Co-reporter:Yanzhen Gan;Ling Yue;Xugeng Guo;Chaoyuan Zhu
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 19) pp:12094-12106
Publication Date(Web):2017/05/17
DOI:10.1039/C6CP08929A
An on-the-fly trajectory surface hopping dynamic simulation has been performed for revealing the multi-state nonadiabatic deactivation mechanism of coumarin. The mechanism involves three adiabatic excited states, S3(ππ*Lb), S2(nπ*, ππ*La) and S1(ππ*La, nπ*), and the ground state S0 at the four state-averaged complete active space self-consistent field, SA4-CASSCF(12,10)/6-31G* level of theory. Upon photoexcitation to the third excited state S3(ππ*Lb) in the Franck–Condon region, 80% sampling trajectories decay to the dark S2(nπ*) state within an average of 5 fs via the conical intersection S3(ππ*Lb)/S2(nπ*), while 20% decay to the S2(ππ*La) state within an average of 11 fs via the conical intersection S3(ππ*Lb)/S2(ππ*La). Then, sampling trajectories via S2(nπ*)/S1(ππ*La) continue with ultrafast decay processes to give a final distribution of quantum yields as follows: 42% stay on the dark S1(nπ*) state, 43.3% go back to the ground S0 state, 12% undergo a ring-opening reaction to the Z-form S0(Z) state, and 2.7% go to the E-form S0(E) state. The lifetimes of the excited states are estimated as follows: the S3 state is about 12 fs on average, the S2 state is about 80 fs, and the S1 state has a fast component of about 160 fs and a slow component of 15 ps. The simulated ultrafast radiationless deactivation pathways of photoexcited coumarin immediately interpret the experimentally observed weak fluorescence emission.
Co-reporter:Yuan Zhao, Nanhao Chen, Chaojie Wang, and Zexing Cao
ACS Catalysis 2016 Volume 6(Issue 4) pp:2145
Publication Date(Web):February 16, 2016
DOI:10.1021/acscatal.5b02855
The highly homologous hydroxynitrile lyases from Manihot esculent (MeHNL) and Hevea brasiliensis (HbHNL) both belong to the α/β-hydrolase superfamily, and they convert cyanohydrins into the corresponding ketone (aldehyde) and hydrocyanic acid, which is important for biosynthesis for carbon–carbon formation. On the basis of extensive MM and ab initio QM/MM MD simulations, one-dimensional and two-dimensional free energy profiles on the whole enzymatic catalysis by MeHNL have been explored, and the effects of key residues around the channel on the delivery of substrate and product have been discussed. The residue Trp128 plays an important gate-switching role to manipulate the substrate access to the active site and product release. In particular, the release of acetone and HCN has been first detected to follow a stepwise mechanism. The release of HCN is quite facile, while the escape of acetone experiences a barrier of ∼10 kcal/mol. The chemical reaction is an endergonic process with a free energy barrier of ∼17.1 kcal/mol, which dominates the entire enzymatic efficiency. Such energy costs can be compensated by the remarkable energy release during the initial substrate binding. Here the carbon–carbon cleavage is the rate-determining step, which differs from that of HbHNL. The protonation state of Lys237 plays an important role in carbon–carbon bond cleavage by restoring the Ser80Ala mutant system to the wild system, which explains the discrepancy between MeHNL and HbHNL at the molecular or atomic scale. The present results provide a basis for understanding the similarity and difference in the enzymatic catalysis by MeHNL and HbHNL.Keywords: biosynthesis; hydroxynitrile lyases; mechanism; product release; QM/MM MD; α/β-hydrolase superfamily
Co-reporter:Ming-Jun Sun, Xinrui Cao, and Zexing Cao
ACS Applied Materials & Interfaces 2016 Volume 8(Issue 26) pp:16551-16554
Publication Date(Web):June 23, 2016
DOI:10.1021/acsami.6b05502
A wide-bandgap SiC4 semiconductor with low density and high elasticity has been designed and characterized by ab initio molecular dynamics simulations and first-principles calculations. The through-space conjugation among the d orbitals of Si and the π* orbitals of ethynyl moieties can remarkably enhance the photoconductivity. This new-type superlight and superflexible semiconductor is predicted to have unique electronic, optical, and mechanical properties, and it is a quite promising material for the high-performance UV optoelectronic devices suitable for various practical demands in a complex environment.
Co-reporter:Xiangfei Zhang and Zexing Cao
Dalton Transactions 2016 vol. 45(Issue 25) pp:10355-10365
Publication Date(Web):17 May 2016
DOI:10.1039/C6DT01154C
The oxidation addition of a series of σ H–X bonds (X = H, B, C, Si, N, P, and O) to a single Al(I) supported by a (NacNac)− bidentate ligand ((NacNac)− = [ArNC(Me)CHC(Me)NAr]− and Ar = 2,6-iPr2C6H3) has been explored through extensive DFT calculations. The presented results show that activation and addition of these σ bonds follow various reaction mechanisms, in which hydride transfer, proton transfer, and Al–X bond coupling steps are involved. The predicted free energy barriers for these oxidative additions range from 8 to 32 kcal mol−1, and all the reactions are remarkably favorable thermodynamically. However, sterically hindered ligands, for most reactants, make the formation of the initial reactant complex difficult and may reduce the efficiency of the reaction. Calculations reveal a strong dependence of the reaction mechanism and low-energy channel on the bonding features of X–H and the local structural environments.
Co-reporter:Jingwei Zhou, Ruibo Wu, Binju Wang, Zexing Cao, Honggao Yan, and Yirong Mo
ACS Catalysis 2015 Volume 5(Issue 5) pp:2805
Publication Date(Web):March 19, 2015
DOI:10.1021/acscatal.5b00079
The conversion of 1-deoxy-D-xylulose 5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) catalyzed by DXP reductoisomerase (DXR) is the committing step in the biosynthesis of terpenoids. This MEP pathway is essential for most pathogenic bacteria but absent in human, and thus, it is an attractive target for the development of novel antibiotics. To this end, it is critical to elucidate the conversion mechanism and identify the transition state, as many drugs are transition-state analogues. Here we performed extensive combined quantum mechanical (density functional theory B3LYP/6-31G*) and molecular mechanical molecular dynamics simulations to elucidate the catalytic mechanism. Computations confirmed the transient existence of two metastable fragments of DXP by the heterolytic C3–C4 bond cleavage, namely, 1-propene-1,2-diol and glycoaldehyde phosphate, in accord with the most recent kinetic isotope effect (KIE) experiments. Significantly, the heterolytic C3–C4 bond cleavage and C2–C4 bond formation are accompanied by proton shuttles, which significantly lower their reaction barriers to only 8.2–6.0 kcal/mol, compared with the normal single carbon–carbon bond energy 83 kcal/mol. This mechanism thus opens a novel way for the design of catalysts in the cleavage or formation of aliphatic carbon–carbon bonds.Keywords: 1-deoxy-D-xylulose 5-phosphate; carbon−carbon bond cleavage; combined QM(DFT)/MM; proton shuttle; reductoisomerase
Co-reporter:Nanhao Chen, Yuan Zhao, Jianing Lu, Ruibo Wu, and Zexing Cao
Journal of Chemical Theory and Computation 2015 Volume 11(Issue 7) pp:3180-3188
Publication Date(Web):June 12, 2015
DOI:10.1021/acs.jctc.5b00045
A full enzymatic catalysis cycle in the inosine–adenosine–guanosine specific nucleoside hydrolase (IAG-NH) was assumed to be comprised of four steps: substrate binding, chemical reaction, base release, and ribose release. Nevertheless, the mechanistic details for the rate-limiting step of the entire enzymatic reaction are still unknown, even though the ribose release was likely to be the most difficult stage. Based on state-of-the-art quantum mechanics and molecular mechanics (QM/MM) molecular dynamics (MD) simulations, the ribose release process can be divided into two steps: “ribose dissociation” and “ribose release”. The “ribose dissociation” includes “cleavage” and “exchange” stages, in which a metastable 6-fold intermediate will recover to an 8-fold coordination shell of Ca2+ as observed in apo- IAG-NH. Extensive random acceleration molecular dynamics and MD simulations have been employed to verify plausible release channels, and the estimated barrier for the rate-determining step of the entire reaction is 13.0 kcal/mol, which is comparable to the experimental value of 16.7 kcal/mol. Moreover, the gating mechanism arising from loop1 and loop2, as well as key residues around the active pocket, has been found to play an important role in manipulating the ribose release.
Co-reporter:Mao-Long Chen, Yu-Hui Hou, Wen-Sheng Xia, Wei-Zheng Weng, Ze-Xing Cao, Zhao-Hui Zhou and Hui-Lin Wan
Dalton Transactions 2014 vol. 43(Issue 23) pp:8690-8697
Publication Date(Web):25 Feb 2014
DOI:10.1039/C4DT00104D
From neutral solutions, dimeric 1,3-propanediaminetetraacetato lanthanides (NH4)2[Ln2(1,3-pdta)2(H2O)4]·8H2O [Ln = La, 1; Ce, 2] and K2[Ln2(1,3-pdta)2(H2O)4]·11H2O [Ln = La, 3; Ce, 4] (1,3-H4pdta = 1,3-propanediaminetetraacetic acid, C11H18N2O8) were isolated in high yields. The reaction of excess strontium nitrate with 1 resulted in the formation of a two dimensional coordination polymer [La2(1,3-pdta)2(H2O)4]n·[Sr2(H2O)6]n·[La2(1,3-pdta)2(H2O)2]n·18nH2O (5) at 70 °C. Complexes 1–4 show a similar central molecular structure. The lanthanide ions are coordinated by two nitrogen atoms, four carboxy oxygen atoms from one 1,3-pdta ligand, two from the neighboring 1,3-pdta ligand forming a four-membered ring and two water molecules. Complex 5 has two kinds of dimeric lanthanum unit and extends into a 2D coordination polymer through strontium ions and bridged oxygen atoms, and forms a fourteen membered ring linked by oxygen atoms from carboxy groups of pdta. Complexes 1–4 are soluble in water. The 13C{1H} NMR experiments for complex 1 were tested in solution. Thermal products from 1 and 5 show good catalytic activities towards the oxidative coupling reaction of methane (OCM). The conversion of methane and selectivity to C2 reached 29.7% and 51.7% at 750 °C for the product of 5. From TGA, XRD and SEM analyses, the thermal products from 1 and 5 are rod- and poly-shaped, which are assigned as lanthanum oxocarbonate and a mixture of La2O3, SrCO3 and La2O2CO3 for 1 and 5, respectively. The precursor method is favorable for the formation of regular shaped mixed oxides.
Co-reporter:Xugeng Guo, Yuan Zhao and Zexing Cao
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 29) pp:15381-15388
Publication Date(Web):02 Jun 2014
DOI:10.1039/C4CP01928H
Extensive ab initio surface-hopping dynamics simulations have been used to explore the excited-state nonadiabatic decay of two biologically relevant hypoxanthine keto-N7H and keto-N9H tautomers in aqueous solution. QM/MM calculations and QM/MM-based MD simulations predict different hydrogen bonding networks around these nucleobase analogues, which influence their photodynamical properties remarkably. Furthermore, different solvent effects on the conical intersection formation of keto-N7H and keto-N9H were found in excited-state MD simulations, which also change the lifetimes of the excited states. In comparison with the gas-phase situation, the S1 → S0 nonradiative decay of keto-N7H is slightly faster, while this decay process of keto-N9H becomes much slower in water. The presence of π-electron hydrogen bonds in the solvated keto-N7H is considered to facilitate the S1 → S0 nonradiative decay process.
Co-reporter:Yuan Zhao, Nanhao Chen, Yirong Mo and Zexing Cao
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 48) pp:26864-26875
Publication Date(Web):24 Oct 2014
DOI:10.1039/C4CP04032E
Hydroxynitrile lyases (HNLs) defend plants from herbivores and microbial attack by releasing cyanide from hydroxynitriles. The reverse process has been productively applied to bioorganic syntheses of pharmaceuticals and agrochemicals. To improve our understanding of the catalytic mechanism of HNLs, extensive ab initio QM/MM and classical MM molecular dynamics simulations have been performed to explore the catalytic conversion of cyanohydrins into aldehyde (or ketone) and HCN by hydroxynitrile lyases from Hevea brasiliensis (HbHNLs). It was found that the catalytic reaction approximately follows a two-stage mechanism. The first stage involves two fast processes including the proton abstraction of the substrate through a double-proton transfer and the C–CN bond cleavage, while the second stage concerns HCN formation and is rate-determining. The complete free energy profile exhibits a peak of ∼18 kcal mol−1. Interestingly, the protonation state of Lys236 influences the efficiency of the enzyme only to some extent, but it changes the entire catalytic mechanism. The dynamical behaviors of substrate delivery and HCN release are basically modulated by the gate movement of Trp128. The remarkable exothermicity of substrate binding and the facile release of HCN may drive the enzyme-catalyzed reaction to proceed along the substrate decomposition efficiently. Computational mutagenesis reveals the key residues which play an important role in the catalytic process.
Co-reporter:Yuan Zhao, Nanhao Chen, Ruibo Wu and Zexing Cao
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 34) pp:18406-18417
Publication Date(Web):15 Jul 2014
DOI:10.1039/C4CP01609B
The glucosamine 6-phosphate deaminase (NagB), which catalyzes the conversion of D-glucosamine 6-phosphate (GlcN6P) into D-fructose 6-phosphate (F6P) and ammonia, determines the final metabolic fate of N-acetylglucosamine (GlcNAc). Here using state-of-the-art ab initio QM/MM MD simulations, we have explored the plausible mechanisms for the enzymatic ring-opening of GlcN6P in the basic environment. Two different proton-shuttle mechanisms have been proposed. Calculations show that the protonated state of the amino group in the substrate dominates the concerted and stepwise catalytic pathways and a catalytic triad plays an important role in mediating the proton transfer and the resulting ring-opening process. The free energy barrier for the rate-determining step in the low-energy stepwise reaction is 17.9 kcal mol−1. In acidic solution, the lid motif prefers a closed state while it always stays in the open state in basic solution upon substrate binding, which is basically dominated by the protonated state of the residue His145.
Co-reporter:Hujun Xie, Qiang Sun, Gerui Ren, and Zexing Cao
The Journal of Organic Chemistry 2014 Volume 79(Issue 24) pp:11911-11921
Publication Date(Web):August 18, 2014
DOI:10.1021/jo501618k
Mechanisms and reactivity differences for the cycloaddition of anhydride to alkyne catalyzed by the palladium and nickel catalysts have been investigated by extensive density functional theory (DFT) calculations. The predicted free energy profiles for the Pd- and Ni-catalyzed reactions have been used to evaluate possible mechanisms for the formation of different products. Calculations show that the formation of isocoumarin via the decarbonylative addition of anhydride to alkyne is kinetically more favorable than the channel to indenone in the Ni-catalyzed reaction. On the contrary, the preparation of naphthalene through sequential liberation of CO2 and CO is kinetically more favorable than that the formation of indenone in the Pd-catalyzed process. The bonding differences between Pd–C and Ni–C bonds, arising from the relativistic effect of late transition metals, play an important role in regulating their catalytic activity. The calculation results show good agreement with the experiments.
Co-reporter:Xugeng Guo, Yuan Zhao, and Zexing Cao
The Journal of Physical Chemistry A 2014 Volume 118(Issue 39) pp:9013-9020
Publication Date(Web):March 20, 2014
DOI:10.1021/jp5020115
The excited-state decay of the biologically relevant allopurinol keto-N9H tautomer populated at the optically bright S1(1ππ*) state in the gas phase and in aqueous solution has been explored theoretically. In solution, the hybrid quantum-mechanical/molecular-mechanical simulations were performed, where the QM region (keto-N9H) was treated at the ab initio SA-CASSCF level, while the MM region (water) was described by the TIP3P model. Here we find that there exist four parallel relaxation pathways in the gas phase, but only two of them occur in aqueous solution. In addition, an ultrafast S1 → S0 internal conversion is found in vacuum, with an estimated excited-state lifetime of 104.7 fs, much faster than that in water (242.8 fs), showing reasonable agreement with the available experimental finding in aqueous solution (τ < 200 fs). Calculations indicate that the presence of water solvent plays an important role in the excited-state dynamics of DNA base, showing the pronounced environmental effects on its decay pathways and excited-state lifetimes.
Co-reporter:Jinxia Liang, Chun Zhu and Zexing Cao
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 33) pp:13844-13851
Publication Date(Web):02 May 2013
DOI:10.1039/C3CP51019K
Plausible mechanisms of the ultrafast electron injection and the significant dependence of the power conversion efficiency on the anchor group for the triphenylamine-based dye-sensitized TiO2 solar cells have been explored by the density functional calculations. Calculations show that the ultrafast charge recombination on the surface trap state of the dye-sensitized TiO2 system can be ascribed to the lack of electron density on the carboxyl group of the A3 dye with the rhodanine group anchor. Predicted electronic and optical properties of the A1-3-adsorbed TiO2 system reveal that the direct electron injection arises from the electronic excitation from HOMO-1 of the dye to the conduction band bottom of TiO2. On the basis of the calculations, the electron density distributions of related frontier orbitals and energy bands of dyes and their adsorbed systems have been discussed, which play an important role in electron injection and charge recombination.
Co-reporter:Xugeng Guo, Zhenggang Lan and Zexing Cao
Physical Chemistry Chemical Physics 2013 vol. 15(Issue 26) pp:10777-10782
Publication Date(Web):23 Apr 2013
DOI:10.1039/C3CP44718A
Nonadiabatic dynamics simulations at the SA-CASSCF level were performed for the two most stable keto-N7H and keto-N9H tautomers of hypoxanthine in order to obtain deep insight into the lifetime of the optically bright S1(1ππ*) excited state and the relevant decay mechanisms. Supporting calculations on the ground-state (S0) equilibrium structures and minima on the crossing seams of both tautomers were carried out at the MR-CIS and CASSCF levels. These studies indicate that there are four slightly different kinds of conical intersections in each tautomer, exhibiting a chiral character, each of which dominates a barrierless reaction pathway. Moreover, both tautomers reveal the ultrafast S1 → S0 decay, in which the S1 state of keto-N9H in the gas phase has a lifetime of 85.5 fs, whereas that of keto-N7H has a longer lifetime of 137.7 fs. An excellent agreement is found between the present results and the experimental value of 130 ± 20 fs in aqueous solution (Chen and Kohler, Phys. Chem. Chem. Phys., 2012, 14, 10677–10689).
Co-reporter:Binju Wang and Zexing Cao
RSC Advances 2013 vol. 3(Issue 33) pp:14007-14015
Publication Date(Web):20 May 2013
DOI:10.1039/C3RA41464G
The detailed catalytic mechanisms of N-heterocyclic carbenes (NHCs) in the formylation of N–H bonds using carbon dioxide and silane were investigated using density functional theory (DFT) calculations. Among all the examined reaction pathways, we found that the most favorable pathway involves collaboration between the covalent bonding activation and general base catalysis. The overall reaction can be divided into four stages, including silane activation through a covalent bonding mechanism, CO2 insertion into the Si–H bond of silane to yield a key intermediate formoxysilane (FOS), the NHC-catalyzed coupling of amine and FOS through a general base mechanism, and C–O bond breaking through general base catalysis to obtain the final amide product. The carbamic acid anion (Me2NCOO−) is an inevitable intermediate from the side reactions, and its formation is almost barrier free. NHC can act as a base to abstract a proton from the nucleophiles (such as amines or alcohol), and facilitate C–N bond or C–O bond formation or cleavage, and such a general base mechanism is remarkably favorable over the covalent binding mechanism for C–N bond (or C–O) bond formation (or cleavage). The calculated thermodynamic properties are in good agreement with the available experimental findings.
Co-reporter:Chun Zhu, Jinxia Liang, and Zexing Cao
The Journal of Physical Chemistry C 2013 Volume 117(Issue 26) pp:13388-13395
Publication Date(Web):June 11, 2013
DOI:10.1021/jp403793f
A new type of metal dicorrole dyes has been designed, and their optical and electronic properties have been characterized by density functional calculations. These novel dicorrole-based sensitizers have a strong light-harvesting ability and an excellent charge separation in the excited states. Their optical and electronic properties can be well-modulated by incorporating the bridge-conjugated group. Introduction of the electron-withdrawing substituent to the meso position of corrole ring regulates the energy levels of key molecular orbitals in the metal–dicorrole dyes to facilitate the regeneration of the oxidized dyes. Calculations show that the metal–dicorrole sensitizers are quite promising for fabrication of the high-performance dye-sensitized solar cells. On the basis of the first-principles calculations, plausible mechanisms for direct and indirect electron injections from the adsorbed dye to TiO2 have been discussed.
Co-reporter:Nanhao Chen, Hu Ge, Jun Xu, Zexing Cao, Ruibo Wu
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2013 Volume 1834(Issue 6) pp:1117-1124
Publication Date(Web):June 2013
DOI:10.1016/j.bbapap.2013.02.005
Although various Trypanosoma vivax purine-specific inosine–adenosine–guanosine nucleoside hydrolase (IAG-NH) crystal structures have been determined and the chemical reaction mechanism of substrate hydrolysis has been studied recently, the mechanistic details for the release of base and ribose are still unclear. Herein molecular dynamics (MD) simulations combined with umbrella sampling technique were utilized to explore the regulation mechanisms of key residues and loops 1 and 2 for the base release. Our results have indicated that the base release process is not the rate-limiting step in the entire hydrolysis process, and the very low barrier of ~ 5.6 kcal/mol can be washed out easily by the notable exothermicity from the substrate hydrolysis step. Moreover, the MD simulations have revealed that Glu82/Trp83 in loop 1 and His247/Arg252 in loop 2 are important to modulate the base release. The partial helix-to-coil change of loop 2 along with the base release process has been observed, showing good agreement with the IAG-NH crystal structures. The local binding site around the ribose after the base release is also discussed.Highlights► The inner-work mechanism of base release in IAG-nucleoside hydrolase was illuminated by MD simulations. ► The key residues promoting the base release have been characterized. ► The helix-to-coil change of loop 2 was revealed and it was in agreement with the XRD's structures. ► Our simulations confirmed the key switches to control the loop's open/closed state and found His247 is a novel controller.
Co-reporter:Shaobin Tang and Zexing Cao
Physical Chemistry Chemical Physics 2012 vol. 14(Issue 48) pp:16558-16565
Publication Date(Web):19 Jun 2012
DOI:10.1039/C2CP41343D
Graphene oxides (GOs) may offer extraordinary potential in the design of novel catalytic systems due to the presence of various oxygen functional groups and their unique electronic and structural properties. Using first-principles calculations, we explore the plausible mechanisms for the oxidative dehydrogenation (ODH) of propane to propene by GOs and the diffusion of the surface oxygen-containing groups under an external electric field. The present results show that GOs with modified oxygen-containing groups may afford high catalytic activity for the ODH of propane to propene. The presence of hydroxyl groups around the active sites provided by epoxides can remarkably enhance the C–H bond activation of propane and the activity enhancement exhibits strong site dependence. The sites of oxygen functional groups on the GO surface can be easily tuned by the diffusion of these groups under an external electric field, which increases the reactivity of GOs towards ODH of propane. The chemically modified GOs are thus quite promising in the design of metal-free catalysis.
Co-reporter:Chun Zhu, Jinxia Liang, Binju Wang, Jun Zhu and Zexing Cao
Physical Chemistry Chemical Physics 2012 vol. 14(Issue 37) pp:12800-12806
Publication Date(Web):18 Jul 2012
DOI:10.1039/C2CP41647F
The electronic and structural features of (oxo)manganese(V) corroles and their catalyzed oxygen atom transfers to thioanisole in different spin states have been investigated by the B3LYP functional calculations. Calculations show that these corrole-based oxidants and their complexes with thioanisole generally have the singlet ground state, and their triplet forms are also accessible in consideration of the spin–orbit coupling interaction. Due to strong d–π conjugation interactions between Mn and the corrole ring arising from the π electron donation of the corrole moiety, the five-coordinated Mn approximately has the stable 18-electron configuration. The predicted free energy barriers for the singlet oxygen atom transfer reactions are generally larger than 22 kcal mol−1, while the spin flip in reaction may remarkably increase the reactivity. In particular, the bromination on β-pyrrole carbon atoms of the meso-substituted (oxo)manganese(V) corrole strikingly enhances the spin–orbit coupling interaction and results in the dramatic increase of reactivity. The multiple spin changes are predicted to be involved in the low-energy reaction pathway. The present results show good agreement with the experimental observation and provide a detailed picture for the oxygen atom transfer reaction induced by the (oxo)manganese(V) corroles.
Co-reporter:Xing Chen, Guangjun Tian, Zilvinas Rinkevicius, Olav Vahtras, Zexing Cao, Hans Ågren, Yi Luo
Chemical Physics 2012 Volume 405() pp:40-45
Publication Date(Web):11 September 2012
DOI:10.1016/j.chemphys.2012.06.004
Abstract
The vibronically resolved spectra of an intermediate and a product involved in the photoreaction of α-santonin have been explored by the density functional theory and the post-SCF methodologies, and a detailed comparison of theory with experiment was conducted to obtain reliable assignments to the observed spectra. The predicted emission energies of photosantonic acid and a topochemical product are found to match with the experimental values reasonably. The further calculations manifest that the absorption spectrum of photosantonic acid exhibits vibrationally resolved features, while the absorption band of topochemical product without vibrational resolution is opposite to the experimental observation. These new computational findings lead to a revised assignment to the observed bands and provide a basis for experimentalists to draw a convinced reaction mechanism for the α-santonin photorearrangement.
Co-reporter:Shaobin Tang and Zexing Cao
The Journal of Physical Chemistry C 2012 Volume 116(Issue 15) pp:8778-8791
Publication Date(Web):March 27, 2012
DOI:10.1021/jp212218w
The interactions of ammonia with graphene oxides (GO) were studied by density functional theory calculations. Our results indicate that the adsorption of NH3 on GO is generally stronger than that on graphene because of the presence of diverse active defect sites, such as the hydroxyl and epoxy functional groups and their neighboring carbon atoms. These surface oxygen sites can form OH···N and O···HN hydrogen bonds with NH3 and enhance charge transfers from NH3 to the graphene oxide. The dissociation of the adsorbed NH3 into the chemisorbed NH2 or NH species through the H atom abstractions leads to hydroxyl group hydrogenation and ring-opening of epoxy group. The reactions of NH3 with the hydroxyl and epoxy groups are predicted to be exothermic with different energy barriers, depending on the oxidation species and the atomic arrangement of these groups. The hydroxyl group exhibits relatively higher reactivity toward hydrogen abstraction from the adsorbed NH3 than the epoxy group in GO with a single oxygen group. The presence of a neighboring OH group may activate the oxygen groups to facilitate the surface reaction of NH3. Followed by the ring-opening of the epoxy group, the newly formed hydroxyl group can be removed by the second H atom abstraction from NH2. The calculated density of states of the adsorbed systems also reveals strong interactions between GO and NH3. The calculated results show good agreement with available experimental observations.
Co-reporter:Ruibo Wu, Wengjin Gong, Ting, Liu, Yingkai Zhang, and Zexing Cao
The Journal of Physical Chemistry B 2012 Volume 116(Issue 6) pp:1984-1991
Publication Date(Web):January 18, 2012
DOI:10.1021/jp211403j
Although various T. vivax purine-specific inosine–adenosine–guanosine nucleoside hydrolase (IAG-NH) crystal structures were determined in recent years, the mechanistic details for the cleavage of N-glycosidic bond and the release of base are still unclear. Herein, the irreversible hydrolysis reaction has been studied by ab initio QM/MM MD simulations, and the results indicate a highly dissociative and concerted mechanism. The protonation of substrate at N7 of inosine is found to strongly facilitate the hydrolysis process, while the hydrolysis reaction is less sensitive to the protonation state of Asp 40 residue. The proton-transfer channel and the dependence of activity on the anti/syn-conformation of substrate are also explored.
Co-reporter:Dr. Xing Chen;Dr. Zilvinas Rinkevicius; Yi Luo; Hans Ågren; Zexing Cao
ChemPhysChem 2012 Volume 13( Issue 1) pp:353-362
Publication Date(Web):
DOI:10.1002/cphc.201100451
Abstract
α-Santonin is the first organic compound observed to feature a photoinduced rearrangement and is now known to undergo a series of photochemical processes under UV irradiation. On the basis of the considerable interest of this system as a prototype, and of the yet limited insights reached for the basic photo mechanisms, we calculate the high-level electronic structures and explore the potential energy surfaces (PES) of α-santonin in the ground and lowest-lying excited states, their couplings, and the possible photoinduced isomerization pathways. The calculations identify the low-lying singlet excited state 1(nπ*) accessible under light irradiation, which decays to the low-energy 3(ππ*) state through an intersystem crossing in the Franck–Condon region to initiate the photoinduced rearrangement. The initial reaction from the C3C5 bond coupling, which takes place on the 3(ππ*) state potential energy surface, leads to a three-membered alkyl-ring compound intermediate state INT. The following photochemical reactions have the possibility to arise from two distinct CC bond cleavages, C4C5 and C3C4, denoted as path A and path B. Path A is favored both dynamically on the excited-state PES and thermodynamically on the ground-state PES in vacuo. Experiments show that it also becomes the dominant photoinduced rearrangement process in the crystal, which can be explained by considering the requirement for less space and the stacking effect under the confined environment. Path B is dynamical advantaged both on the ground- and excited-state PESs in a weak polar solvent, such as dioxane. Once the biradical intermediate B-INT is accessible on the ground-state PES, the formation of the product B-P is almost barrier free.
Co-reporter:Binju Wang ;Dr. Zexing Cao
Angewandte Chemie 2011 Volume 123( Issue 14) pp:3324-3328
Publication Date(Web):
DOI:10.1002/ange.201008239
Co-reporter:Binju Wang ;Dr. Zexing Cao
Angewandte Chemie International Edition 2011 Volume 50( Issue 14) pp:3266-3270
Publication Date(Web):
DOI:10.1002/anie.201008239
Co-reporter:Xing Chen, Zilvinas Rinkevicius, Yi Luo, Hans Ågren, and Zexing Cao
The Journal of Physical Chemistry A 2011 Volume 115(Issue 26) pp:7815-7822
Publication Date(Web):May 31, 2011
DOI:10.1021/jp203369b
The CASSCF and CASPT2 methodologies have been used to explore the potential energy surfaces of lumisantonin in the ground and low-lying triplet states along the photoisomerization pathways. Calculations indicate that the 1(nπ*) state is the accessible low-lying singlet state with a notable oscillator strength under an excitation wavelength of 320 nm and that it can effectively decay to the 3(ππ*) state through intersystem crossing in the region of minimum surface crossings with a notable spin–orbital coupling constant. The 3(ππ*) state, derived from the promotion of an electron from the π-type orbital mixed with the σ orbital localized on the C—C bond in the three-membered alkyl ring to the π* orbital of conjugation carbon atoms, plays a critical role in C—C bond cleavage. Based on the different C—C bond rupture patterns, the reaction pathways can be divided into paths A and B. Photolysis along path A arising from C1—C5 bond rupture is favorable because of the dynamic and thermodynamic preferences on the triplet excited-state PES. Path B is derived from the cleavage of the C5—C6 bond, leading first to a relatively stable species, compared to intermediate A-INT formed on the ground state PES. Accordingly, path B is relatively facile for the pyrolytic reaction. The present results provide a basis to interpret the experimental observations.
Co-reporter:Jinxia Liang ; Shaobin Tang
The Journal of Physical Chemistry C 2011 Volume 115(Issue 38) pp:18802-18809
Publication Date(Web):August 22, 2011
DOI:10.1021/jp205847u
The structures and electronic and optical properties of B2CN sheet and single-walled B2CN nanotubes were investigated by the first-principles density functional calculations. By rolling up the planar low-energy B2CN nanosheets along various chiral vectors, four types of zigzag and armchair B2CN nanotubes were constructed. The present calculations show that the structural and electronic properties of B-rich B2CN nanotubes strongly depend on their sizes and chiralities. The zigzag and armchair B2CN nanotubes with the small diameter generally are semiconductors, and their band gaps decrease as the tube-radius increases. When the diameter of tubes is large enough, the four kinds of nanotubes may produce the electronic behavior transitions from semiconductor to metal. Owing to the electronic affinity difference among B, C, and N atoms, there are remarkable charge transfers from B to C and N atoms in B2CN nanostructures. The predicted dielectric and optical properties show that the zigzag and armchair B2CN nanotubes are the optical anisotropy with respect to light polarization, and their absorption spectra are sensitive to the chirality of tube.
Co-reporter:Binju Wang ;Dr. Zexing Cao
Chemistry - A European Journal 2011 Volume 17( Issue 42) pp:11919-11929
Publication Date(Web):
DOI:10.1002/chem.201101274
Abstract
The acid-catalyzed reactions of twisted amides in water solution were investigated by using cluster-continuum model calculations. In contrast to the previous widely suggested concerted hydration of the CO group, our calculations show that the reaction proceeds in a practically stepwise manner, and that the hydration and hydrolysis channels of the CN bond compete. The Eigen ion (H3O+) is the key species involved in the reaction, and it modulates the hydration and hydrolysis reaction pathways. The phenyl substitution in the twisted amide not only activates the NCO bond, but also stabilizes the hydrolysis product through nNπphenyl delocalization, leading exclusively to the hydrolysis product of the ring-opened carboxylic acid. Generally, the twisted amides are more active than the planar amides, and such a rate acceleration results mainly from the increase in exothermicity in the first N-protonation step; the second step of the nucleophilic attack is less affected by the twisting of the amide bond. The present results show good agreement with the available experimental observations.
Co-reporter:Shaobin Tang and Zexing Cao
Physical Chemistry Chemical Physics 2010 vol. 12(Issue 10) pp:2313-2320
Publication Date(Web):21 Jan 2010
DOI:10.1039/B920754F
First-principles calculations within the local spin-density approximation have been used to investigate the electronic and magnetic properties of carbon chain-doped zigzag born nitride nanoribbons (ZBNNRs). Our results indicate that doped half-bare ZBNNRs with an H-passivated B edge and a bare C edge generally have a spin-polarized ground state with the ferromagnetic spin ordering localized at the C edge, independent of the doping concentration and the ribbon width. In particular, doped half-bare ZBNNRs for all widths may produce half-semiconducting → half-metallic → metallic behavior transitions without an external electric field as the doping proceeds gradually from the N edge to the B edge. The breakage of the symmetric spin distribution in the bipartite lattice and the coexistence of the edge state and the border state arising from charge transfer in these doped ZBNNRs are responsible for their tunable electronic and magnetic properties.
Co-reporter:Shaobin Tang, Zexing Cao
Chemical Physics Letters 2010 Volume 488(1–3) pp:67-72
Publication Date(Web):12 March 2010
DOI:10.1016/j.cplett.2010.01.073
The first-principles calculations have been used to determine structures, stabilities, and electronic properties of the completely hydrogenated boron nitride sheets and nanoribbons. Calculations show that these hydrogenated boron nitride systems have favorable formation energies and they still maintain a hexagonal network structure during full geometry relaxation. The hydrogenated zigzag boron nitride nanoribbons with various widths generally have ferromagnetic metallicity in their ground states, while the hydrogenated armchair boron nitride nanoribbons behave as nonmagnetic semiconductors with the wide direct band gaps. Predicted electronic properties of these hydrogenated boron nitride sheets and nanoribbons show remarkable size and structural dependences.The first-principles calculations were used to determine structural and electronic properties of the completely hydrogenated boron nitride sheets and nanoribbons.
Co-reporter:Congjie Zhang, Pei Wang, Jinxia Liang, Wenhong Jia, Zexing Cao
Journal of Molecular Structure: THEOCHEM 2010 Volume 941(1–3) pp:41-46
Publication Date(Web):15 February 2010
DOI:10.1016/j.theochem.2009.10.036
Based on the most stable structure of C3B2H4 and its substitution of H with -Cl, -CH2OH, -CHOH, -CO and -COOH groups, a series of derivatives containing the planar tetracoordinate carbon (ptC) atoms as well as crown ether-like compounds from the assembling of C3B2H4 units have been constructed. At the B3LYP/6-311++G** and MP2/6-31G** levels of theory, these ptC compounds were predicted to be stable and they generally have large HOMO–LUMO gaps. The IR characteristic bands arising from the symmetrical and asymmetrical stretching vibrations of C–ptC, the stretching vibrations of C–B and B–H as well as the breath vibration of the two three-membered rings of C3B2 appear at 1000, 1250, 1600, 2800, and 1700 cm−1, respectively. Calculations also show that these ptC molecules have strong aromaticities and the ptC atom obeys the octal rule. Furthermore, the derivatives C3B2H2(COOH)2 and tetra-C3B2H2-16-crown-4 can serve as the chelate ligands and form stable complexes with uranyl.
Co-reporter:Binju Wang and Zexing Cao
The Journal of Physical Chemistry A 2010 Volume 114(Issue 49) pp:12918-12927
Publication Date(Web):November 17, 2010
DOI:10.1021/jp106560s
The acid-catalyzed hydrolysis of formamide in aqueous solutions was investigated by ab initio calculations. Solvent effects on the hydrolysis reaction were reasonably considered by the cluster-continuum model with explicit water molecules in the first solvation shell, and the selection of hydration cluster plays an important role in reliable estimation of thermodynamic values for the hydrolysis reaction. Possible concerted and stepwise mechanisms of the O-protonated and N-protonated pathways were investigated by extensive calculations. On the basis of unbiased theoretical treatments on all plausible pathways, the O-protonated stepwise pathway was shown to be the favored mechanism, and the predicted activation free energies for the rate-determining step and the breaking of the C−N bond are 21.8 and 9.4 kcal/mol by B3LYP, respectively. The present results show good agreement with experiment and provide a complete description of the acid-catalyzed hydrolysis of formamide.
Co-reporter:Jinglai Zhang, Xugeng Guo, Zexing Cao
International Journal of Mass Spectrometry 2010 290(2–3) pp: 113-119
Publication Date(Web):
DOI:10.1016/j.ijms.2009.12.013
Co-reporter:Congjie Zhang, Wenhong Jia and Zexing Cao
The Journal of Physical Chemistry A 2010 Volume 114(Issue 30) pp:7960-7966
Publication Date(Web):July 9, 2010
DOI:10.1021/jp102678v
We have investigated the structures, stabilities, aromaticities, and Wiberg bond indices of four types of compounds (8-like, trapezia, umbrella-like, and quadrangle) containing planar tetracoordinate carbon (ptC), and the stability rules for the compound with ptC were concluded on the basis of extensive calculations. Generally, the stability or viability of compound with ptC strongly depends on the number of three-membered ring and conjugated three-membered ring, as well as π electrons. These rules can be successfully used to identify the stability of other compounds reported in previous studies. On the basis of these rules, eight stable compounds with planar tetracoordinate nitrogen (ptN) are successfully constructed.
Co-reporter:Hujun Xie and Zexing Cao
Organometallics 2010 Volume 29(Issue 2) pp:436-441
Publication Date(Web):December 16, 2009
DOI:10.1021/om9008197
The oxidative half-reaction of oxygen atom transfer from nitrate to the MoIV complex has been investigated by the density functional approach, based on the model cluster [(Me2C2S2)2Mo(MeS2)]− derived from the newly identified structure of nitrate reductase. Calculations show that the reduction of nitrate to nitrite can occur through an association of nitrate to the Mo center, followed by rupture of the Mo−O−NO2− bond. In reaction mechanism i, Mo−SCys bond cleavage coupling with the coordination of nitrate to Mo is the rate-determining step with a barrier of 19.8 kcal mol−1. In reaction mechanism iii, the direct coordination of nitrate to Mo is an almost barrier-free process, and the barrier for the rate-determining step of the Mo−O−NO2− bond cleavage is about 11.7 kcal mol−1, significantly lower than those in other plausible mechanisms. Present calculations lend support to the notion that the presence of a disulfide bond in the active site can influence the interconversion of MoIV to MoVI.
Co-reporter:Congjie ZHANG;Wenhong JIA
Chinese Journal of Chemistry 2009 Volume 27( Issue 5) pp:882-886
Publication Date(Web):
DOI:10.1002/cjoc.200990148
Abstract
Fullerene[51] containing quasi-planar tetracoordinate carbons and its eight modificational compounds with quasi-planar tetracoordinate carbons have been constructed. Using B3LYP method, their structures, stabilities, and bonding properties have been investigated, indicating that the nine novel structures are stable and have big vertical detachment energies and relatively small vertical electron affinities. The structures of the nine compounds contain five- and six-membered rings, as well as bigger ten-membered rings.
Co-reporter:Yuchun Lin, Zexing Cao and Yirong Mo
The Journal of Physical Chemistry B 2009 Volume 113(Issue 14) pp:4922-4929
Publication Date(Web):March 11, 2009
DOI:10.1021/jp810651m
Molecular dynamics simulations on the wild-type AmtB protein and its D160A homology model have been performed. Although no significant structural changes due to the mutation of Asp160 were observed, calculations confirmed the critical role of Asp160 for the recognition and binding of NH4+ in AmtB. The carboxyl group of Asp160 is ∼8 Å from NH4+, but their favorable through-space electrostatic interaction is further enhanced by a hydrogen bond chain involving Ala162 (the backbone carbonyl group) and Gly163 (the backbone amide group). This explains the occurrence of the second binding site in AmtB which does not exist in the D160A mutant, as shown in the computed energy profiles. As the initially buried carboxyl group of Asp160 links to the ammonium ion in the periplasmic binding vestibule through a chain of water molecules, a likely deprotonation venue thus is from ammonium to Asp160. Combined QM(PM3)/MM molecular dynamics simulations showed that indeed Asp160 can serve as the proton acceptor and the overall proton transfer process needs to overcome a barrier of merely 7.7 kcal/mol, which is in good agreement with our previous QM(DFT)/MM optimizations. Significantly, the proton transfer adopts an unconventional mechanism by migrating the negative charge from the carboxyl group of Asp160 to NH4+ via two water molecules, which can be illustrated as −CO2−···H2O···H2O···NH4+ → −COOH···H2O···OH−···NH4+ → −COOH···H2O···H2O···NH3. Apparently, this is also a charge recombination process and thus is exothermic.
Co-reporter:Bin Liu;Hujun Xie;Huijuan Wang;Liqiong Wu;Qianyi Zhao;Jinxiang Chen;TingBin Wen Dr., Dr. ;Haiping Xia Dr.
Angewandte Chemie 2009 Volume 121( Issue 30) pp:5569-5572
Publication Date(Web):
DOI:10.1002/ange.200902238
Co-reporter:Bin Liu;Hujun Xie;Huijuan Wang;Liqiong Wu;Qianyi Zhao;Jinxiang Chen;TingBin Wen Dr., Dr. ;Haiping Xia Dr.
Angewandte Chemie International Edition 2009 Volume 48( Issue 30) pp:5461-5464
Publication Date(Web):
DOI:10.1002/anie.200902238
Co-reporter:Ruibo Wu, Hujun Xie, Yirong Mo and Zexing Cao
The Journal of Physical Chemistry A 2009 Volume 113(Issue 43) pp:11595-11603
Publication Date(Web):May 27, 2009
DOI:10.1021/jp901093g
l-Rhamnose isomerase (l-RhI) has been found in many microorganisms and catalyzes the reversible isomerization between l-rhamnose and l-rhamnulose. Interestingly, Pseudomonas stutzeri l-RhI (P. stutzeri l-RhI) exhibits a much broader substrate specificity than others such as Escherichia coli l-RhI (E. coli l-RhI) and catalyzes the interconversion of many aldoses and ketoses. To elucidate the uniqueness of P. stutzeri l-RhI and the mechanism of enzymatic catalysis, we performed dual-level combined QM/MM molecular dynamics simulations on P. stutzeri l-RhI with a number of substrates. Calculations show that the reversible process between aldoses and ketoses can be rationalized by a zwitterion intermediate mechanism that involves both proton and hydride transfers. Predicted free energy barriers in the rate-determining step are 8.9 kcal/mol for l-rhamnose and 13.6 kcal/mol for d-allose, respectively, in good agreement with the experimental characterization of relative substrate reactivity. Conformational and hydrogen bond analyses of the active domain and evaluation of electrostatic and van der Waals (vdW) interactions between substrates and surrounding residues provide a basis to understand the catalytic role of conserved residues, the substrate specificity, and the relative activity of favorable substrates in P. stutzeri l-RhI.
Co-reporter:Shaobin Tang and Zexing Cao
The Journal of Physical Chemistry A 2009 Volume 113(Issue 19) pp:5685-5690
Publication Date(Web):April 20, 2009
DOI:10.1021/jp810435c
Density functional calculations have been used to investigate adsorption and decomposition of 1-propanethiol on the Ga-rich GaAs (001) surface. The dissociative adsorption of 1-propanethiol on GaAs (001) to the chemisorbed propanethiolate and hydrogen was predicted to be quite facile. Followed by the C−S bond scission of the propanethiolate species, the surface propyl species was formed with a barrier of 47.2 kcal/mol for the low-energy route. The propyl species is an important precursor to propane through the C−H bond coupling and to propene via the β-H elimination. Predicted activation free energies for the surface processes from the propyl species to propane and propene are 45.2 and 37.0 kcal/mol at 298.1 K, respectively, while the corresponding overall Gibbs free energies of reaction ΔG are −49.3 and −21.2 kcal/mol relative to free 1-propanethiol. Therefore, both reaction routes are competitive, resulting in a product mixture, although the β-H elimination from the propyl species is initially remarkably favorable dynamically. On the basis of our calculations, detailed mechanisms for adsorption and thermal decomposition of 1-propanethiol on the GaAs (001) surface were proposed, and the calculated results show good agreement with experimental observations.
Co-reporter:Cong-Jie ZHANG;Jin-Xia LIANG ;Ze-Xing CAO
Chinese Journal of Chemistry 2008 Volume 26( Issue 2) pp:243-248
Publication Date(Web):
DOI:10.1002/cjoc.200890048
Abstract
The geometries and vibrational frequencies of C7H22− and C7H32− dianions, as well as their corresponding anions were investigated theoretically using HF, MP2, CCSD and CISD methods. The lowest energy structures are C2C(H2)C42− and C2CHCHCHC22− for C7H22− and C7H32− dianions, respectively. Analysis of possible detachment channels of the two structures indicates that the two isomers are stable with respect to fragmentation into two monoanions. However, the vertical and adiabatic detachment energies of the two structures show that C2C(H2)C42− is electronically stable, while C2CHCHCHC22− is not.
Co-reporter:Hujun Xie, Ruibo Wu, Zhaohui Zhou and Zexing Cao
The Journal of Physical Chemistry B 2008 Volume 112(Issue 36) pp:11435-11439
Publication Date(Web):August 16, 2008
DOI:10.1021/jp803616z
Density functional theory and combined quantum mechanics and molecular mechanics (QM/MM) calculations have been used to explore structural features of the FeMo cofactor with an interstitial atom X (X = N, C, or O) and its interactions with CO and N2. Predicted frequencies of the metal-bound CO, QM/MM-optimized geometries, and calculated redox potentials of the FeMo cofactor with different central ligands show that the oxygen atom is the candidate for the interstitial atom. Calculations on the interactions of the FeMo cofactor with CO and N2 reveal that there is a remarkable dependence of the binding energy on the binding site and the interstitial atom. Generally, the Fe2 site of the FeMo cofactor has stronger interactions with CO and N2 than Fe6, and both the Fe2 and Fe6 sites in the N-centered and O-centered clusters of the FeMo cofactor can effectively bind N2 while the coordination of N2 to the Fe6 site of the C-centered active cluster is unfavorable energetically. Present results indicate that the protein environment is important for computational characterization of the structure of the FeMo cofactor and properties of the metal-bound CO and N2 are sensitive to the interstitial atom.
Co-reporter:Zexing Cao Dr.;Yirong Mo Dr.;Walter Thiel Dr.
Angewandte Chemie 2007 Volume 119(Issue 36) pp:
Publication Date(Web):2 AUG 2007
DOI:10.1002/ange.200701348
Stufenweiser Verlauf: Im Ammoniak-Kanalprotein AmtB kann die Deprotonierung von NH4+ über eine Abfolge aus zwei wasserstoffverbrückten H2O-Molekülen verlaufen, die am Protonenakzeptor, der Carboxylatgruppe von Asp160, endet (siehe Bild). Quantenmechanischen und quantenmechanisch/molekülmechanischen Rechnungen zufolge liegt kein konzertierter, sondern ein stufenweiser Mechanismus vor.
Co-reporter:Zexing Cao Dr.;Yirong Mo Dr.;Walter Thiel Dr.
Angewandte Chemie International Edition 2007 Volume 46(Issue 36) pp:
Publication Date(Web):2 AUG 2007
DOI:10.1002/anie.200701348
All wired up: In the ammonia-channel protein AmtB, the deprotonation of NH4+ can occur along a hydrogen-bond wire that contains two water molecules and terminates at the proton acceptor, the carboxylate group of the residue Asp160 (see picture). The results of quantum-mechanical and quantum-mechanical/molecular-mechanical calculations suggest that a stepwise rather than a concerted mechanism is involved.
Co-reporter:Kuo Zeng;Ze-Xing Cao
Chinese Journal of Chemistry 2006 Volume 24(Issue 3) pp:
Publication Date(Web):13 MAR 2006
DOI:10.1002/cjoc.200690056
Density functional theory and ab initio calculations have been used to determine structures and stabilities of the protonated aromatics species AH+ and AH22+ (A=pyrrole, furan). Possible mechanisms and relative energetics for protonation of pyrrole and furan by H3O+ and AH4+ in the gas phase have been explored. Calculations show that the Cα-protonated species was the most stable structure for AH+, and the protonated AH+ might accommodate the second proton to yield AH22+ if the free proton was available. The gas-phase H3O+ could protonate pyrrole and furan with significant exothermicity and almost without barrier. The proton transfer from AH4+ to pyrrole and furan has a barrier ranging from 33.5 to 39.3 kJ/mol in the gas phase.
Co-reporter:Zexing Cao Dr.;Qianer Zhang
Chemistry - A European Journal 2004 Volume 10(Issue 8) pp:
Publication Date(Web):7 APR 2004
DOI:10.1002/chem.200305572
Density functional theory and CASSCF calculations have been used to optimize the geometries of binuclear gold(I) complexes [H3PAu(CC)nAuPH3] (n=1–6) in their ground states and selected lowest energy 3(ππ*) excited states. Vertical excitation energies obtained by time-dependent density functional calculations for the spin-forbidden singlet–triplet transitions have exponential-decay size dependence. The predicted singlet–triplet splitting limit of [H3PAu(CC)∝AuPH3] is about 8317 cm−1. Calculated singlet–triplet transition energies are in reasonable agreement with available experimental observations. The effect of the heavy atom Au spin-orbit coupling on the 3(ππ*) emission of these metal-capped one-dimensional carbon allotropes has been investigated by MRCI calculations. The contribution of the spin- and dipole-allowed singlet excited state to the spin-orbit-coupling wave function of the 3(ππ*) excited state makes the low-lying acetylenic triplet excited states become sufficiently allowed so as to appear in both electronic absorption and emission.
Co-reporter:Zhang Cong-Jie;Zhang Li-Ling;Cao Ze-Xing;Zhang Qian-Er
Chinese Journal of Chemistry 2003 Volume 21(Issue 2) pp:
Publication Date(Web):26 AUG 2010
DOI:10.1002/cjoc.20030210206
Density functional theory calculations with the B3LYP functional are used to study the structure and stabilities of C5H2 isomers and possible isomerization mechanisms on the triplet and singlet potential energy surfaces. Calculated results show that isomerization of C5H2 is likely to occur on the triplet potential energy surface while direct conversions of the singlet C5H2 isomers via 1,3-hydrogen migration transition states are extremely difficult dynamically. In such isomerization processes, the hydrogen transfer processes in carbon chains are the rate-determining steps. The triplet species except the linear ground state X3 Σ are rather less stable than their singlet forms, although the singlet and triplet species have similar geometries.
Co-reporter:Zexing Cao Dr.;Qianer Zhang ;Sigrid D. Peyerimhoff Dr.
Chemistry - A European Journal 2001 Volume 7(Issue 9) pp:
Publication Date(Web):26 APR 2001
DOI:10.1002/1521-3765(20010504)7:9<1927::AID-CHEM1927>3.0.CO;2-P
Photoexcitations and photoisomerizations due to low-lying nπ* and ππ* excited states of dimethylpyridines are investigated by density functional theory, CASSCF, CASPT2 and MRCI methodologies. Mechanistic details for the formation of Dewar dimethylpyridines and the interconversions of dimethylpyridines are rationalized through the characterization of minima and transition states on the singlet and triplet potential energy surfaces of relevant intermediates. Our present theoretical schemes suggest that Möbius dimethylpyridine intermediate 14 and azabenzvalene intermediate 10 can serve as possible precursors to Dewar dimethylpyridines and singlet phototransposition products, respectively. The calculations suggest that an S1(ππ*)/S0 conical intersection in dimethylpyridines 2 is involved in the formation of 14. An azabenzvalene 10 might be formed through S2(ππ*)/S1(nπ*) interaction followed by an S1/S0 decay in dimethylpyridine 6. Calculated barriers of isomerizations from 14 to Dewar dimethylpyridine 7 and from 10 to 4 are 8.4 and 28.5 kcal mol−1 at the B3LYP/6–311G** level, respectively. In the suggested triplet multistage transposition mechanism, an out-of-plane distorted geometry 19 due to vibrational relaxation of the T1(3B1) excited state of 3,5-dimethylpyridine 6 is a precursor of the interconversion of 6 to 2,4-dimethylpyridine 4. The formation of a triplet azaprefulvene 21 with a barrier of 20.7 kcal mol−1 is a key step during the triplet migration process leading to another out-of-plane distorted structure 27. Subsequent rearomatization of 27 completes the interconversion of 6 with 4. Present calculations provide some insight into the photochemistry of dimethylpyridines at 254 nm.
Co-reporter:Ruibo Wu ; Zhenyu Lu ; Zexing Cao ;Yingkai Zhang
Journal of the American Chemical Society () pp:
Publication Date(Web):April 1, 2011
DOI:10.1021/ja111104p
It is of significant biological interest and medical importance to develop class- and isoform-selective histone deacetylase (HDAC) modulators. The impact of the linker component on HDAC inhibition specificity has been revealed but is not understood. Using Born−Oppenheimer ab initio QM/MM MD simulations, a state-of-the-art approach to simulating metallo-enzymes, we have found that the hydroxamic acid remains to be protonated upon its binding to HDAC8, and thus disproved the mechanistic hypothesis that the distinct zinc−hydroxamate chelation modes between two HDAC subclasses come from different protonation states of the hydroxamic acid. Instead, our simulations suggest a novel mechanism in which the chelation mode of hydroxamate with the zinc ion in HDACs is modulated by water access to the linker binding channel. This new insight into the interplay between the linker binding and the zinc chelation emphasizes its importance and gives guidance regarding linker design for the development of new class-IIa-specific HDAC inhibitors.
Co-reporter:Shaobin Tang and Zexing Cao
Physical Chemistry Chemical Physics 2012 - vol. 14(Issue 48) pp:NaN16565-16565
Publication Date(Web):2012/06/19
DOI:10.1039/C2CP41343D
Graphene oxides (GOs) may offer extraordinary potential in the design of novel catalytic systems due to the presence of various oxygen functional groups and their unique electronic and structural properties. Using first-principles calculations, we explore the plausible mechanisms for the oxidative dehydrogenation (ODH) of propane to propene by GOs and the diffusion of the surface oxygen-containing groups under an external electric field. The present results show that GOs with modified oxygen-containing groups may afford high catalytic activity for the ODH of propane to propene. The presence of hydroxyl groups around the active sites provided by epoxides can remarkably enhance the C–H bond activation of propane and the activity enhancement exhibits strong site dependence. The sites of oxygen functional groups on the GO surface can be easily tuned by the diffusion of these groups under an external electric field, which increases the reactivity of GOs towards ODH of propane. The chemically modified GOs are thus quite promising in the design of metal-free catalysis.
Co-reporter:Chun Zhu, Jinxia Liang, Binju Wang, Jun Zhu and Zexing Cao
Physical Chemistry Chemical Physics 2012 - vol. 14(Issue 37) pp:NaN12806-12806
Publication Date(Web):2012/07/18
DOI:10.1039/C2CP41647F
The electronic and structural features of (oxo)manganese(V) corroles and their catalyzed oxygen atom transfers to thioanisole in different spin states have been investigated by the B3LYP functional calculations. Calculations show that these corrole-based oxidants and their complexes with thioanisole generally have the singlet ground state, and their triplet forms are also accessible in consideration of the spin–orbit coupling interaction. Due to strong d–π conjugation interactions between Mn and the corrole ring arising from the π electron donation of the corrole moiety, the five-coordinated Mn approximately has the stable 18-electron configuration. The predicted free energy barriers for the singlet oxygen atom transfer reactions are generally larger than 22 kcal mol−1, while the spin flip in reaction may remarkably increase the reactivity. In particular, the bromination on β-pyrrole carbon atoms of the meso-substituted (oxo)manganese(V) corrole strikingly enhances the spin–orbit coupling interaction and results in the dramatic increase of reactivity. The multiple spin changes are predicted to be involved in the low-energy reaction pathway. The present results show good agreement with the experimental observation and provide a detailed picture for the oxygen atom transfer reaction induced by the (oxo)manganese(V) corroles.
Co-reporter:Xugeng Guo, Yuan Zhao and Zexing Cao
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 29) pp:NaN15388-15388
Publication Date(Web):2014/06/02
DOI:10.1039/C4CP01928H
Extensive ab initio surface-hopping dynamics simulations have been used to explore the excited-state nonadiabatic decay of two biologically relevant hypoxanthine keto-N7H and keto-N9H tautomers in aqueous solution. QM/MM calculations and QM/MM-based MD simulations predict different hydrogen bonding networks around these nucleobase analogues, which influence their photodynamical properties remarkably. Furthermore, different solvent effects on the conical intersection formation of keto-N7H and keto-N9H were found in excited-state MD simulations, which also change the lifetimes of the excited states. In comparison with the gas-phase situation, the S1 → S0 nonradiative decay of keto-N7H is slightly faster, while this decay process of keto-N9H becomes much slower in water. The presence of π-electron hydrogen bonds in the solvated keto-N7H is considered to facilitate the S1 → S0 nonradiative decay process.
Co-reporter:Xiangfei Zhang and Zexing Cao
Dalton Transactions 2016 - vol. 45(Issue 25) pp:NaN10365-10365
Publication Date(Web):2016/05/17
DOI:10.1039/C6DT01154C
The oxidation addition of a series of σ H–X bonds (X = H, B, C, Si, N, P, and O) to a single Al(I) supported by a (NacNac)− bidentate ligand ((NacNac)− = [ArNC(Me)CHC(Me)NAr]− and Ar = 2,6-iPr2C6H3) has been explored through extensive DFT calculations. The presented results show that activation and addition of these σ bonds follow various reaction mechanisms, in which hydride transfer, proton transfer, and Al–X bond coupling steps are involved. The predicted free energy barriers for these oxidative additions range from 8 to 32 kcal mol−1, and all the reactions are remarkably favorable thermodynamically. However, sterically hindered ligands, for most reactants, make the formation of the initial reactant complex difficult and may reduce the efficiency of the reaction. Calculations reveal a strong dependence of the reaction mechanism and low-energy channel on the bonding features of X–H and the local structural environments.
Co-reporter:Yanzhen Gan, Ling Yue, Xugeng Guo, Chaoyuan Zhu and Zexing Cao
Physical Chemistry Chemical Physics 2017 - vol. 19(Issue 19) pp:NaN12106-12106
Publication Date(Web):2017/04/13
DOI:10.1039/C6CP08929A
An on-the-fly trajectory surface hopping dynamic simulation has been performed for revealing the multi-state nonadiabatic deactivation mechanism of coumarin. The mechanism involves three adiabatic excited states, S3(ππ*Lb), S2(nπ*, ππ*La) and S1(ππ*La, nπ*), and the ground state S0 at the four state-averaged complete active space self-consistent field, SA4-CASSCF(12,10)/6-31G* level of theory. Upon photoexcitation to the third excited state S3(ππ*Lb) in the Franck–Condon region, 80% sampling trajectories decay to the dark S2(nπ*) state within an average of 5 fs via the conical intersection S3(ππ*Lb)/S2(nπ*), while 20% decay to the S2(ππ*La) state within an average of 11 fs via the conical intersection S3(ππ*Lb)/S2(ππ*La). Then, sampling trajectories via S2(nπ*)/S1(ππ*La) continue with ultrafast decay processes to give a final distribution of quantum yields as follows: 42% stay on the dark S1(nπ*) state, 43.3% go back to the ground S0 state, 12% undergo a ring-opening reaction to the Z-form S0(Z) state, and 2.7% go to the E-form S0(E) state. The lifetimes of the excited states are estimated as follows: the S3 state is about 12 fs on average, the S2 state is about 80 fs, and the S1 state has a fast component of about 160 fs and a slow component of 15 ps. The simulated ultrafast radiationless deactivation pathways of photoexcited coumarin immediately interpret the experimentally observed weak fluorescence emission.
Co-reporter:Mao-Long Chen, Yu-Hui Hou, Wen-Sheng Xia, Wei-Zheng Weng, Ze-Xing Cao, Zhao-Hui Zhou and Hui-Lin Wan
Dalton Transactions 2014 - vol. 43(Issue 23) pp:NaN8697-8697
Publication Date(Web):2014/02/25
DOI:10.1039/C4DT00104D
From neutral solutions, dimeric 1,3-propanediaminetetraacetato lanthanides (NH4)2[Ln2(1,3-pdta)2(H2O)4]·8H2O [Ln = La, 1; Ce, 2] and K2[Ln2(1,3-pdta)2(H2O)4]·11H2O [Ln = La, 3; Ce, 4] (1,3-H4pdta = 1,3-propanediaminetetraacetic acid, C11H18N2O8) were isolated in high yields. The reaction of excess strontium nitrate with 1 resulted in the formation of a two dimensional coordination polymer [La2(1,3-pdta)2(H2O)4]n·[Sr2(H2O)6]n·[La2(1,3-pdta)2(H2O)2]n·18nH2O (5) at 70 °C. Complexes 1–4 show a similar central molecular structure. The lanthanide ions are coordinated by two nitrogen atoms, four carboxy oxygen atoms from one 1,3-pdta ligand, two from the neighboring 1,3-pdta ligand forming a four-membered ring and two water molecules. Complex 5 has two kinds of dimeric lanthanum unit and extends into a 2D coordination polymer through strontium ions and bridged oxygen atoms, and forms a fourteen membered ring linked by oxygen atoms from carboxy groups of pdta. Complexes 1–4 are soluble in water. The 13C{1H} NMR experiments for complex 1 were tested in solution. Thermal products from 1 and 5 show good catalytic activities towards the oxidative coupling reaction of methane (OCM). The conversion of methane and selectivity to C2 reached 29.7% and 51.7% at 750 °C for the product of 5. From TGA, XRD and SEM analyses, the thermal products from 1 and 5 are rod- and poly-shaped, which are assigned as lanthanum oxocarbonate and a mixture of La2O3, SrCO3 and La2O2CO3 for 1 and 5, respectively. The precursor method is favorable for the formation of regular shaped mixed oxides.
Co-reporter:Yuan Zhao, Nanhao Chen, Ruibo Wu and Zexing Cao
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 34) pp:NaN18417-18417
Publication Date(Web):2014/07/15
DOI:10.1039/C4CP01609B
The glucosamine 6-phosphate deaminase (NagB), which catalyzes the conversion of D-glucosamine 6-phosphate (GlcN6P) into D-fructose 6-phosphate (F6P) and ammonia, determines the final metabolic fate of N-acetylglucosamine (GlcNAc). Here using state-of-the-art ab initio QM/MM MD simulations, we have explored the plausible mechanisms for the enzymatic ring-opening of GlcN6P in the basic environment. Two different proton-shuttle mechanisms have been proposed. Calculations show that the protonated state of the amino group in the substrate dominates the concerted and stepwise catalytic pathways and a catalytic triad plays an important role in mediating the proton transfer and the resulting ring-opening process. The free energy barrier for the rate-determining step in the low-energy stepwise reaction is 17.9 kcal mol−1. In acidic solution, the lid motif prefers a closed state while it always stays in the open state in basic solution upon substrate binding, which is basically dominated by the protonated state of the residue His145.
Co-reporter:Jinxia Liang, Chun Zhu and Zexing Cao
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 33) pp:NaN13851-13851
Publication Date(Web):2013/05/02
DOI:10.1039/C3CP51019K
Plausible mechanisms of the ultrafast electron injection and the significant dependence of the power conversion efficiency on the anchor group for the triphenylamine-based dye-sensitized TiO2 solar cells have been explored by the density functional calculations. Calculations show that the ultrafast charge recombination on the surface trap state of the dye-sensitized TiO2 system can be ascribed to the lack of electron density on the carboxyl group of the A3 dye with the rhodanine group anchor. Predicted electronic and optical properties of the A1-3-adsorbed TiO2 system reveal that the direct electron injection arises from the electronic excitation from HOMO-1 of the dye to the conduction band bottom of TiO2. On the basis of the calculations, the electron density distributions of related frontier orbitals and energy bands of dyes and their adsorbed systems have been discussed, which play an important role in electron injection and charge recombination.
Co-reporter:Shaobin Tang and Zexing Cao
Physical Chemistry Chemical Physics 2010 - vol. 12(Issue 10) pp:NaN2320-2320
Publication Date(Web):2010/01/21
DOI:10.1039/B920754F
First-principles calculations within the local spin-density approximation have been used to investigate the electronic and magnetic properties of carbon chain-doped zigzag born nitride nanoribbons (ZBNNRs). Our results indicate that doped half-bare ZBNNRs with an H-passivated B edge and a bare C edge generally have a spin-polarized ground state with the ferromagnetic spin ordering localized at the C edge, independent of the doping concentration and the ribbon width. In particular, doped half-bare ZBNNRs for all widths may produce half-semiconducting → half-metallic → metallic behavior transitions without an external electric field as the doping proceeds gradually from the N edge to the B edge. The breakage of the symmetric spin distribution in the bipartite lattice and the coexistence of the edge state and the border state arising from charge transfer in these doped ZBNNRs are responsible for their tunable electronic and magnetic properties.
Co-reporter:Yuan Zhao, Nanhao Chen, Yirong Mo and Zexing Cao
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 48) pp:NaN26875-26875
Publication Date(Web):2014/10/24
DOI:10.1039/C4CP04032E
Hydroxynitrile lyases (HNLs) defend plants from herbivores and microbial attack by releasing cyanide from hydroxynitriles. The reverse process has been productively applied to bioorganic syntheses of pharmaceuticals and agrochemicals. To improve our understanding of the catalytic mechanism of HNLs, extensive ab initio QM/MM and classical MM molecular dynamics simulations have been performed to explore the catalytic conversion of cyanohydrins into aldehyde (or ketone) and HCN by hydroxynitrile lyases from Hevea brasiliensis (HbHNLs). It was found that the catalytic reaction approximately follows a two-stage mechanism. The first stage involves two fast processes including the proton abstraction of the substrate through a double-proton transfer and the C–CN bond cleavage, while the second stage concerns HCN formation and is rate-determining. The complete free energy profile exhibits a peak of ∼18 kcal mol−1. Interestingly, the protonation state of Lys236 influences the efficiency of the enzyme only to some extent, but it changes the entire catalytic mechanism. The dynamical behaviors of substrate delivery and HCN release are basically modulated by the gate movement of Trp128. The remarkable exothermicity of substrate binding and the facile release of HCN may drive the enzyme-catalyzed reaction to proceed along the substrate decomposition efficiently. Computational mutagenesis reveals the key residues which play an important role in the catalytic process.
Co-reporter:Xugeng Guo, Zhenggang Lan and Zexing Cao
Physical Chemistry Chemical Physics 2013 - vol. 15(Issue 26) pp:NaN10782-10782
Publication Date(Web):2013/04/23
DOI:10.1039/C3CP44718A
Nonadiabatic dynamics simulations at the SA-CASSCF level were performed for the two most stable keto-N7H and keto-N9H tautomers of hypoxanthine in order to obtain deep insight into the lifetime of the optically bright S1(1ππ*) excited state and the relevant decay mechanisms. Supporting calculations on the ground-state (S0) equilibrium structures and minima on the crossing seams of both tautomers were carried out at the MR-CIS and CASSCF levels. These studies indicate that there are four slightly different kinds of conical intersections in each tautomer, exhibiting a chiral character, each of which dominates a barrierless reaction pathway. Moreover, both tautomers reveal the ultrafast S1 → S0 decay, in which the S1 state of keto-N9H in the gas phase has a lifetime of 85.5 fs, whereas that of keto-N7H has a longer lifetime of 137.7 fs. An excellent agreement is found between the present results and the experimental value of 130 ± 20 fs in aqueous solution (Chen and Kohler, Phys. Chem. Chem. Phys., 2012, 14, 10677–10689).
