Influenza A(A/H_(x)N_(y))is a significant public health concern due to its high infectiousness and mortality.Neuraminidase,which interacts with sialic acid(SIA)in host cells,has become an essential target since its hi...Influenza A(A/H_(x)N_(y))is a significant public health concern due to its high infectiousness and mortality.Neuraminidase,which interacts with sialic acid(SIA)in host cells,has become an essential target since its highly conserved catalytic center structure,while resistance mutations have already generated.Here,a detailed investigation of the drug resistance mechanism caused by mutations was performed for subtype N9(A/H7N9).Molecular dynamics simulation and alanine-scanning-interaction-entropy method(ASIE)were used to explore the critical differences between N9 and Zanamivir(ZMR)before and after R294K mutation.The results showed that the mutation caused the hydrogen bond between Arg294 and ZMR to break,then the hydrogen bonding network was disrupted,leading to weakened binding ability and resistance.While in wild type(A/H7N9^(WT)),this hydrogen bond was initially stable.Meanwhile,N9 derived from A/H11N9 was obtained as an R292K mutation.Then the relative binding free energy of N9 with five inhibitors(SIA,DAN,ZMR,G28,and G39)was predicted,basically consistent with experimental values,indicating that the calculated results were reliable by ASIE.In addition,Arg292 and Tyr406 were hot spots in the A/H11N9^(WT)-drugs.However,Lys292 was not observed as a favorable contributing residue in A/H11N9^(R292K),which may promote resistance.In comparison,Tyr406 remained the hotspot feature when SIA,ZMR,and G28 binding to A/H11N9^(R292K).Combining the two groups,we speculate that the resistance was mainly caused by the disruption of the hydrogen bonding network and the transformation of hotspots.This study could guide novel drug delivery of drug-resistant mutations in the treatment of A/H_(x)N9.展开更多
Reduced graphene oxide is the precursor to produce graphene in a large scale;however,to date,there has been no consensus on the electronic structure of reduced graphene oxide.In this study,we carried out an ab initio ...Reduced graphene oxide is the precursor to produce graphene in a large scale;however,to date,there has been no consensus on the electronic structure of reduced graphene oxide.In this study,we carried out an ab initio molecular dynamics simulation to investigate the adsorption process of hydroxyl groups on graphene surface.During the adsorption process,the OH group needs to firstly pass through a physical adsorption complex with the OH above the bridge site of two carbon atoms,next to surmount a transition state,then to be adsorbed at the atop site of a carbon atom.With a 5×5 graphene surface,up to 6 hydroxyl groups can be adsorbed on the graphene surface,indicating the concentration coverage of the hydroxyl groups on graphene surface is about 12%.The simulation results show that the negative adsorption energy increases linearly as the number of adsorbed hydroxyl groups increases,and the band gap also increases linearly with the number of adsorbed hydroxyl groups.展开更多
The geometric and electronic structures of several possible adsorption configurations of the pyrazine(C4H4N2)molecule covalently attached to Si(100)surface,which is of vital importance in fabricating functional nano-d...The geometric and electronic structures of several possible adsorption configurations of the pyrazine(C4H4N2)molecule covalently attached to Si(100)surface,which is of vital importance in fabricating functional nano-devices,have been investigated using X-ray spectroscopies.The Carbon K-shell(1s)X-ray photoelectron spectroscopy(XPS)and near-edge X-ray absorption fine structure(NEXAFS)spectroscopy of predicted adsorbed structures have been simulated by density functional theory with cluster model calculations.Both XPS and NEXAFS spectra demonstrate the structural dependence on different adsorption configurations.In contrast to the XPS spectra,it is found that the NEXAFS spectra exhibiting conspicuous dependence on the structures of all the studied pyrazine/Si(100)systems can be well utilized for structural identification.In addition,according to the classification of carbon atoms,the spectral components of carbon atoms in different chemical environments have been investigated in the NEXAFS spectra as well.展开更多
The structure-property relationship of diarylethene(DAE)-derivative molecular isomers,which involve ring-closed and ring-open forms,is investigated by employing the nonequilibrium Green’s function formalism combined ...The structure-property relationship of diarylethene(DAE)-derivative molecular isomers,which involve ring-closed and ring-open forms,is investigated by employing the nonequilibrium Green’s function formalism combined with density functional theory.Molecular junctions are formed by the isomers connecting to Au(111)electrodes through flanked pyridine groups.The difference in electronic structures caused by different geometry structures for the two isomers,particularly the interatomic alternative single bond and double bond of the ring-closed molecule,contributes to the vastly different low-bias conductance values.The lowest unoccupied molecular orbital(LUMO)of the isomers is the main channel for electron transport.In addition,more electrons transferred to the ring-closed molecular junction in the equilibrium condition,thereby decreasing the LUMO energy to near the Fermi energy,which may contribute to a larger conductance value at the Fermi level.Our findings are helpful for understanding the mechanism of low-bias conductance and are conducive to the design of high-performance molecular switching based on diarylethene or diarylethene-derivative molecules.展开更多
The present work concerns the study of solvent effects on the geometrical structures, as well as one- and two-photon absorption (TPA) processes, for two series of alkyne and alkene π-bridging molecules, within the ...The present work concerns the study of solvent effects on the geometrical structures, as well as one- and two-photon absorption (TPA) processes, for two series of alkyne and alkene π-bridging molecules, within the framework of the polarization continuum model. Particular emphasis was put on the characterization of solvent effects on the molecular geometrical structures and geometric distortion, which were measured by the bond-length-alternation parameter. The π centres in the compounds are seen to play a decisive role in increasing the TPA cross section and nonlinear optical properties. All studied molecules have relatively strong TPA characteristics, while the alkyne π-bridging ones yield larger TPA cross sections.展开更多
Two-photon fluorescence dyes have shown promising applications in biomedical imaging.However,the substitution site effect on geometric structures and photophysical properties of fluorescence dyes is rarely illustrated...Two-photon fluorescence dyes have shown promising applications in biomedical imaging.However,the substitution site effect on geometric structures and photophysical properties of fluorescence dyes is rarely illustrated in detail.In this work,a series of new lipid droplets detection dyes are designed and studied,molecular optical properties and non-radiative transitions are analyzed.The intramolecular weak interaction and electron-hole analysis reveal its inner mechanisms.All dyes are proven to possess excellent photophysical properties with high fluorescence quantum efficiency and large stokes shift as well as remarkable two-photon absorption cross section.Our work reasonably elucidates the experimental measurements and the effects of substitution site on two-photon absorption and excited states properties of lipid droplets detection NAPBr dyes are highlighted,which could provide a theoretical perspective for designing efficient organic dyes for lipid droplets detection in biology and medicine fields.展开更多
In this work, the optical properties of fluorescent probes used for detection of biothiol were studied by employing time-dependent density functional theory. By calculating the single photon absorption and emission pr...In this work, the optical properties of fluorescent probes used for detection of biothiol were studied by employing time-dependent density functional theory. By calculating the single photon absorption and emission properties of probe Mol.1, Mol.2 and Mol.3 before and after reaction with cysteine and homocysteine, we have investigated the effect of carboncarbon triple bond and benzene ring on the properties of fluorescent probes. It is found that the oscillator strength of probe molecules increases gradually with the improvement of the structure of the electron donor triphenylamine and the addition of carbon-carbon triple bonds, and better properties of fluorescence probes have also been demonstrated. At the same time, the effect of different number of side branches on the molecular properties of the probe was also studied. The results showed that compared with single-branched molecule Z1 and tribranched probe Mol.3, two side probe molecules Z2 had higher oscillator strength and better detection effect. In addition, the new single-branched probe Mol.4 with the addition of carbon-carbon triple bonds and benzene rings has better probe properties and simpler structure than the tribranched probe Mol.3.展开更多
Moleculardeviceswith highswitchingperformance and/or the perfect spin filtering effect have always been the pursuit with the development of molecular electronics.Hereb,yusingthe 2001.0V nonequilibrium.Green's func...Moleculardeviceswith highswitchingperformance and/or the perfect spin filtering effect have always been the pursuit with the development of molecular electronics.Hereb,yusingthe 2001.0V nonequilibrium.Green's function method in combination with the density functionaltheory,the switching performance and spin filtering properties of dimethyldihydropyrene(DHP)/cyclophanediene(CPD)photoswitchable molecule connected by carbon atomic chains(CACs)to two zigzag graphene nanoribbon electrodes have been theoretically investigated.The results show that DHP is more conductive than CPD and therefore an evident switching effect is demonstrated,and the switching ratio(RON/OFF)can reach 4.5×103.It is further revealed that the RoON/OF of DHP/CPD closely depends on the length of CACs.More specifically,the RoN/OFF values of DHP/CPD with odd-numbered CACs are larger than those with even-numbered CACs.More interestingly,a high or even perfect spin filtering effect can be obtained in these investigated DHP/CPD single-molecule devices.Our study is helpful for future design of single-molecule switches and spin filters and provides a way to optimize their performance by means of varying the length of bridging CACs.展开更多
基金supported by the National Natural Science Foundation of China(No.11774207)。
文摘Influenza A(A/H_(x)N_(y))is a significant public health concern due to its high infectiousness and mortality.Neuraminidase,which interacts with sialic acid(SIA)in host cells,has become an essential target since its highly conserved catalytic center structure,while resistance mutations have already generated.Here,a detailed investigation of the drug resistance mechanism caused by mutations was performed for subtype N9(A/H7N9).Molecular dynamics simulation and alanine-scanning-interaction-entropy method(ASIE)were used to explore the critical differences between N9 and Zanamivir(ZMR)before and after R294K mutation.The results showed that the mutation caused the hydrogen bond between Arg294 and ZMR to break,then the hydrogen bonding network was disrupted,leading to weakened binding ability and resistance.While in wild type(A/H7N9^(WT)),this hydrogen bond was initially stable.Meanwhile,N9 derived from A/H11N9 was obtained as an R292K mutation.Then the relative binding free energy of N9 with five inhibitors(SIA,DAN,ZMR,G28,and G39)was predicted,basically consistent with experimental values,indicating that the calculated results were reliable by ASIE.In addition,Arg292 and Tyr406 were hot spots in the A/H11N9^(WT)-drugs.However,Lys292 was not observed as a favorable contributing residue in A/H11N9^(R292K),which may promote resistance.In comparison,Tyr406 remained the hotspot feature when SIA,ZMR,and G28 binding to A/H11N9^(R292K).Combining the two groups,we speculate that the resistance was mainly caused by the disruption of the hydrogen bonding network and the transformation of hotspots.This study could guide novel drug delivery of drug-resistant mutations in the treatment of A/H_(x)N9.
基金supported by the National Natural Science Foundation of China(No.11774206)Taishan Scholarship Fund from Shandong Province。
文摘Reduced graphene oxide is the precursor to produce graphene in a large scale;however,to date,there has been no consensus on the electronic structure of reduced graphene oxide.In this study,we carried out an ab initio molecular dynamics simulation to investigate the adsorption process of hydroxyl groups on graphene surface.During the adsorption process,the OH group needs to firstly pass through a physical adsorption complex with the OH above the bridge site of two carbon atoms,next to surmount a transition state,then to be adsorbed at the atop site of a carbon atom.With a 5×5 graphene surface,up to 6 hydroxyl groups can be adsorbed on the graphene surface,indicating the concentration coverage of the hydroxyl groups on graphene surface is about 12%.The simulation results show that the negative adsorption energy increases linearly as the number of adsorbed hydroxyl groups increases,and the band gap also increases linearly with the number of adsorbed hydroxyl groups.
基金the National Natural Science Foundation of China(No.11874242,No.11804196,No.11804197)support provided by China Scholarship Council(CSC)for Yong Ma to Royal Institute of Technology(KTH)is acknowledgedsupport of the Taishan Scholar Project of Shandong Province。
文摘The geometric and electronic structures of several possible adsorption configurations of the pyrazine(C4H4N2)molecule covalently attached to Si(100)surface,which is of vital importance in fabricating functional nano-devices,have been investigated using X-ray spectroscopies.The Carbon K-shell(1s)X-ray photoelectron spectroscopy(XPS)and near-edge X-ray absorption fine structure(NEXAFS)spectroscopy of predicted adsorbed structures have been simulated by density functional theory with cluster model calculations.Both XPS and NEXAFS spectra demonstrate the structural dependence on different adsorption configurations.In contrast to the XPS spectra,it is found that the NEXAFS spectra exhibiting conspicuous dependence on the structures of all the studied pyrazine/Si(100)systems can be well utilized for structural identification.In addition,according to the classification of carbon atoms,the spectral components of carbon atoms in different chemical environments have been investigated in the NEXAFS spectra as well.
基金supported by the National Natural Science Foundation of China(No.11874242 and No.21933002)the Natural Science Foundation of Shandong Province,China(No.ZR2019PA022).
文摘The structure-property relationship of diarylethene(DAE)-derivative molecular isomers,which involve ring-closed and ring-open forms,is investigated by employing the nonequilibrium Green’s function formalism combined with density functional theory.Molecular junctions are formed by the isomers connecting to Au(111)electrodes through flanked pyridine groups.The difference in electronic structures caused by different geometry structures for the two isomers,particularly the interatomic alternative single bond and double bond of the ring-closed molecule,contributes to the vastly different low-bias conductance values.The lowest unoccupied molecular orbital(LUMO)of the isomers is the main channel for electron transport.In addition,more electrons transferred to the ring-closed molecular junction in the equilibrium condition,thereby decreasing the LUMO energy to near the Fermi energy,which may contribute to a larger conductance value at the Fermi level.Our findings are helpful for understanding the mechanism of low-bias conductance and are conducive to the design of high-performance molecular switching based on diarylethene or diarylethene-derivative molecules.
文摘The present work concerns the study of solvent effects on the geometrical structures, as well as one- and two-photon absorption (TPA) processes, for two series of alkyne and alkene π-bridging molecules, within the framework of the polarization continuum model. Particular emphasis was put on the characterization of solvent effects on the molecular geometrical structures and geometric distortion, which were measured by the bond-length-alternation parameter. The π centres in the compounds are seen to play a decisive role in increasing the TPA cross section and nonlinear optical properties. All studied molecules have relatively strong TPA characteristics, while the alkyne π-bridging ones yield larger TPA cross sections.
基金This work was supported by the National Natural Science Foundation of China(No.11804196 and No.11904210)the Project funded by China Postdoctoral Science Foundation(No.2018M642689)the Open Fund of Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates,(South China University of Technology)(No.2019B030301003).
文摘Two-photon fluorescence dyes have shown promising applications in biomedical imaging.However,the substitution site effect on geometric structures and photophysical properties of fluorescence dyes is rarely illustrated in detail.In this work,a series of new lipid droplets detection dyes are designed and studied,molecular optical properties and non-radiative transitions are analyzed.The intramolecular weak interaction and electron-hole analysis reveal its inner mechanisms.All dyes are proven to possess excellent photophysical properties with high fluorescence quantum efficiency and large stokes shift as well as remarkable two-photon absorption cross section.Our work reasonably elucidates the experimental measurements and the effects of substitution site on two-photon absorption and excited states properties of lipid droplets detection NAPBr dyes are highlighted,which could provide a theoretical perspective for designing efficient organic dyes for lipid droplets detection in biology and medicine fields.
基金supported by the National Natural Science Foundation of China (No.11604185 and No.11804196)the Taishan Scholar Program of Shandong Province of China
文摘In this work, the optical properties of fluorescent probes used for detection of biothiol were studied by employing time-dependent density functional theory. By calculating the single photon absorption and emission properties of probe Mol.1, Mol.2 and Mol.3 before and after reaction with cysteine and homocysteine, we have investigated the effect of carboncarbon triple bond and benzene ring on the properties of fluorescent probes. It is found that the oscillator strength of probe molecules increases gradually with the improvement of the structure of the electron donor triphenylamine and the addition of carbon-carbon triple bonds, and better properties of fluorescence probes have also been demonstrated. At the same time, the effect of different number of side branches on the molecular properties of the probe was also studied. The results showed that compared with single-branched molecule Z1 and tribranched probe Mol.3, two side probe molecules Z2 had higher oscillator strength and better detection effect. In addition, the new single-branched probe Mol.4 with the addition of carbon-carbon triple bonds and benzene rings has better probe properties and simpler structure than the tribranched probe Mol.3.
基金This work is supported by the National Natural Sci-ence Foundation China(No.22173052 of and No.11974217).
文摘Moleculardeviceswith highswitchingperformance and/or the perfect spin filtering effect have always been the pursuit with the development of molecular electronics.Hereb,yusingthe 2001.0V nonequilibrium.Green's function method in combination with the density functionaltheory,the switching performance and spin filtering properties of dimethyldihydropyrene(DHP)/cyclophanediene(CPD)photoswitchable molecule connected by carbon atomic chains(CACs)to two zigzag graphene nanoribbon electrodes have been theoretically investigated.The results show that DHP is more conductive than CPD and therefore an evident switching effect is demonstrated,and the switching ratio(RON/OFF)can reach 4.5×103.It is further revealed that the RoON/OF of DHP/CPD closely depends on the length of CACs.More specifically,the RoN/OFF values of DHP/CPD with odd-numbered CACs are larger than those with even-numbered CACs.More interestingly,a high or even perfect spin filtering effect can be obtained in these investigated DHP/CPD single-molecule devices.Our study is helpful for future design of single-molecule switches and spin filters and provides a way to optimize their performance by means of varying the length of bridging CACs.