Molecular surface functionalization of In_(2)O_(3) to tune interfacial microenvironment for enhanced catalytic performance of CO_(2) electroreduction

Indium-based materials(e.g.,In_(2)O_(3))are a class of promising non-noble metal-based catalysts for electroreduction of carbon dioxide(CO_(2)).However,competitive hydrogen reduction reaction(HER)on indium-based catalysts hampers CO_(2) reduction reaction(CO_(2)RR)process.We herein tune the interfacial microenvironment of In_(2)O_(3) through chemical graft of alkyl phosphoric acid molecules using a facile solution-processed strategy for the first time,which is distinguished from other researches that tailor intrinsic activity of In_(2)O_(3) themselves.The surface functionalization of alkyl phosphoric acids over In_(2)O_(3) is demonstrated to remarkably boost CO_(2) conversion.For example,octadecylphosphonic acid modified In_(2)O_(3) exhibits Faraday efficiency for H_(2) H_(2) H_(2)(FE)of as low as 6.6%and FEHCOOH of 86.5%at-0.67 V vs.RHE,which are far superior to parent In_(2)O_(3) counterparts(FE of 24.0%and FEHCOOH of 63.1%).Moreover,the enhancing effect of alkyl phosphoric acid functionalization is found to be closely related to the length of alkyl chains.By virtue of comprehensive experimental characterizations and molecular dynamics simulations,it is revealed that the modification of alkyl phosphoric acids significantly alters the interface microenvironment of the electrocatalyst,which changes the electrocatalyst surface from hydrophilic and aerophobic to hydrophobic and aerophilic.In this case,the water molecules are pushed away and more CO_(2) molecules are trapped,increasing local CO_(2) concentration at In_(2)O_(3) active sites,thus leading to the significantly enhanced CO_(2)RR and suppressed HER.This work highlights the importance of regulating the interfacial microenvironment of inorganic catalysts by molecular surface functionalization as a means for promoting the electrochemical performance in electrosynthesis and beyond.

Surface Molecular Encapsulation with Cyclodextrin in Promoting the Activity and Stability of Fe Single-Atom Catalyst for Oxygen Reduction Reaction

Fe single-atom catalysts(Fe-SACs)have been extensively studied as a highly efficient electrocatalyst toward the oxygen reduction reaction(ORR).Nonetheless,they suffer from stability issue induced by dissolution of Fe metal center and the OH^(−)blocking.Herein,a surface molecular engineering strategy is developed by usingβ-cyclodextrins(CDs)as a localized molecular encapsulation.The CD-modified Fe-SAC(Fe-SNC-β-CD)shows obviously improved activity toward the ORR with 0.90 V,4.10 and 4.09 mA cm^(-2)for E_(1/2),J_(0)and Jk0.9,respectively.Meanwhile,the Fe-SNC-β-CD shows the excellent long-term stability against aggressive stress and the poisoning.It is confirmed through electrochemical investigation that modification ofβ-CD can,on one hand,regulate the atomic Fe coordination chemistry through the interaction between the CD and FeN_(x) moiety,while on the other mitigate the strong adsorption of OH^(−)and function as protective barrier against the poisoning molecules leading to enhanced ORR activity and stability for the Fe-SACs.The molecular encapsulation strategy demonstrates the uniqueness of post-pyrolysis surface molecular engineering for the design of single-atom catalyst.

Between Algorithm and Model:Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field.In this work,two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface:the blobby surface,an implicit Gaussian atom centered surface,and the skin surface.As figures of merit,we considered surface differentiability and surface area continuity with respect to atom positions,and the agreement with explicit solvent simulations.Geometric analysis seems to privilege the skin to the blobby surface,and points to an unexpected relationship between the non connectedness of the surface,caused by interstices in the solute volume,and the surface area dependence on atomic centers.In order to assess the ability to reproduce explicit solvent results,specific software tools have been developed to enable the use of the skin surface in PoissonBoltzmann calculations with the DelPhi solver.The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.

Poisson-Boltzmann Calculations:van der Waals or Molecular Surface?

The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules,but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric.The default choice for the dielectric boundary has been the molecular surface,but the use of the van der Waals surface has also been advocated.Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations.The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface.However,this assignment may not be as unrealistic as previously thought,since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.

Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters（hexamer and above）, the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster,vacancy formation, filling, and shifting can be observed from the results.

A MOLECULAR BEAM INVESTIGATION ON ACTIVATED CHEMISORPTION OF N_2 ON Ni SURFACE AND La FILM

The activated chemisorption of N2 on Ni （poly） and La film was performed on a molecular beam—surface scattering apparatus. Experimental results indicate that the initial sticking probability so increases linearly from 0 to 0.03 as normal component of translational energy of the molecuar beam En increases from 11.00 to 19.91 kcal/mol for N2/Ni system and S0 from 0 to 0. 10 as En from 10. 40 to 19.91 kcal/mol for N2/La system. The apparent activation energy △E are 6.16 kcal/mol and 5.30 kcal/mol for N2/Ni and N2/La systems respectively.

Exploring unbinding mechanism of drugs from SERT via molecular dynamics simulation and its implication in antidepressants

The human serotonin transporter(SERT)terminates neurotransmission by removing serotonin from the synaptic cleft,which is an essential process that plays an important role in depression.In addition to natural substrate serotonin,SERT is also the target of the abused drug cocaine and,clinically used antidepressants,escitalopram,and paroxetine.To date,few studies have attempted to investigate the unbinding mechanism underlying the orthosteric and allosteric modulation of SERT.In this article,the conserved property of the orthosteric and allosteric sites(S1 and S2)of SERT was revealed by combining the high resolutions of x-ray crystal structures and molecular dynamics(MD)simulations.The residues Tyr95 and Ser438 located within the S1 site,and Arg104 located within the S2 site in SERT illustrate conserved interactions(hydrogen bonds and hydrophobic interactions),as responses to selective serotonin reuptake inhibitors.Van der Waals interactions were keys to designing effective drugs inhibiting SERT and further,electrostatic interactions highlighted escitalopram as a potent antidepressant.We found that cocaine,escitalopram,and paroxetine,whether the S1 site or the S2 site,were more competitive.According to this potential of mean force(PMF)simulations,the new insights reveal the principles of competitive inhibitors that lengths of trails from central SERT to an opening were~18A for serotonin and~22 A for the above-mentioned three drugs.Furthermore,the distance between the natural substrate serotonin and cocaine(or escitalopram)at the allosteric site was~3A.Thus,it can be inferred that the potent antidepressants tended to bind at deeper positions of the S1 or the S2 site of SERT in comparison to the substrate.Continuing exploring the processes of unbinding four ligands against the two target pockets of SERT,this study observed a broad pathway in which serotonin,cocaine,escitalopram(at the S1 site),and paroxetine all were pulled out to an opening between MT1b and MT6a,which may be helpful to understand the dissociation mechanism of antidepressants.

Prediction of aqueous solubility of PCBs based on molecular structure

The thermodynamic relationships among aqueous solubility and molar volume (MV) , total molecular surface area (TSA) and molecular connectivity index (MCI) for highly hydrophobic chemicals. PCBs are established and discussed, respectively. Good linear relationships exist among In Cs and MV, TSA or MCI.

Structure and switching of single-stranded DNA tethered to a charged nanoparticle surface

Using a molecular theory, we investigate the temperature-dependent self-assembly of single-stranded DNA（ss DNA）tethered to a charged nanoparticle surface. Here the size, conformations, and charge properties of ss DNA are taken into account. The main results are as follows： i） when the temperature is lower than the critical switching temperature, the ss DNA will collapse due to the existence of electrostatic interaction between ss DNA and charged nanoparticle surface; ii）for the short ss DNA chains with the number of bases less than 10, the switching of ss DNA cannot happen, and the critical temperature does not exist; iii） when the temperature increases, the electrostatic attractive interaction between ss DNA and charged nanoparticle surface becomes weak dramatically, and ss DNA chains will stretch if the electrostatic attractive interaction is insufficient to overcome the elastic energy of ss DNA and the electrostatic repulsion energy. These findings accord well with the experimental observations. It is predicted that the switching of ss DNA will not happen if the grafting densities are too high.

Helium nano-bubble bursting near the nickel surface

We have investigated the expansion and bursting of a helium nano-bubble near the surface of a nickel matrix using a molecular dynamics simulation. The helium atoms erupt from the bubble in an instantaneous and volcano-like process,which leads to surface deformation consisting of cavity formation on the surface, along with modification and atomic rearrangement at the periphery of the cavity. During the kinetic releasing process, the channel may undergo the ＂open＂ and＂close＂ states more than once due to the variation of the stress inside the nano-bubble. The ratio between the number of helium atoms and one of vacancies can directly reflect the releasing rate under different temperatures and crystallographic orientation conditions, respectively. Moreover, a special relationship between the stress and He-to-vacancy ratio is also determined. This model is tested to compare with the experimental result from Hastelloy N alloys implanted by helium ions and satisfactory agreement is obtained.

Combination of multiple tools for surface manipulation of polar molecules

A scheme of surface manipulation and control of polar molecules is proposed, which combines three tools of electrostatic velocity filtering, bunching, and storing. In the scheme, a slow molecular beam is produced from an effusive beam by surface velocity filtering. Then the velocity spread of the slow molecular beam is compressed by a buncher consisting of a series of electrodes. Following that the molecular beam with a narrow velocity spread is stored in a storage ring. Using ND3 molecule as a tester, the feasibility of our scheme is analyzed theoretically and verified via numerical simulations that cover all three manipulation processes. The results show that cold molecular samples can be prepared from a thermal gas reservoir and stored in the storage ring with more than 10 round trips. Our combined scheme facilitates the production and manipulation of polar molecules, offering new opportunities for basic research and intriguing applications such as quantum information science and cold collisions.

Predictive and Comparative Study of Chromatographic Retention Index for 75 Chloronaphthalene Congeners

Chloronaphthalenes （PCNs, polychlorinated naphthalenes） are a group of persistent environmental pollutants. In the present study, geometrical optimization and electrostatic potential calculations have been performed for all 75 PCNs at the HF/6-31G^＊ level of theory. A number of statistic based parameters have been extracted. Linear relationships between gas-chromatographic retention index （RI） of 62 PCNs in a non-polar column （DB-5） and the structural descriptors have been established by stepwise multiple regression technique. The result shows that two quantities derived from electrostatic potential on molecular surface, ∑Vs- and σ＋^2, together with the number of chlorine （ NCl ） and the energy of the highest occupied molecular orbital （EHOMO） can be well used to express the quantitative structure-retention relationship （QSRR） of PCNs. Predictive capability of the model has been demonstrated by leave-one-out cross-validation with the cross-validated correlation coefficient （Rcv^2） of 0.997, and further compared with the results from similar researches published recently. Furthermore, when splitting the 62 PCNs into training and validation sets in the ratio of 2：1, a similar treatment yields an equation of almost equal statistical quality and very similar regression coefficients, validating the robustness and prediction capability of our model. The QSRR model established may provide a new powerful method for predicting chromatographic properties of polychlorinated naphthalenes.

Theoretical Studies on the Hydrogen Bonds of Different Position Action Mechanisms of Thymine with Uracil

In this research, the hydrogen bonds Y···H-X （X = C, N; Y = N, O） of thymine and uracil have been theoretically studied. The results show that hydrogen bond leads to bond length elongation and stretches the frequency red-shift of N-H···Y. Meanwhile, the C-H···O bonds shorten and stretch the frequency blue-shift. They all belong to traditional hydrogen bonds. The intermolecular charge transfer caused by the intermolecular hyperconjugation s＊（N–H） → n（Y） and intramolecular charge redistribution by intramolecular hyperconjugation σ（C-H） →σ＊（C-N） play important roles in the formation of hydrogen bonds. According to thejudgment standards proposed by Bader and Popelier, these hydrogen bonds have typical electron density topological properties. Electrostatic surface potential （ESP） is a useful physicochemical property of a molecule that provides insights into inter- and intramolecular associations, as well as the prediction of likely sites of electrophilic and nucleophilic metabolic attack.

Tunable CO_(2)enrichment on functionalized Au surface for enhanced CO_(2)electroreduction

Electrochemical conversion of carbon dioxide(CO_(2))to higher-value products provides a forward-looking way to solve the problems of environmental pollution and energy shortage.However,the low solubility of CO_(2)in aqueous electrolytes,sluggish kinetics,and low selectivity hamper the efficient conversion of CO_(2).Here,we report a Au-based hybrid nanomaterial by modifying Au nanoparticles(NPs)with the macrocyclic molecule cucurbit[6]uril(Au@CB[6]).Au@CB[6]displays the optimal selectivity of CO,with the highest CO Faraday efficiency(FECO)reaching 99.50%at−0.6 V vs.reversible hydrogen electrode(RHE).The partial current density of CO formed by Au@CB[6]increases dramatically,as 3.18 mA/cm2 at−0.6 V,which is more than ten times as that of oleylamine-coated Au NPs(Au@OAm,0.31 mA/cm2).Operando electrochemical measurement combined with density functional theory(DFT)calculations reveals that CB[6]can gather CO_(2)and lead the increased local CO_(2)concentration near metal interface,which realizes significantly enhanced electrochemical CO_(2)reduction reaction(CO_(2)RR)performance.

Rupintrivir is a promising candidate for treating severe cases of Enterovirus-71 infection

AIM:To evaluate the suitability of rupintrivir against Enterovirus 71(EV71)induced severe clinical symptoms using computational methods. METHODS:The structure of EV71 3C protease was predicted by homology modeling.The binding free energies between rupintrivir and EV71 3C and human rhinovirus 3C protease were computed by molecular dynamics and molecular mechanics Poisson-Boltzmann/ surface area and molecular mechanics generalized-born/ surface area methods.EV71 3C fragments obtained from clinical samples collected during May to July 2008 in Shanghai were amplified by reverse-transcription and polymerase chain reaction and sequenced. RESULTS:We observed that rupintrivir had favorable binding affinity with EV71 3C protease(-10.76 kcal/mol). The variability of the 3C protein sequence in isolates of various outbreaks,including those obtained in our hospital from May to July 2008,were also analyzed to validate the conservation of the drug binding pocket. CONCLUSION:Rupintrivir,whose safety profiles had been proved,is an attractive candidate and can be quickly utilized for treating severe EV71 infection.

Molecular Dynamics Simulation of Tensile Deformation and Fracture of γ-TiAl with and without Surface Defects

Molecular dynamics simulation of uniaxial tension along [001] has been performed to study the influence of various surface defects on the initiation of plastic deformation and fracture of γ-TiAl single crystals.The results indicate that brittle fracture occurs in perfect bulk; surfaces and edges will be detrimental to the strength of materials and provide dislocation nucleation site. The defects on surfaces and edges cause further weakening with various effects depending on defect type, size, position and orientation,while the edge dimples are the most influential. For γ-TiAl rods with surface dimples, dislocations nucleate from an edge of the rod when dimples are small, dimple dislocation nucleation occurs only when the dimples are larger than a strain rate dependent critical size. The dislocations nucleated upon [001]tension are super dislocations with Burger vectors 〈011] or 1/2 〈 112] containing four 1/6 〈 112 〉 partials. The effects of surface scratches are orientation and shape sensitive. Scratches parallel to the loading direction have little influence, while sharp ones perpendicular to the loading direction may cause crack and thus should be avoided. This simulation also shows that, any type of surface defect would lower strength,and cause crack in some cases. But some may facilitate dislocation nucleation and improve ductility of TiAl if well controlled.

Coupled quantum molecular cavity optomechanics with surface plasmon enhancement

Cavity optomechanics is applied to study the coupling behavior of interacting molecules in surface plasmon systems driven by two-color laser beams. Different from the traditional force–distance measurement, due to a resonant frequency shift or a peak splitting on the probe spectrum, we have proposed a convenient method to measure the van der Waals force strength and interaction energy via nonlinear spectroscopy. The minimum force value can reach approximately 10^(-15) N, which is 3 to 4 orders of magnitude smaller than the widely applied atomic force microscope(AFM). It is also shown that two adjacent molecules with similar chemical structures and nearly equal vibrational frequencies can be easily distinguished by the splitting of the transparency peak. Based on this coupled optomechanical system, we also conceptually design a tunable optical switch by van der Waals interaction. Our results will provide new approaches for understanding the complex and dynamic interactions inmolecule–plasmon systems.

POLYMER CHAIN DIFFUSION AT A TEMPERATURE BELOW ITS BULK GLASS TRANSITION TEMPERATURE

In this study, it was examined whether the dynamics of polymer chains at a surface is different from that in thebulk, and if so, to what extent they differ in terms of surface glass transition temperature and diffusion coefficient. Obtainedresults clearly indicate that surface chains can travel for a relatively large distance in comparison with the characteristiclength scale of usual segmental motion even at a temperature below its bulk glass transition temperature, T_g^b. This isconsistent with our previous results that the surface glass transition temperature is much lower than the corresponding T_g^b.Also, it was experimentally revealed that there was a gradient of molecular motion in the surface region.

Surface molecularly imprinted polymers for solid-phase extraction of （-）-epigallocatechin gallate from toothpaste

Surface molecularly imprinted polymers （SMIPs） have been synthesized to selectively determine （-）-epigallocatechin gallate in aqueous media. SMIPs were prepared using a surface grafting copolymerization method on a functionalized silica gel modified with β-cyclodextrin and vinyl groups. The morphology and composition of the SMIPs were investigated by scanning electron microscopy, Fourier transform-infrared spectroscopy and thermogravimetric analysis. In addition, the molecular binding capacity, recognition properties and selectivity of the SMIPs were evaluated. The imprinted polymers were found to have a highly specific recognition and binding capacity for aqueous media which is （-）-epigallocatechin gallate in the result of the hydrophobic properties of the β-cyclodextrin and the hydrogen-bonding interactions of methacrylic acid. The SMIPs were successfully employed as solid-phase extraction adsor- bents prior to the HPLC determination of （-）-epigallocatechin gallate in toothpaste. The HPLC analysis had a linear dynamic range of 0.5-50.0 μg·mL^-1 with a correlation coefficient of 0.9998 and the recoveries ranged from 89.4% to 97.0% with relative standard deviations less than 4.8%. The limit of detection and limit of quantification were 0.17 and 0.33 μg·mL^-1, respectively. The method provides a promising approach for the preparation of selective materials for the purification and determination of complex samples.

Evaluation on performance of MM/PBSA in nucleic acid-protein systems

The molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) method has been widely used in predicting the binding affinity among ligands,proteins,and nucleic acids.However,the accuracy of the predicted binding energy by the standard MM/PBSA is not always good,especially in highly charged systems.In this work,we take the protein-nucleic acid complexes as an example,and showed that the use of screening electrostatic energy(instead of Coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA.In particular,the Pearson correlation coefficient of dataset Ⅱ in the modified MM/PBSA(i.e.,screening MM/PBSA) is about 0.52,much better than that(<0.33)in the standard MM/PBSA.Further,we also evaluate the effect of solute dielectric constant and salt concentration on the performance of the screening MM/PBSA.The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.