In chemical science,the vertical ionization potential(VIP)is a crucial metric for understanding the electronegativity,hardness and softness of chemical material systems as well as the electronic structure and stabilit...In chemical science,the vertical ionization potential(VIP)is a crucial metric for understanding the electronegativity,hardness and softness of chemical material systems as well as the electronic structure and stability of molecules.Ever since the last century,the model chemistry composite methods have witnessed tremendous developments in computing the thermodynamic properties as well as the barrier heights.However,their performance in realm of the vertical electron processes of molecular systems has been rarely explored.In this study,we for the first time benchmarked the model chemistry composite methods(e.g.,CBS-QB3,G4 and W1BD)in comparison with the commonly used Koopmans's theorem(KT),electron propagator theory(e.g.,OVGF,D2,P3 and P3+)and CCSD(T)methods in calculating the VIP for up to 613 molecular systems with available experimental measurements.The large-scale test calculations strongly showed that the CBS-QB3 model chemistry composite technique can be well recommended to calculate VIP from the perspectives of accuracy,economy and applicability.Notably,the VIP values of up to 7 molecules were identified to have the absolute errors of larger than 0.3 e V at all calculation levels,which have strong hints that their VIP experimental values should be re-investigated.展开更多
Urban rainwater runoff is an important source of nonpoint source pollution due to its transport of diverse contaminants,including polycyclic aromatic hydrocarbons(PAHs)and chlorinated derivatives.Importantly,these chl...Urban rainwater runoff is an important source of nonpoint source pollution due to its transport of diverse contaminants,including polycyclic aromatic hydrocarbons(PAHs)and chlorinated derivatives.Importantly,these chlorinated polycyclic aromatic hydrocarbons(Cl-PAHs)exhibit elevated toxicological potential compared to their non-halogenated parent compounds.In this study,we proposed an approach that combined multivariate receptor model with integration of SHapley Additive exPlanations and Random Forest model.This method identifies the possible sources and reveals the impact of source apportionment results and environmental driving factors(such as geographical and meteorological data)on pollutant concentrations.Sixteen PAHs and nine ClPAHs were detected in 79 runoff samples from all three sites.TheΣ_(16)PAHs average concentration(2923.93 to 6071.83 ng/L)was significantly higher than theΣ_(9)Cl-PAHs(384.34 to 1314.73 ng/L).The source apportionment was conducted by positive matrix factorization(PMF),and six potential pollution sources for PAHs and three for Cl-PAHs were quantified.PAHs primarily originate from the combustion of fossil fuels such as traffic,industrial emissions and coal tar,while Cl-PAHs are mainly derived from atmospheric deposition and industrial emissions.Meanwhile,the self‑organizing map classified PAHs and Cl-PAHs into 2 and 3 groups,respectively.The k-means algorithm yielded 4 clusters for runoff samples.Among machine learning models,Random Forest(RF)demonstrated optimal predictive performance and integrated with SHapley Additive exPlanations(RF-SHAP)revealed the effects of driving factors on the predicted concentration of PAHs and Cl-PAHs in urban runoff samples.展开更多
Control over charge transport in molecular–scale devices requires a deep understanding of how minute structural changes influence electronic properties.Here,we demonstrate dual transport regimes in tunnel junctions o...Control over charge transport in molecular–scale devices requires a deep understanding of how minute structural changes influence electronic properties.Here,we demonstrate dual transport regimes in tunnel junctions of n-alk-1-yne(CnA)molecules with gold electrodes driven by conformational bifurcation—the emergence of two nearly isoenergetic(planar and skewed)molecular conformers(dihedral anglesα=180°andα≈65°at the alkyne terminus in the gas phase).Although the energy differences are small,these subtle conformational differences manifest as distinct transport behaviors,uncovered through unsupervised machine learning,which identified two junction groups:“short”and“long”chains,with distinct attenuation factors(β_(short)≈1.0 vs.β_(long)≈0.74)and contact conductances(G_(c,short)≈200μS vs.G_(c,long)≈8μS).This dramatic impact of the dihedral angle exceeds the impact of the inter-ring twist angle in biphenyl-based junctions and rivals changes induced by switching from gold to platinum electrodes or from monothiol to dithiol anchors in oligoacene and oligophenylene junctions.X-ray photoelectron spectroscopy(XPS)confirmed this bifurcation,linking the“short”and“long”groups to planar and skewed conformers,with dihedrals remarkably agreeing with the gas-phase values.This work establishes conformational bifurcation as a promising route for designing programmable nanotransport properties through anchor-group control.展开更多
Glutathione transferases（GSTs） play an important role in the detoxification of xenobiotic/endobiotic toxic compounds. The α-, π-, and/l-classes of cytosolic GSTs have been studied extensively, while Gtt2 from Sacc...Glutathione transferases（GSTs） play an important role in the detoxification of xenobiotic/endobiotic toxic compounds. The α-, π-, and/l-classes of cytosolic GSTs have been studied extensively, while Gtt2 from Saccharo- myces cerevisiae, a novel atypical GST, is still poorly understood. In the present study, we investigated the gluta- thione（GSH） activation mechanism of Gtt2 using the density functional theory（DFT） with the hybrid functional B3LYP. The computational results show that a water molecule could assist a proton transfer between the GSH thiol and the N atom of His133. The energy barrier of proton transfer is 46.0 kJ/mol. The GSH activation mechanism and the characteristics of active site are different from those of classic cytosolic GSTs.展开更多
In this study, in order to explain the solvent and spin state effects on the molecular structure of catechol-Fe complex [Fe(cat)3]n﹣?where n = 2 and 3, Hartree Fock (HF)-Density Functional Theory (DFT) hybrid calcula...In this study, in order to explain the solvent and spin state effects on the molecular structure of catechol-Fe complex [Fe(cat)3]n﹣?where n = 2 and 3, Hartree Fock (HF)-Density Functional Theory (DFT) hybrid calculations are performed at the B3LYP/6-311g(d,p) level of theory. The binding energies of Fe2+ and Fe3+ in high-spin state are higher than intermediate and low-spin states which show that the complex formation in a high spin state is more favorable. The calculated binding energies at different solvents indicate that the binding energies in polar solvents are lower than non-polar solvents. Furthermore, spectroscopic studies including FTIR and Raman spectrum in various solvents reveal that the formation of intermolecular bonds between the oxygen atom of carbonyl group and the hydrogen atom of solvent causes a spectral red shift. The calculated FTIR and geometry parameters are in good agreement with previous experimental data. Donor-acceptor interaction energies are evaluated due to the importance of the charge transfer in the complex formation. It is observed that the free electrons of oxygen atom interact with the antibonding orbitals of the iron. Finally, some correlations between the quantum chemical reactivity indices of the complexes and solvent polarity are considered. The study indicates a linear correlation between chemical hardness and binding energies of [Fe(cat)3]3﹣?complex.展开更多
The Michael addition reactions of Z and E benzaldoximes with propene were investigated theoretically by DFT method at B3LYP/6-31G^＊ level. The calculation results show that both addition reactions are concerted proce...The Michael addition reactions of Z and E benzaldoximes with propene were investigated theoretically by DFT method at B3LYP/6-31G^＊ level. The calculation results show that both addition reactions are concerted processes accompanied by the migration of hydrogen from the atom oxygen to carbon. Both products Z and E nitrones have dipolar charge distributions and activities. Z isomer is more favorable in the reaction due to the barrier is lower.展开更多
The density functional theory was employed to study the structures, ionization potentials（IPs）, electron affinities（EAs）, and HOMO-LUMO gaps（ΔH-L） of the oligomers. The time-dependent density functional theory...The density functional theory was employed to study the structures, ionization potentials（IPs）, electron affinities（EAs）, and HOMO-LUMO gaps（ΔH-L） of the oligomers. The time-dependent density functional theory（TD-DFT） and ZINDO were employed to study the lowest excitation energies（Egs） and the absorption and emission spectra of the oligomers of polyfluorene（PF） and poly（fluorene-co-thiophene）（PFT）. By extrapolating ΔH-L and Egs to those of infinite chain length, band gaps and effective conjugation lengths of the corresponding polymers were obtained. The IPs, EAs and 2abs of the polymers were obtained by extrapolating those of the oligomers to the inverse chain length equal to zero（I/n=0）. The outcome shows the decreased dihedral angle between fluorene and thiophene units in the PFT compared to that between fluorene units in the PF results in the increased efficient conjugation of PFT. These cause both the maximal absorption and emission wavelengths of PFT red-shifted compared with those of PF.展开更多
By using the iterative method in functional theory, an analytic expression of the Poisson-Boltzmann equation (PB eq.), which describes the distribution of the potential of electrical double layer of a spherical micell...By using the iterative method in functional theory, an analytic expression of the Poisson-Boltzmann equation (PB eq.), which describes the distribution of the potential of electrical double layer of a spherical micelle, has been carried out under the general potential condition for the first time. The method also can give the radius, the surface potential, and the thickness of the layer.展开更多
The molecular structures and electron affinities of 5- and 6-halouracils（XU, X=F, Cl, Br） were determined by means of five different density functional methods. The basis set used in this work is of double-（plus po...The molecular structures and electron affinities of 5- and 6-halouracils（XU, X=F, Cl, Br） were determined by means of five different density functional methods. The basis set used in this work is of double-（plus polariza- tion（DZP） quality with additional diffuse s- and p-type functions, denoted DZP＋＋. The geometries were fully optimized with each density functional theory（DFT） method, and discussed. Three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity（AEA）, the vertical electron affinity（VEA）, and the vertical detachment energy（VDE）. An excellent agreement between our B3LYP results and those obtained by other calculations regarding the structural modifications and electron affinities of neutral and anion 5XU was found. The differences in charge distribution between uracil and halogenated uracils were indicated, thus the ability to form the hydrogen bonds of halogenated uracils was discussed. It shows the applicability of the DFT/DZP＋＋ method to predict the similar molecular models at a highly economical computational cost.展开更多
Based on the vibrational potential curves coupled with the minimum energy reaction path, the partial potential energy surface of the reaction I＋HI→IH＋I was constructed at the QCISD（T）//MP4SDQ level with pseudo po...Based on the vibrational potential curves coupled with the minimum energy reaction path, the partial potential energy surface of the reaction I＋HI→IH＋I was constructed at the QCISD（T）//MP4SDQ level with pseudo potential method. And the formation mechanism of the scattering resonance states of this reaction was well interpreted with the partial potential energy surface. The scattering resonance states of this reaction should belong to Feshbach resonance because of the coupling of the vibrational mode and the translational mode. With the one-dimensional square potential well model, the resonance width and lifetime of the I＋HI（v=0）→IH（v＇=0）＋I state-to-state reaction were calculated, which preferably explained the high-resolved threshold photodetachment spectroscopy of the IHI- anion performed by Neumark et al..展开更多
The partial potential energy surface was constructed by ab initio method [QCISD（T）/6- 311＋＋G（2df,2pd）]for F＋CH4→HF＋CH3 reaction system. It not only explained the reaction mechanism brought forward by Diego Tr...The partial potential energy surface was constructed by ab initio method [QCISD（T）/6- 311＋＋G（2df,2pd）]for F＋CH4→HF＋CH3 reaction system. It not only explained the reaction mechanism brought forward by Diego Troya by means of quasiclassical trajectory （QCT） but also successfully validated Kopin Liu＇s experimental phenomena about the existence of the reactive resonance. The lifetime of the scattering resonance state was about 0.07 ps. All these were in agreement with the experiments.展开更多
The ONIOM quantum mechanics method is used to study the reaction of one-carbon unit transfer from an imidazolidine to 6- aminouracil model with the participation of water molecules.The computation results show that in...The ONIOM quantum mechanics method is used to study the reaction of one-carbon unit transfer from an imidazolidine to 6- aminouracil model with the participation of water molecules.The computation results show that in this reaction the participation of H_2O molecule makes the energy barrier lower because of the H-bond interaction.展开更多
A series of dye molecules was designed theoretically.Particularly,azoles and their derivatives were chosen as the modifying groups linking to ancillary ligands of [Ru（dcbpyH2）2（NCS）2]（N3,dcbpy=4,4＇-dicarboxy2,2...A series of dye molecules was designed theoretically.Particularly,azoles and their derivatives were chosen as the modifying groups linking to ancillary ligands of [Ru（dcbpyH2）2（NCS）2]（N3,dcbpy=4,4＇-dicarboxy2,2＇-bipyridine;NCS=thiocyanato）.Density functional theory（DFT） based approaches were applied to exploring the electronic structures and properties of all these systems.The dye molecule with 1,2,4-triazole groups which exhibits a very high intensity of absorption in visible region,was obtained.Time-dependent DFT（TD-DFT） results indicate that the ancillary ligand dominates the molecular orbital（MO） energy levels and masters the absorption transition nature to a certain extent.The deprotonation of anchoring ligand not only affects the frontier MO energy levels but also controls the energy gaps of the highest occupied MO（HOMO） to the lowest unoccupied MO（LUMO） and LUMO to LUMO＋1 orbital.If the gap between LUMO-LUMO＋1 is small enough,the higher efficiency of dye-sensitized solar cell（DSSC） should be expected.展开更多
The density functional theory at the B3LYP/6-311G（d, p） level was applied to exploring the inhibition mechanism of cholinesterases by carbamate. The results indicate that the inhibition reactions with or without the...The density functional theory at the B3LYP/6-311G（d, p） level was applied to exploring the inhibition mechanism of cholinesterases by carbamate. The results indicate that the inhibition reactions with or without the catalytic effect of the catalytic triad in eholinesterases underwent a two-step addition-elimination mechanism, which is in good agreement with the proposed mechanism. The solvent has a strong effect on the inhibition reactions and the reaction with the catalytic triad in the solvent phase is close to the real reaction under biological condition.展开更多
The single chain antibody scFv2F3 can be converted into selenium-containing Se-scFv2F3 by chemical mutation of the Ser residues. With antibody fragment 1NQB as a template, the catalytic domain of scFv2F3 was built by ...The single chain antibody scFv2F3 can be converted into selenium-containing Se-scFv2F3 by chemical mutation of the Ser residues. With antibody fragment 1NQB as a template, the catalytic domain of scFv2F3 was built by using homology modeling and molecular dynamics（MD） simulations. On the basis of the 3D model, we discussed the importance of Ser52 as the chemical modification site and redesigned the protein groups nearby Ser52 via intro- ducing a catalytic triad. The following 10 ns MD results show that the designed Ser52-Trp29-Gln72 catalytic triad is stable enough and high close to the local structural features of native glutathione peroxidases（GPX）. Our results may be useful for creating a new abzyme with higher catalytic efficiency and stability.展开更多
The mechanism and kinetics for the reaction of propene(CH_(3)CH=CH_(2))molecule with O(1D)atom were investigated theoretically.The electronic structure information of the potential energy surface(PES)was obtained at t...The mechanism and kinetics for the reaction of propene(CH_(3)CH=CH_(2))molecule with O(1D)atom were investigated theoretically.The electronic structure information of the potential energy surface(PES)was obtained at the B3LYP/6-311+G(d,p)level,and the single-point energies were refined by the multi-level MCG3-MPWB method.The calculated results show that O(1D)atom can attack CH_(3)CH=CH_(2)via the barrierless insertion mechanism to form four energy-riched intermediates CH_(3)C(OH)CH_(2)(IM1),CH_(3)CHCHOH(IM2),CH_(2)OHCHCH_(2)(IM3)and cyclo CH_(2)OCHCH_(3)(IM4),respectively,on the singlet PES.The branching ratios as well as the pressure and temperature dependence of various product channels for this multi-well reaction were predicted by variational transition-state and Rice-Ramsperger-Kassel-Marcus(RRKM)theories.The present results will be useful to gain a deep insight into the reaction mechanism and kinetics of CH_(3)CH=CH_(2)+O(1D)reaction.展开更多
The mechanisms about the water’s and methanol’s effects on the alcoholysis of N-benzyl-3-oxo-β-sultam together with their differences have been studied by using density func- tional theory at the B3LYP/6-31G＊ leve...The mechanisms about the water’s and methanol’s effects on the alcoholysis of N-benzyl-3-oxo-β-sultam together with their differences have been studied by using density func- tional theory at the B3LYP/6-31G＊ level. The results, in comparison with a previous study on the relative reaction without the assistance of water and methanol, show that the added water or methanol can remarkably reduce the energy barrier of alcoholysis reaction of N-benzyl-3-oxo- β-sultam and the most favorite pathway is the breaking of C–N bond instead of S–N. It is also found that the reaction energy barrier of methanol-assisted alcoholysis is a little higher than that of the water-assisted one.展开更多
2,4-diphenylpentane- and 2,4-di-p-tolylpentane-2,4-diols were investigated employing experimental and density functional theory （DFT） method at B3LYP/6-31G （d） level. The structure of syn-2,4-di-p-tolylpentane-2,4...2,4-diphenylpentane- and 2,4-di-p-tolylpentane-2,4-diols were investigated employing experimental and density functional theory （DFT） method at B3LYP/6-31G （d） level. The structure of syn-2,4-di-p-tolylpentane-2,4-diol （2b） was characterized by X-ray diffraction and compared with the crystal structures of anti- and syn-2,4-diphenylpentane-2,4-diols （la and lb）. X-ray diffraction indicates that inter and intra-molecular hydrogen bonds are formed in the crystal structures. There is n-n staking interaction in lb and 2b. Good linear correlations and similar results are found between the experimental 1H and 13C NMR chemical shifts （6~exp） and GIAO （Gauge Independent Atomic Orbital） method calculated magnetic isotropic shielding tensors （acalc）. HOMO and LUMO molecular orbitals were calculated at the same levels with the different results. UV-vis absorption spectra of the compounds were recorded in EtOH, MeCN, n-BuOH and cyclohexane with different dielectric constants. It is found that the solvent effect is obvious when e is 24.85（EtOH）, 35.69（MeCN） and it is weak when e is decreased to 17.33（n-BuOH）, 1.18 （cyclohexane）.展开更多
With the aid of high-level B3LYP and MP2 calculations, three new neutral structures of glycine （iin, ivn and vn, see Fig. 2） were obtained and validated by frequency calculations. The structural and energetic analys...With the aid of high-level B3LYP and MP2 calculations, three new neutral structures of glycine （iin, ivn and vn, see Fig. 2） were obtained and validated by frequency calculations. The structural and energetic analyses showed that iin, ivn and vn are enantiomers to the previous IIn, IVn and Vn （J. Am. Chem. Soc. 1992, 114, 9568.）, respectively. Owing to the presence of these novel conformers, a redistribution of the populations of glycine conformers is resulted in and causes the remarkable decrease of the most stabilized Ip （from 48% to 38%）. It indicated that the simple glycine molecule can show chirality under certain conditions. The interacting modes of glycine enantiomeric pairs （e.g., ivn and IVn） with PG showed large differences （Fig. 4）; in addition, their interaction energies corrected with basis set superposition errors （BSSE） were calculated to be --66.81 and -46.99 kJ tool^-1, respectively. Accordingly, the glycine enantiomers can be potentially applied to the chiral recognition in biological and pharmaceutical areas.展开更多
With the help of the method of separation of variables and the Debye-Hüchel approximation, the Poisson-Boltzmann equation that describes the distribution of the potential in the electrical double layer of a cylin...With the help of the method of separation of variables and the Debye-Hüchel approximation, the Poisson-Boltzmann equation that describes the distribution of the potential in the electrical double layer of a cylindrical particle with a limited length has been firstly solved under a very low potential condition. Then with the help of the functional analysis theory this equation has been further analytically solved under general potential conditions and consequently, the corresponding surface charge densities have been obtained. Both the potential and the surface charge densities cointide with those results obtained from the Debye-Hüchel approximation when the very low potential of zeψ〈〈kT is introduced.展开更多
基金funded by the National Natural Science Foundation of China(Nos.22073069,21773082)Science Research Project of Hebei Education Department(No.QN2024255)。
文摘In chemical science,the vertical ionization potential(VIP)is a crucial metric for understanding the electronegativity,hardness and softness of chemical material systems as well as the electronic structure and stability of molecules.Ever since the last century,the model chemistry composite methods have witnessed tremendous developments in computing the thermodynamic properties as well as the barrier heights.However,their performance in realm of the vertical electron processes of molecular systems has been rarely explored.In this study,we for the first time benchmarked the model chemistry composite methods(e.g.,CBS-QB3,G4 and W1BD)in comparison with the commonly used Koopmans's theorem(KT),electron propagator theory(e.g.,OVGF,D2,P3 and P3+)and CCSD(T)methods in calculating the VIP for up to 613 molecular systems with available experimental measurements.The large-scale test calculations strongly showed that the CBS-QB3 model chemistry composite technique can be well recommended to calculate VIP from the perspectives of accuracy,economy and applicability.Notably,the VIP values of up to 7 molecules were identified to have the absolute errors of larger than 0.3 e V at all calculation levels,which have strong hints that their VIP experimental values should be re-investigated.
基金supported by Guangdong Basic and Applied Basic Research Foundation(Nos.2021B1515120055 and 2022A1515010499).
文摘Urban rainwater runoff is an important source of nonpoint source pollution due to its transport of diverse contaminants,including polycyclic aromatic hydrocarbons(PAHs)and chlorinated derivatives.Importantly,these chlorinated polycyclic aromatic hydrocarbons(Cl-PAHs)exhibit elevated toxicological potential compared to their non-halogenated parent compounds.In this study,we proposed an approach that combined multivariate receptor model with integration of SHapley Additive exPlanations and Random Forest model.This method identifies the possible sources and reveals the impact of source apportionment results and environmental driving factors(such as geographical and meteorological data)on pollutant concentrations.Sixteen PAHs and nine ClPAHs were detected in 79 runoff samples from all three sites.TheΣ_(16)PAHs average concentration(2923.93 to 6071.83 ng/L)was significantly higher than theΣ_(9)Cl-PAHs(384.34 to 1314.73 ng/L).The source apportionment was conducted by positive matrix factorization(PMF),and six potential pollution sources for PAHs and three for Cl-PAHs were quantified.PAHs primarily originate from the combustion of fossil fuels such as traffic,industrial emissions and coal tar,while Cl-PAHs are mainly derived from atmospheric deposition and industrial emissions.Meanwhile,the self‑organizing map classified PAHs and Cl-PAHs into 2 and 3 groups,respectively.The k-means algorithm yielded 4 clusters for runoff samples.Among machine learning models,Random Forest(RF)demonstrated optimal predictive performance and integrated with SHapley Additive exPlanations(RF-SHAP)revealed the effects of driving factors on the predicted concentration of PAHs and Cl-PAHs in urban runoff samples.
基金financial support from the National Key R&D Program of China(2023YFA1407100)the National Natural Science Foundation of China(22373026)+1 种基金Guangdong Science and Technology Department(2021B0301030005,STKJ2023072,GDZX2304005,GDZX2504001,and 2021QN02X538)Ioan Bâldea gratefully acknowledges computational support by the state of Baden-Württemberg through bwHPC and the German Research Foundation through Grant Nos.INST 40/575-1,35/1597-1,and 35/1134-1(JUSTUS 2,bwUniCluster 2/3,and bwForCluster/MLS&WISO/HELIX 2).
文摘Control over charge transport in molecular–scale devices requires a deep understanding of how minute structural changes influence electronic properties.Here,we demonstrate dual transport regimes in tunnel junctions of n-alk-1-yne(CnA)molecules with gold electrodes driven by conformational bifurcation—the emergence of two nearly isoenergetic(planar and skewed)molecular conformers(dihedral anglesα=180°andα≈65°at the alkyne terminus in the gas phase).Although the energy differences are small,these subtle conformational differences manifest as distinct transport behaviors,uncovered through unsupervised machine learning,which identified two junction groups:“short”and“long”chains,with distinct attenuation factors(β_(short)≈1.0 vs.β_(long)≈0.74)and contact conductances(G_(c,short)≈200μS vs.G_(c,long)≈8μS).This dramatic impact of the dihedral angle exceeds the impact of the inter-ring twist angle in biphenyl-based junctions and rivals changes induced by switching from gold to platinum electrodes or from monothiol to dithiol anchors in oligoacene and oligophenylene junctions.X-ray photoelectron spectroscopy(XPS)confirmed this bifurcation,linking the“short”and“long”groups to planar and skewed conformers,with dihedrals remarkably agreeing with the gas-phase values.This work establishes conformational bifurcation as a promising route for designing programmable nanotransport properties through anchor-group control.
基金Supported by the National Natural Science Foundation of China(No.20903045)the Specialized Research Fund for the Doctoral Program of Higher Education of China(No.20070183046)the Specialized Fund for the Basic Research of Jilin University,China(No.200810018)
文摘Glutathione transferases（GSTs） play an important role in the detoxification of xenobiotic/endobiotic toxic compounds. The α-, π-, and/l-classes of cytosolic GSTs have been studied extensively, while Gtt2 from Saccharo- myces cerevisiae, a novel atypical GST, is still poorly understood. In the present study, we investigated the gluta- thione（GSH） activation mechanism of Gtt2 using the density functional theory（DFT） with the hybrid functional B3LYP. The computational results show that a water molecule could assist a proton transfer between the GSH thiol and the N atom of His133. The energy barrier of proton transfer is 46.0 kJ/mol. The GSH activation mechanism and the characteristics of active site are different from those of classic cytosolic GSTs.
文摘In this study, in order to explain the solvent and spin state effects on the molecular structure of catechol-Fe complex [Fe(cat)3]n﹣?where n = 2 and 3, Hartree Fock (HF)-Density Functional Theory (DFT) hybrid calculations are performed at the B3LYP/6-311g(d,p) level of theory. The binding energies of Fe2+ and Fe3+ in high-spin state are higher than intermediate and low-spin states which show that the complex formation in a high spin state is more favorable. The calculated binding energies at different solvents indicate that the binding energies in polar solvents are lower than non-polar solvents. Furthermore, spectroscopic studies including FTIR and Raman spectrum in various solvents reveal that the formation of intermolecular bonds between the oxygen atom of carbonyl group and the hydrogen atom of solvent causes a spectral red shift. The calculated FTIR and geometry parameters are in good agreement with previous experimental data. Donor-acceptor interaction energies are evaluated due to the importance of the charge transfer in the complex formation. It is observed that the free electrons of oxygen atom interact with the antibonding orbitals of the iron. Finally, some correlations between the quantum chemical reactivity indices of the complexes and solvent polarity are considered. The study indicates a linear correlation between chemical hardness and binding energies of [Fe(cat)3]3﹣?complex.
基金supported by the National Natural Science Foundation of China(No.20373033).
文摘The Michael addition reactions of Z and E benzaldoximes with propene were investigated theoretically by DFT method at B3LYP/6-31G^＊ level. The calculation results show that both addition reactions are concerted processes accompanied by the migration of hydrogen from the atom oxygen to carbon. Both products Z and E nitrones have dipolar charge distributions and activities. Z isomer is more favorable in the reaction due to the barrier is lower.
基金Supported by the State Basic Research Development Program of China(No.2002CB613406)the National Natural Science Foundation of China(No.20673045)the Open Project of State Key Laboratory of Superamolecular Structure and Materials of Jilin University(No.SKLSSM200716)
文摘The density functional theory was employed to study the structures, ionization potentials（IPs）, electron affinities（EAs）, and HOMO-LUMO gaps（ΔH-L） of the oligomers. The time-dependent density functional theory（TD-DFT） and ZINDO were employed to study the lowest excitation energies（Egs） and the absorption and emission spectra of the oligomers of polyfluorene（PF） and poly（fluorene-co-thiophene）（PFT）. By extrapolating ΔH-L and Egs to those of infinite chain length, band gaps and effective conjugation lengths of the corresponding polymers were obtained. The IPs, EAs and 2abs of the polymers were obtained by extrapolating those of the oligomers to the inverse chain length equal to zero（I/n=0）. The outcome shows the decreased dihedral angle between fluorene and thiophene units in the PFT compared to that between fluorene units in the PF results in the increased efficient conjugation of PFT. These cause both the maximal absorption and emission wavelengths of PFT red-shifted compared with those of PF.
基金We wish to thank to the National Natural Science Foundation of China(to grant No,29903006 and 29973023)the Visiting Scholar Foundation of Key Laboratory in University of China for financial suppor.
文摘By using the iterative method in functional theory, an analytic expression of the Poisson-Boltzmann equation (PB eq.), which describes the distribution of the potential of electrical double layer of a spherical micelle, has been carried out under the general potential condition for the first time. The method also can give the radius, the surface potential, and the thickness of the layer.
基金Supported by the National Natural Science Foundation of China(No.20573042)
文摘The molecular structures and electron affinities of 5- and 6-halouracils（XU, X=F, Cl, Br） were determined by means of five different density functional methods. The basis set used in this work is of double-（plus polariza- tion（DZP） quality with additional diffuse s- and p-type functions, denoted DZP＋＋. The geometries were fully optimized with each density functional theory（DFT） method, and discussed. Three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity（AEA）, the vertical electron affinity（VEA）, and the vertical detachment energy（VDE）. An excellent agreement between our B3LYP results and those obtained by other calculations regarding the structural modifications and electron affinities of neutral and anion 5XU was found. The differences in charge distribution between uracil and halogenated uracils were indicated, thus the ability to form the hydrogen bonds of halogenated uracils was discussed. It shows the applicability of the DFT/DZP＋＋ method to predict the similar molecular models at a highly economical computational cost.
基金Ⅴ. ACKN0WLEDGMENTS This work was supported by the National Natural Science Foundation of China （No.20573064） and Ph.D. Special Research Foundation of Chinese Education Department.
文摘Based on the vibrational potential curves coupled with the minimum energy reaction path, the partial potential energy surface of the reaction I＋HI→IH＋I was constructed at the QCISD（T）//MP4SDQ level with pseudo potential method. And the formation mechanism of the scattering resonance states of this reaction was well interpreted with the partial potential energy surface. The scattering resonance states of this reaction should belong to Feshbach resonance because of the coupling of the vibrational mode and the translational mode. With the one-dimensional square potential well model, the resonance width and lifetime of the I＋HI（v=0）→IH（v＇=0）＋I state-to-state reaction were calculated, which preferably explained the high-resolved threshold photodetachment spectroscopy of the IHI- anion performed by Neumark et al..
基金the support of the Grant from the National Natural Science Foundation of China No.20573064 Ph.D.Special Research Foundation of Chinese Education Department.
文摘The partial potential energy surface was constructed by ab initio method [QCISD（T）/6- 311＋＋G（2df,2pd）]for F＋CH4→HF＋CH3 reaction system. It not only explained the reaction mechanism brought forward by Diego Troya by means of quasiclassical trajectory （QCT） but also successfully validated Kopin Liu＇s experimental phenomena about the existence of the reactive resonance. The lifetime of the scattering resonance state was about 0.07 ps. All these were in agreement with the experiments.
文摘The ONIOM quantum mechanics method is used to study the reaction of one-carbon unit transfer from an imidazolidine to 6- aminouracil model with the participation of water molecules.The computation results show that in this reaction the participation of H_2O molecule makes the energy barrier lower because of the H-bond interaction.
基金Supported by the National Natural Science Foundation of China(Nos.20973076,21003057)the Specialized Research Fund for the Doctoral Program of Higher Education,China(No.20110061110018)
文摘A series of dye molecules was designed theoretically.Particularly,azoles and their derivatives were chosen as the modifying groups linking to ancillary ligands of [Ru（dcbpyH2）2（NCS）2]（N3,dcbpy=4,4＇-dicarboxy2,2＇-bipyridine;NCS=thiocyanato）.Density functional theory（DFT） based approaches were applied to exploring the electronic structures and properties of all these systems.The dye molecule with 1,2,4-triazole groups which exhibits a very high intensity of absorption in visible region,was obtained.Time-dependent DFT（TD-DFT） results indicate that the ancillary ligand dominates the molecular orbital（MO） energy levels and masters the absorption transition nature to a certain extent.The deprotonation of anchoring ligand not only affects the frontier MO energy levels but also controls the energy gaps of the highest occupied MO（HOMO） to the lowest unoccupied MO（LUMO） and LUMO to LUMO＋1 orbital.If the gap between LUMO-LUMO＋1 is small enough,the higher efficiency of dye-sensitized solar cell（DSSC） should be expected.
基金Supported by the National Natural Science Foundation of China(Nos.20333050 and 20673044), PCSIRT(No.IRT0625) Key Subject of Science and Technology by Jilin Province, China
文摘The density functional theory at the B3LYP/6-311G（d, p） level was applied to exploring the inhibition mechanism of cholinesterases by carbamate. The results indicate that the inhibition reactions with or without the catalytic effect of the catalytic triad in eholinesterases underwent a two-step addition-elimination mechanism, which is in good agreement with the proposed mechanism. The solvent has a strong effect on the inhibition reactions and the reaction with the catalytic triad in the solvent phase is close to the real reaction under biological condition.
基金Supported by the National Natural Science Foundation of China(Nos.20333050,20673044)Program for Changjiang Scho-lars and Innovative Research Team in University of China(No.IRT0625) Key Subject of Science and Technology by Jilin Province,China
文摘The single chain antibody scFv2F3 can be converted into selenium-containing Se-scFv2F3 by chemical mutation of the Ser residues. With antibody fragment 1NQB as a template, the catalytic domain of scFv2F3 was built by using homology modeling and molecular dynamics（MD） simulations. On the basis of the 3D model, we discussed the importance of Ser52 as the chemical modification site and redesigned the protein groups nearby Ser52 via intro- ducing a catalytic triad. The following 10 ns MD results show that the designed Ser52-Trp29-Gln72 catalytic triad is stable enough and high close to the local structural features of native glutathione peroxidases（GPX）. Our results may be useful for creating a new abzyme with higher catalytic efficiency and stability.
基金Supported by the National Natural Science Foundation of China(Nos.20303007,20333050,20973077)the Program for New Century Excellent Talents(NCET)in Universities of China
文摘The mechanism and kinetics for the reaction of propene(CH_(3)CH=CH_(2))molecule with O(1D)atom were investigated theoretically.The electronic structure information of the potential energy surface(PES)was obtained at the B3LYP/6-311+G(d,p)level,and the single-point energies were refined by the multi-level MCG3-MPWB method.The calculated results show that O(1D)atom can attack CH_(3)CH=CH_(2)via the barrierless insertion mechanism to form four energy-riched intermediates CH_(3)C(OH)CH_(2)(IM1),CH_(3)CHCHOH(IM2),CH_(2)OHCHCH_(2)(IM3)and cyclo CH_(2)OCHCH_(3)(IM4),respectively,on the singlet PES.The branching ratios as well as the pressure and temperature dependence of various product channels for this multi-well reaction were predicted by variational transition-state and Rice-Ramsperger-Kassel-Marcus(RRKM)theories.The present results will be useful to gain a deep insight into the reaction mechanism and kinetics of CH_(3)CH=CH_(2)+O(1D)reaction.
基金This work was supported by the National Natural Science Foundation of China (No. 20373034 and 20603030)Post-doctor Research Foundation of Shandong Province (No. 200601007)
文摘The mechanisms about the water’s and methanol’s effects on the alcoholysis of N-benzyl-3-oxo-β-sultam together with their differences have been studied by using density func- tional theory at the B3LYP/6-31G＊ level. The results, in comparison with a previous study on the relative reaction without the assistance of water and methanol, show that the added water or methanol can remarkably reduce the energy barrier of alcoholysis reaction of N-benzyl-3-oxo- β-sultam and the most favorite pathway is the breaking of C–N bond instead of S–N. It is also found that the reaction energy barrier of methanol-assisted alcoholysis is a little higher than that of the water-assisted one.
基金Projects(21072053,20772028)supported by the National Natural Science Foundation of ChinaProjects(10K025,11C0527)supported by the Scientific Research Fund of Hunan Provincial Education Department,ChinaProject(LKF0901)supported by the Open Foundation of Key Laboratory of Theoretical Chemistry and Molecular Simulation of Ministry of Education,Hunan University of Science and Technology,China
文摘2,4-diphenylpentane- and 2,4-di-p-tolylpentane-2,4-diols were investigated employing experimental and density functional theory （DFT） method at B3LYP/6-31G （d） level. The structure of syn-2,4-di-p-tolylpentane-2,4-diol （2b） was characterized by X-ray diffraction and compared with the crystal structures of anti- and syn-2,4-diphenylpentane-2,4-diols （la and lb）. X-ray diffraction indicates that inter and intra-molecular hydrogen bonds are formed in the crystal structures. There is n-n staking interaction in lb and 2b. Good linear correlations and similar results are found between the experimental 1H and 13C NMR chemical shifts （6~exp） and GIAO （Gauge Independent Atomic Orbital） method calculated magnetic isotropic shielding tensors （acalc）. HOMO and LUMO molecular orbitals were calculated at the same levels with the different results. UV-vis absorption spectra of the compounds were recorded in EtOH, MeCN, n-BuOH and cyclohexane with different dielectric constants. It is found that the solvent effect is obvious when e is 24.85（EtOH）, 35.69（MeCN） and it is weak when e is decreased to 17.33（n-BuOH）, 1.18 （cyclohexane）.
基金supported by the Major State Basic Research Development Programs (No. 2004CB719902)the National Natural Science Foundation of China (No. 20633060)the Talented Funds of Northeast Forestry University (No. 220-602042)
文摘With the aid of high-level B3LYP and MP2 calculations, three new neutral structures of glycine （iin, ivn and vn, see Fig. 2） were obtained and validated by frequency calculations. The structural and energetic analyses showed that iin, ivn and vn are enantiomers to the previous IIn, IVn and Vn （J. Am. Chem. Soc. 1992, 114, 9568.）, respectively. Owing to the presence of these novel conformers, a redistribution of the populations of glycine conformers is resulted in and causes the remarkable decrease of the most stabilized Ip （from 48% to 38%）. It indicated that the simple glycine molecule can show chirality under certain conditions. The interacting modes of glycine enantiomeric pairs （e.g., ivn and IVn） with PG showed large differences （Fig. 4）; in addition, their interaction energies corrected with basis set superposition errors （BSSE） were calculated to be --66.81 and -46.99 kJ tool^-1, respectively. Accordingly, the glycine enantiomers can be potentially applied to the chiral recognition in biological and pharmaceutical areas.
基金Supported by the National Natural Science Foundation of China(No.20473034) the Taihu Scholar Foundation of SouthernYangtze University(2003).
文摘With the help of the method of separation of variables and the Debye-Hüchel approximation, the Poisson-Boltzmann equation that describes the distribution of the potential in the electrical double layer of a cylindrical particle with a limited length has been firstly solved under a very low potential condition. Then with the help of the functional analysis theory this equation has been further analytically solved under general potential conditions and consequently, the corresponding surface charge densities have been obtained. Both the potential and the surface charge densities cointide with those results obtained from the Debye-Hüchel approximation when the very low potential of zeψ〈〈kT is introduced.
