this computational study are expected to stimulate further biochemical studies on the structures and mechanisms of EIE and other members of the plant α/β hydrolases.

Ultralow-Energy-Barrier H_(2)O_(2)Dissociation on Coordinatively Unsaturated Metal Centers in Binary Ce-Fe Prussian Blue Analogue for Efficient and Stable Photo-Fenton Catalysis

The low intrinsic activity of Fenton catalytic site and high demand for light-energy input inhibit the organic-pollution control efficiency of photo-Fenton process.Here,through structural design with density functional theory(DFT)calculations,Ce is predicted to enable the construction of coordinatively unsaturated metal centers(CUCs)in Prussian blue analogue(PBA),which can strongly adsorb H_(2)O_(2)and donate sufficient electrons for directly splitting the O-O bond to produceOH.Using a substitution-co-assembly strategy,binary Ce-Fe PBA is then prepared,which rapidly degrades sulfamethoxazole with the pseudo-first-order kinetic rate constant exceeding reported values by 1-2 orders of magnitude.Meanwhile,the photogenerated electrons reduce Fe(Ⅲ)and Ce(Ⅳ)to promote the metal valence cycle in CUCs and make sulfamethoxazole degradation efficiency only lose 6.04%in 5 runs.Overall,by introducing rare earth metals into transition metal-organic frameworks,this work guides the whole process for highly active CUCs from design and construction to mechanism exploration with DFT calculations,enabling ultrafast and stable photo-Fenton catalysis.

Direct atomic-level insight into oxygen reduction reaction on size-dependent Pt-based electrocatalysts from density functional theory calculations

Developing novel oxygen reduction reaction(ORR)catalysts with high activity is urgent for proton exchange membrane fuel cells.Herein,we investigated a group of size-dependent Pt-based catalysts as promising ORR catalysts by density functional theory calculations,ranging from single-atom,nanocluster to bulk Pt catalysts.The results showed that the ORR overpotential of these Pt-based catalysts increased when its size enlarged to the nanoparticle scale or reduced to the single-atom scale,and the Pt_(38)cluster had the lowest ORR overpotential(0.46 V)compared with that of Pt_(111)(0.57 V)and single atom Pt(0.7 V).Moreover,we established a volcano curve relationship between the ORR overpotential and binding energy of O*(ΔE_(O*),confirming the intermediate species anchored on Pt38cluster with suitable binding energy located at top of volcano curve.The interaction between intermediate species and Pt-based catalysts were also investigated by the charge distribution and projected density of state and which further confirmed the results of volcano curve.

Simulation Prediction of Heat Transport with Machine Learning in Tokamak Plasmas

Machine learning opens up new possibilities for research of plasma confinement. Specifically, models constructed using machine learning algorithms may effectively simplify the simulation process. Previous firstprinciples simulations could provide physics-based transport information, but not fast enough for real-time applications or plasma control. To address this issue, this study proposes SExFC, a surrogate model of the Gyro-Landau Extended Fluid Code(ExFC). As an extended version of our previous model ExFC-NN, SExFC can capture more features of transport driven by the ion temperature gradient mode and trapped electron mode,using an extended database initially generated with ExFC simulations. In addition to predicting the dominant instability, radially averaged fluxes and radial profiles of fluxes, the well-trained SExFC may also be suitable for physics-based rapid predictions that can be considered in real-time plasma control systems in the future.

A TD-DFT Study for the Excited State Calculations of Microhydration of N-Acetyl-Phenylalaninylamide (NAPA)

Investigating the impact of microhydration on the excited-states and electronic excitation properties of biomolecules has remained one of the important yet challenging aspects of science because of the complexity of developing models. However, with the advent of computational chemistry methods such as TD-DFT, many useful insights about the electronic excitation energy and excited-state nature of biomolecules can be explored. Accordingly, in our study, we have incorporated the TD-DFT/wB97XD/cc-pVTZ method to study the excited state properties of N-acetyl phenylalanine amide (NAPA-A(H2O) n) (n = 1 to 4) clusters from ground to the tenth lowest gaseous singlet excited state. We found that the C=O bond length gradually increases both in N-terminal amide and C-terminal amide after the sequential addition of water molecules because of intermolecular H-bonding and this intermolecular H-bonding becomes weaker after the sequential addition of H2O molecules. The UV absorption maxima of NAPA-A (H2O)n (n = 1 - 4) clusters consisted of two peaks that are S5←S0 (1st absorption) and S6←S0 (2nd absorption) excitations. The first absorption maxima were blue-shifted with the increase in oscillator strength. This means that strong H-bonds reduce the charge transfer and make clusters more rigid. On the other hand, the second absorption maxima were red-shifted with the decrease in oscillator strength. In the ECD spectra, the negative bands indicate the presence of an amide bond and L-configuration of micro hydrated NAPA-A clusters. Finally, our calculated absorption and fluorescence energy confirm that all the NAPA-A (H2O) n (n = 0 - 4) clusters revert to the ground state from the fluorescent state by emitting around 5.490 eV of light.

Concerted versus stepwise mechanisms of cyclic proton transfer:Experiments, simulations, and current challenges

Proton transfer(PT) is a process of fundamental importance in hydrogen(H)-bonded systems. At cryogenic or moderate temperatures, pronounced quantum tunneling may happen due to the light mass of H. Single PT processes have been extensively studied. However, for PT involving multiple protons, our understanding remains in its infancy stage due to the complicated interplay between the high-dimensional nature of the process and the quantum nature of tunneling. Cyclic H-bonded systems are typical examples of this, where PT can happen separately via a “stepwise” mechanism or collectively via a “concerted” mechanism. In the first scenario, some protons hop first, typically resulting in metastable intermediate states(ISs) and the reaction pathway passes through multiple transition states. Whilst in the concerted mechanism, all protons move simultaneously, resulting in only one barrier along the path. Here, we review previous experimental and theoretical studies probing quantum tunneling in several representative systems for cyclic PT, with more focus on recent theoretical findings with path-integral based methods. For gas-phase porphyrin and porphycene, as well as porphycene on a metal surface, theoretical predictions are consistent with experimental observations, and enhance our understanding of the processes. Yet, discrepancies in the PT kinetic isotope effects between experiment and theory appear in two systems,most noticeably in water tetramer adsorbed on NaCl(001) surface, and also hinted in porphycene adsorbed on Ag(110)surface. In ice Ih, controversy surrounding concerted PT remains even between experiments. Despite of the recent progress in both theoretical methods and experimental techniques, multiple PT processes in cyclic H-bonded systems remain to be mysterious.

Acetate coverage effect on the reactivity of vinyl acetate synthesis on Pd/Au alloy surfaces

Vinyl acetate （VA） synthesis on Pd/Au（111） and Pd/Au（100） surfaces has been systematically investigated through first-principles density functional theory （DFT） calculations. The DFr results showed that for VA synthesis, the ＇Samanos＇ reaction mechanism （i.e., direct coupling of coadsorbed ethylene and acetate species and subsequent/%hydride elimination to form VA） is more favorable than the ＇Moiseev＇ mechanism （i.e., ethylene first dehydrogenates to form vinyl species which then couple with the coadsorbed acetate species to form VA）. More importantly, it was found the surface coverage of acetate has a significant effect on the reactivity of VA synthesis, and the activation energy of the rate- controlling step on Pd/Au（100） surface is smaller than that on Pd/Au（111） surface （0.88 vs. 0.95 eV）, indicating the former is more active than the latter.

Molecular Simulation of CO2/H2 Mixture Separation in Metal-organic Frameworks： Effect of Catenation and Electrostatic Interactions

In this work grand canonical Monte Carlo simulations were performed to study gas separation in three pairs of isoreticular metal-organic frameworks (IRMOFs) with and without catenation at room temperature.Mixture composed of CO2 and H2 was selected as the model system to separate.The results show that CO2 selectivity in catenated MOFs with multi-porous frameworks is much higher than their non-catenated counterparts.The simulations also show that the electrostatic interactions are very important for the selectivity,and the contributions of different electrostatic interactions are different,depending on pore size,pressure and mixture composition.In fact,changing the electrostatic interactions can even qualitatively change the adsorption behavior.A general conclusion is that the electrostatic interactions between adsorbate molecules and the framework atoms play a dominant role at low pressures,and these interactions in catenated MOFs have much more pronounced effects than those in their non-catenated counterparts,while the electrostatic interactions between adsorbate molecules become evident with increasing pressure,and eventually dominant.

Multi sites vs single site for catalytic combustion of methane over Co3O4(110):A first-principles kinetic Monte Carlo study

Single-atom catalysts have been applied in many processes recently.The difference of their kinetic behavior compared to the traditional heterogeneous catalysts has not been extensively discussed yet.Herein a complete catalytic cycle of CH4 combustion assuming to be confined at isolated single sites of the Co3O4(110)surface is computationally compared with that on multi sites.The macroscopic kinetic behaviors of CH4 combustion on Co3O4(110)is systematically and quantitatively compared between those on the single site and multi sites utilizing kinetic Monte Carlo simulations upon the energetic information from the PBE+U calculation and statistic mechanics.The key factors governing the kinetics of CH4 combustion are disclosed for both the catalytic cycles respectively following the single-site and multi-site mechanisms.It is found that cooperation of multi active sites can promote the activity of complete CH4 combustions substantially in comparison to separated single-site catalyst whereas the confinement of active sites could regulate the selectivity of CH4 oxidation.The quantitative understanding of catalytic mechanism paves the way to improve the activity and selectivity for CH4 oxidation.

Activity and selectivity of propane oxidative dehydrogenation over VO_3/CeO_2(111) catalysts: A density functional theory study

The oxidative dehydrogenation（ODH） of propane on monomeric VO3 supported by CeO2（111）（VO3/CeO 2（111）） is studied by periodic density functional theory calculations. Detailed energetic, structural, and electronic properties of these reactions are determined. The calculated activation energies of the breaking of the first and second C–H bonds of propane on the VO3/CeO2（111） catalyst are compared, and it is found that both the unique structural and electronic effects of the VO3/CeO2（111） catalyst contribute to the relatively easy rupture of the first C–H bond of the propane molecule during the ODH reaction. In particular, the so-called new empty localized states that are mainly constituted of O2 porbitals of the ceria-supported VO3 species are determined to be crucial for assisting the cleavage of the first C–H bond of the propane molecule. Following this they become occupied and the remaining C–H bonds become increasingly difficult to break owing to the increasing repulsion between the localized 4 felectrons at the Cecations, resulting in the adsorption of more H and other moieties. This work illustrates that CeO2-supported monomeric vanadium oxides can exhibit unique activity and selectivity for the catalytic ODH of alkanes to alkenes.

Benchmark Calculations on the Atomization Enthalpy,Geometry and Vibrational Frequencies of UF_6 with Relativistic DFT Methods

Benchmark calculations on the molar atomization enthalpy, geometry, and vibrational frequencies of uranium hexafluoride （UF6） have been performed by using relativistic density functional theory （DFT） with various levels of relativistic effects, different types of basis sets, and exchange-correlation functionals. Scalar relativistic effects are shown to be critical for the structural properties. The spin-orbit coupling effects are important for the calculated energies, but are much less important for other calculated ground-state properties of closed-shell UF6. We conclude through systematic investigations that ZORA- and RECP-based relativistic DPT methods are both appropriate for incorporating relativistic effects. Comparisons of different types of basis sets （Slater, Gaussian, and plane-wave types） and various levels of theoretical approximation of the exchange-correlation functionals were also made.

Estimation of Critical Temperature of Thermal Explosion for Energetic Materials Based on Non-isothermal Kinetic Equation dα/dt =A_0 exp(bT)[1+(T–T_0 )b]f(α)

Critical temperature（Tb） of thermal explosion for energetic materials is estimated from Semenov＇s thermal explosion theory and the non-isothermal kinetic equation da/dt=Aoexp（bT）[1＋（T-T0）b][（a） deduced via reasonable hypotheses, where To is the initial point of the deviation from the baseline of DSC curve. The final formula is （Tb-Te0）{ 1＋1/[1＋（ Tb-T00）b]}=1. We can easily obtain the initial temperature（T0/） and onset temperature（Tci） from the non-isothermal DSC curves, the values of Too and Tc0 from the equation TOi or ei=T00 or c0＋α1βi＋a2βi^2＋…＋aL-2L-2βiL-2, i=1,2,…L, the value of b from the equation： In[β/（Tei-T0i）]=ln[A0/G（a）]＋bTei, so as to calculate the value of Tb. The result obtained with this method coincides completely with the value of Tb obtained by Hu-Yang-Liang-Wu method.