Co-reporter:Binbin Xie, Ganglong Cui, and Wei-Hai Fang
Journal of Chemical Theory and Computation June 13, 2017 Volume 13(Issue 6) pp:2717-2717
Publication Date(Web):April 24, 2017
DOI:10.1021/acs.jctc.7b00153
In the present work, the quantum trajectory mean-field (QTMF) approach is numerically implemented by ab initio calculation at the level of the complete active space self-consistent field, which is used to simulate photoisomerization of acetylacetone at ∼265 nm. The simulated results shed light on the possible nonadiabatic pathways from the S2 state and mechanism of the photoisomerization. The in-plane proton transfer and the subsequent S2 → S1 transition through the E-S2/S1-1 intersection region is the predominant route to the S1 state. Meanwhile, rotational isomerization occurs in the S2 state, which is followed by internal conversion to the S1 state in the vicinity of the E-S2/S1-2 conical intersection. As a minor pathway, the direct S2 → S1 → S0 transition can take place via the E-S2/S1/S0 three-state intersection region. The rotamerization in the S1 state was determined to be the key step for formation of nonchelated enolic isomers. The final formation yield is predicted to be 0.57 within the simulated period. The time constant for the S2 proton transfer was experimentally inferred to be ∼70.0 fs in the gas phase and ∼50.0 fs in dioxane, acetonitrile, and n-hexane, which is well-reproduced by the present QTMF simulation. The S1 lifetime of 2.11 ps simulated here is in excellent agreement with the experimentally inferred values of 2.12, 2.13, and 2.25 ps in n-hexane, acetonitrile, and dioxane, respectively. The present study provides clear evidence that a direct ab initio QTMF approach is a reliable tool for simulating multiple-state nonadiabatic dynamics processes.
Co-reporter:Yating Yang, Wei-Hai Fang, and Run Long
The Journal of Physical Chemistry Letters December 7, 2017 Volume 8(Issue 23) pp:5771-5771
Publication Date(Web):November 12, 2017
DOI:10.1021/acs.jpclett.7b02779
Two-dimensional transition metal dichalcogenides (TMDs) heterojunctions are appealing candidates for optoelectronics and photovoltaics. Using time-domain density functional theory combined with nonadiabatic (NA) molecular dynamics, we show that photoexcitation dynamics exhibit a significant difference in the vertical and lateral MoS2/WSe2 heterojunctions arising from the disparity in the donor–acceptor interaction and fundamental band alignment. The obtained electron transfer time scale in the vertical heterojunction shows excellent agreement with experiment. Hole transfer proceeds 1.5 times slower. The electron–hole recombination is 3 orders of magnitude longer than the charge separation, which favors solar cell applications. On the contrary, the lateral heterojunction shows no band offsets steering charge separation. The excited electron is localized at the interface that attracts holes to form an exciton-like state due to Coulomb interaction, suggesting potential applications in light-emitting devices. The coupled electron and hole wave functions increase NA coupling and the coherence time, accelerating electron–hole recombination by a factor of 3 compared with the vertical case. The atomistic studies advance our understanding of the photoinduced charge–phonon dynamics in TMDs heterojunctions.
Co-reporter:Chenchen Qin;Jinbo Fei;Ganglong Cui;Xiangyang Liu;Weihai Fang;Xiaoke Yang;Xingcen Liu;Junbai Li
Physical Chemistry Chemical Physics 2017 vol. 19(Issue 35) pp:23733-23739
Publication Date(Web):2017/09/13
DOI:10.1039/C7CP02543B
Herein, we show that a molecular assembly offers tremendous opportunities of affording existing building units with new physicochemical properties, holding promise in wide applications. Herein, we develop a facile covalent assembly using a natural occurring linker, genipin, to efficiently transform a traditional chemo drug, doxorubicin, into a nanophotomedicine. A possible mechanism is proposed, in which doxorubicin reacts with genipin through covalent bonding to produce poorly soluble units, which further form nuclei and mediate the interfacial assembly to generate uniform nanoparticles. Such assembled nanophotomedicine shows remarkably enhanced singlet oxygen generation ability (about 1000 folds), leading to a much higher photodynamic activity. Moreover, this self-carried nanodrug exhibits adjustable size, excellent colloidal stability, high capacity and preferable endocytosis. These favorable features lead to greatly improved anticancer efficiency under light at the same dosage, compared to that of pure doxorubin. We believe this study brings a new dimension to develop advanced drug delivery systems by molecular assembly.
Co-reporter:Xiang-Yang Liu;Ganglong Cui
Theoretical Chemistry Accounts 2017 Volume 136( Issue 1) pp:
Publication Date(Web):2017 January
DOI:10.1007/s00214-016-2029-z
Two-state conical intersection optimization methods at both QM and QM/MM levels have been extensively implemented in many commercial and noncommercial packages in the past decade. In contrast, three-state conical intersection optimization methods are less concerned, in particular the QM/MM-based ones. In this work, we have developed a penalty function-based three-state conical intersection optimization approach in the framework of the QM/MM method. We first present the fundamental formulation of this approach, and its algorithm and implementation in our package; then, we have carried out several pilot applications on molecular systems in vacuo and aqueous solution to demonstrate the efficiency of our implemented method. Our current developments enable efficient determination of three-state conical intersection structures of molecules in solution and biological systems, which is at the heart of understanding the photophysical and photochemical mechanisms of large systems at the atomistic level.
Co-reporter:Huizhen Su, Xuebo Chen, and Weihai Fang
Analytical Chemistry 2014 Volume 86(Issue 1) pp:891
Publication Date(Web):December 16, 2013
DOI:10.1021/ac4034592
An ab initio multiconfigurational (CASPT2//CASSCF) approach has been employed to map radiative and nonradiative relaxation pathways for a cyclam-methylbenzimidazole fluorescent sensor and its metal ion (Zn2+, Cd2+, and Cu2+) complexes to provide an universal understanding of ON–OFF fluorescent mechanisms for the selective identification of these metal ions. The photoinduced electron transfer (PET) between the receptor and the signaling unit is quantitatively attributed for the first time to a newly generated transition of S0→SCT(1nπ*), which is a typical 1nπ* excitation but exhibits a significant charge transfer character and zwitterionic radical configuration. The present study contributes the two theoretical models of the competitive coexistence of radiative/nonradiative decay channel in 1ππ*/SCT(1nπ*) states for the detection of metal ions with d10 configuration (i.e., Zn2+, Cd2+, etc.) and a downhill ladder relaxation pathway through multi nona-diabatic relays for the probing of d9 cations (Cu2+, etc.). These computational results will establish a benchmark for ON–OFF mechanisms of a fluorescent sensor that coordinates various transition metal ions with different electron configuration and radius.
Co-reporter:Hongjuan Wang, Xuebo Chen and Weihai Fang
Physical Chemistry Chemical Physics 2014 vol. 16(Issue 46) pp:25432-25441
Publication Date(Web):15 Oct 2014
DOI:10.1039/C4CP04130E
The photolyase enzyme absorbs blue light to repair damaged DNA through a cyclic electron transfer reaction. A description of the underlying mechanism has proven to be a challenging issue for both experimental and theoretical studies. In the present work, combined CASPT2//CASSCF/AMBER (QM/MM) calculations have been performed for damaged DNA in photolyase. A proton-coupled electron transfer (PCET) mechanism has been determined for restoring cyclobutane pyrimidine dimer (CPD) to two normal thymine bases by irradiation of photolyase. A well-defined water wire between FADH− and CPD was determined as a bridge to assist the PCET process within FADH− and thereby trigger the forward electron transfer to CPD. The subsequent CPD splitting and the alternation of the H-bond pattern proceed in a concerted way, which makes the productive backward electron transfer occur on an ultrafast timescale. A local minimum of SCT(1ππ*)-LMin was identified on the pathway of the futile backward electron transfer (BET), which is stabilized by the strong H-bond interaction between the water wire and CPD. As a result, the futile BET process is endothermic by ∼18.0 kcal mol−1, which is responsible for a 2.4 ns timescale inferred experimentally for the futile BET process. Besides the unbiased interpretation for the majority of the experimental findings, the present study provides a new excited-state PCET mechanism, which leads to a significant step toward a deeper understanding of the photo-repair process of damaged-DNA by the photolyase enzyme.
Co-reporter:Zhi-Zhong Xie, Wen-Juan Liao, Jun Cao, Li-Ping Guo, Francis Verpoort, and Weihai Fang
Organometallics 2014 Volume 33(Issue 10) pp:2448-2456
Publication Date(Web):May 15, 2014
DOI:10.1021/om401092h
A DFT study on the reaction of diazoacetate with primary allyl alcohol mediated by dirhodium catalyst has been carried out in detail. Calculations indicate that the major O–H insertion product can be obtained via either a [1,3]-proton shift of the free enol or a [1,2]-proton shift of the free oxonium ylide, which are regulated by the orientation of the ester group. In the case of a [1,3]-proton shift the reaction begins with the nucleophilic attack of the alcohol at the carbenoid, generating a metal-associated oxonium ylide followed by a [1,4]-proton shift to the adjacent carbonyl oxygen atom of the ester group, resulting in a metal-associated enol. Subsequently, its decomposition liberates a free enol intermediate. The whole process requires an overall barrier of 4.2 kcal/mol and is exergonic by 6.4 kcal/mol. The [1,3]-proton shift of the enol also readily provides the final O–H insertion product, which has a barrier of 11.7 kcal/mol using a three-alcohol cluster as catalyst. For the free oxonium ylide pathway, formation of an alternative metal-associated oxonium ylide is also straightforward, having an overall barrier of 4.5 kcal/mol. In the presence of extra alcohol molecules, the decomposition of the metal-associated oxonium ylide can generate an alcohol-stabilized free oxonium ylide (endergonic by only 4.1 kcal/mol). Afterward, it undergoes a [1,2]-proton shift, resulting in the O–H insertion product, which requires an energy barrier of 4.7 kcal/mol. In comparison, the competitive [2,3]-sigmatropic rearrangement for the metal-associated oxonium ylides is not sensitive to the orientation of the ester, which has a similar activation free energy around 14.0 kcal/mol. Accordingly, it is always disfavored over the O–H insertion, which kinetically agrees well with the experimental observations, in which traces of [2,3]-sigmatropic rearrangement product were obtained for the primary allyl alcohol.
Co-reporter:Lihong Liu, Shuhua Xia, and Wei-Hai Fang
The Journal of Physical Chemistry A 2014 Volume 118(Issue 39) pp:8977-8985
Publication Date(Web):April 17, 2014
DOI:10.1021/jp5019923
In this article, structures and energies of cyclopropenone in the low-lying electronic states have been determined by the CASSCF and MS-CASPT2 calculations with different basis sets. Two minimum-energy conical intersections (CI-1 and CI-2) between S0 and S1 were obtained and their topographic characters were characterized by the SA4-CAS(10,9) calculated energy gradients and nonadiabatic coupling vectors. The AIMS method was used to carry out nonadiabatic dynamics simulation with ab initio calculation performed at the SA4-CAS(10,9) level. On the basis of time evolution of wave functions simulated here, the S1 lifetime is fitted to be 125 fs with a pure exponential decay for the S1 electronic population. The CI-1 intersection is mainly responsible for ultrafast S1→S0 nonadiabatic transition and the photoinduced decarbonylation is a sequential process, where the first C—C bond is broken in the S1 state and fission of the second C—C bond occurs in the S0 state as a result of the S1→S0 internal conversion via the CI-1 region. As a minor channel through the CI-2 region, the decarbonylation proceeds in an asynchronous concerted way. Effects of the S1 excess energies and the S1–S0 energy gap on the nonadiabatic dynamics were examined, which reveals that the S1→S0 nonadiabatic transition occurs within a small energy gap and high-energy conical intersection regions can play an important role. The present study provides new insights into mechanistic photochemistry of cyclopropenones and reveals that the AIMS dynamics simulation at a high-accuracy ab initio level is a powerful tool for exploring a mechanism of an ultrafast photochemical reaction.
Co-reporter:Cong Hou;Dr. Ya-Jun Liu;Dr. Nicolas Ferré;Dr. Wei-Hai Fang
Chemistry - A European Journal 2014 Volume 20( Issue 26) pp:7979-7986
Publication Date(Web):
DOI:10.1002/chem.201400253
Abstract
Bacterial bioluminescence (BL) has been successfully applied in water-quality monitoring and in vivo imaging. The attention of researchers has been attracted for several decades, but the mechanism of bacterial BL is still largely unknown due to the complexity of the multistep reaction process. Debates mainly focus on three key questions: How is the bioluminophore produced? What is the exact chemical form of the bioluminophore? How does the protein environment affect the light emission? Using quantum mechanics (QM), combined QM and molecular mechanics (QM/MM) and molecular dynamic (MD) calculations in gas-phase, solvent and protein environments, the entire process of bacterial BL was investigated, from flavin reduction to light emission. This investigation revealed that: 1) the chemiluminescent decomposition of flavin peroxyhemiacetal does not occur through the intramolecular chemical initiated electron exchange luminescence (CIEEL) or the “dioxirane” mechanism, as suggested in the literature. Instead, the decomposition occurs according to the charge-transfer initiated luminescence (CTIL) mechanism for the thermolysis of dioxetanone. 2) The first excited state of 4a-hydroxy-4a,5-dihydroFMN (HFOH) was affirmed to be the bioluminophore of bacterial BL. This study provides details regarding the mechanism by which bacterial BL is produced and is helpful in understanding bacterial BL in general.
Co-reporter:Juan Han, Lin Shen, Xuebo Chen and Weihai Fang
Journal of Materials Chemistry A 2013 vol. 1(Issue 27) pp:4227-4235
Publication Date(Web):02 May 2013
DOI:10.1039/C3TC30692E
A comprehensive theoretical model of electron exchange-induced energy transfer combined with the CASPT2//CASSCF theory is first applied to explore the mechanism of tunable emission for the single-dopant WOLED of FPt and the related photophysical processes. The monomer-like bluish emission is demonstrated to depend on the efficiency of direction-specific charge transfer along O1 → Pt → pyridinyl ring, while the dimer-like reddish emission from the TLC state is dominated by the electron exchange that takes place between the TMLCTx and TLC states via the ground state. The strategy of molecular design is proposed to improve the efficiency of emission for the analogous C⁁NPt(O⁁O) complex on the basis of accurate electronic structure calculations and quantitative rates of Dexter energy transfer as well as comparisons with the case of Pt-4.
Co-reporter:Dr. Ganglong Cui;Dr. Xiao-Yan Cao;Dr. Wei-Hai Fang;Dr. Michael Dolg;Dr. Walter Thiel
Angewandte Chemie 2013 Volume 125( Issue 39) pp:10471-10475
Publication Date(Web):
DOI:10.1002/ange.201305487
Co-reporter:Dr. Ganglong Cui;Dr. Xiao-Yan Cao;Dr. Wei-Hai Fang;Dr. Michael Dolg;Dr. Walter Thiel
Angewandte Chemie International Edition 2013 Volume 52( Issue 39) pp:10281-10285
Publication Date(Web):
DOI:10.1002/anie.201305487
Co-reporter:Xuebo Chen, Qiangqiang Zhang, Yanchang Xu, Weihai Fang, and David Lee Phillips
The Journal of Organic Chemistry 2013 Volume 78(Issue 11) pp:5677-5684
Publication Date(Web):May 14, 2013
DOI:10.1021/jo4008783
An unusual photochemistry of water-assisted self-photoredox of 3-(hydroxymethyl) benzophenone 1 has been investigated by CASPT2//CASSCF computations. The water-assisted self-photoredox is found to proceed via three sequential reactions: an excited-state intermolecular proton transfer (ESIPT), a photoinduced deprotonation, and a self-redox reaction. Upon photoexcitation at 243 nm, the system of 1 is taken to the Franck–Condon region of a short-distance charge transfer (SCT) state of SSCT(1ππ*) and then undergoes ESIPT with a small barrier of ∼3.4 kcal/mol producing the intermediate 2. Subsequently, the singlet–triplet crossing (STC) of STC (1ππ*/3ππ*) relays 2 by intersystem crossing to the TSCT(3ππ*) state followed by a deprotonation reaction overcoming a moderate barrier of ∼8.0 kcal/mol and finally produces the triplet biradical intermediate 3. Another moderate barrier (∼5.8 kcal/mol) in the TSCT(3ππ*) state has to be overcome so as to relax to a second singlet–triplet crossing STC(T/S0) that allows an efficient spin-forbidden decay to the ground state. The self-redox reaction aided by water molecules occurs with tiny barriers in the S0 state via two steps, protonation of the benzhydrol carbon to produce intermediate 4 and then deprotonation from the benzylic oxygen to yield the final product 3-formylbenzhydrol 5.
Co-reporter:Ming-Juan Li, Ming-Xia Liu, Yan-Ying Zhao, Ke-Mei Pei, Hui-Gang Wang, and Xuming Zheng and Wei Hai Fang
The Journal of Physical Chemistry B 2013 Volume 117(Issue 39) pp:11660-11669
Publication Date(Web):August 23, 2013
DOI:10.1021/jp403798d
The resonance Raman spectroscopic study of the excited state structural dynamics of 1,3-dimethyluracil (DMU), 5-bromo-1,3-dimethyluracil (5BrDMU), uracil, and thymine in water and acetonitrile were reported. Density functional theory calculations were carried out to help elucidate the ultraviolet electronic transitions associated with the A-, and B-band absorptions and the vibrational assignments of the resonance Raman spectra. The effect of the methylation at N1, N3 and C5 sites of pyrimidine ring on the structural dynamics of uracils in different solvents were explored on the basis of the resonance Raman intensity patterns. The relative resonance Raman intensities of DMU and 5BrDMU are computed at the B3LYP-TD level. Huge discrepancies between the experimental resonance Raman intensities and the B3LYP-TD predicted ones were observed. The underlying mechanism was briefly discussed. The decay channel through the S1(1nπ*)/S2(1ππ*) conical intersection and the S1(1nπ*)/T1(3ππ*) intersystem crossing were revealed by using the CASSCF(8,7)/6-31G(d) level of theory calculations.
Co-reporter:Ling Yue ; Ya-Jun Liu
Journal of the American Chemical Society 2012 Volume 134(Issue 28) pp:11632-11639
Publication Date(Web):June 21, 2012
DOI:10.1021/ja302979t
The peroxide decomposition that generates the excited-state carbonyl compound is the key step in most organic chemiluminescence, and chemically initiated electron exchange luminescence (CIEEL) has been widely accepted for decades as the general mechanism for this decomposition. The firefly dioxetanone, which is a peroxide, is the intermediate in firefly bioluminescence, and its decomposition is the most important step leading to the emission of visible light by a firefly. However, the firefly dioxetanone decomposition mechanism has never been explored at a reliable theoretical level, because the decomposition process includes biradical, charge-transfer (CT) and several nearly degenerate states. Herein, we have investigated the thermolysis of firefly dioxetanone in its neutral (FDOH) and anionic (FDO–) forms using second-order multiconfigurational perturbation theories in combination with the ground-state intrinsic reaction coordinate calculated via the combined hybrid functional with Coulomb attenuated exchange-correlation, and considered the solvent effect on the ground-state reaction path using the combined hybrid functional with Coulomb attenuated exchange-correlation. The calculated results indicate that the chemiluminescent decomposition of FDOH or FDO– does not take place via the CIEEL mechanism. An entropic trap was found to lead to an excited-state carbonyl compound for FDOH, and a gradually reversible CT initiated luminescence (GRCTIL) was proposed as a new mechanism for the decomposition of FDO–.
Co-reporter:Liu Yang, Weihai Fang and Yong Zhang
Chemical Communications 2012 vol. 48(Issue 32) pp:3842-3844
Publication Date(Web):27 Feb 2012
DOI:10.1039/C2CC31016C
HNO binds to many different metals in organometallic and bioinorganic chemistry. To help understand experimentally observed metal centre effects, a quantum chemical investigation was performed, revealing clear general binding trends with respect to metal centre characteristics and the electronic origin for the first time.
Co-reporter:Yue Chen ; Juan Han
Inorganic Chemistry 2012 Volume 51(Issue 9) pp:4938-4946
Publication Date(Web):April 9, 2012
DOI:10.1021/ic202097c
In the present work, photoinduced O2 evolution from the [Cp2Os–OH]+ complex in aqueous solution has been studied by the DFT, CASSCF, and CASPT2 methods. The CASPT2//CASSCF calculations predict that the S3 state is initially populated and the subsequent deprotonation of [Cp2Os–OH]+ proceeds very easily along the T1 pathway as a result of the efficient S3 → T1 intersystem crossing. It is found that the O–O bond is formed via the acid–base mechanism, which is different from the direct oxo–oxo coupling mechanism suggested in the experimental study. Formation of the O–O bond is the rate-determining step and has an activation energy and activation free energy of 81.3 and 90.4 kcal/mol, respectively. This is consistent with the low quantum yield observed for generating molecular oxygen upon irradiation at 350 nm (∼ 82 kcal/mol). The O2 release from an intermediate complex has to overcome a small barrier on the triplet pathway first and then pass through the triplet–singlet intersection, generating the O2 molecules in either the lowest singlet or triplet state. The formed 3O2 molecule can be converted into the 1O2 molecule by the heavy atom effect in the Os complexes, which is probably the reason only the 1O2 molecule was detected experimentally.
Co-reporter:Xin Zhang, Xiaojia Guo, Yue Chen, Yanhui Tang, Ming Lei and Weihai Fang
Physical Chemistry Chemical Physics 2012 vol. 14(Issue 17) pp:6003-6012
Publication Date(Web):06 Mar 2012
DOI:10.1039/C2CP23936A
In this paper, the mechanism of ketone hydrogenation catalyzed by five Ru bifunctional catalysts with different structural frameworks was studied in detail using density functional theory (DFT). This mechanism contains hydrogen transfer, dehydrogenation of alcohol, and dihydrogen activation fundamental reactions. The involvement of alcohol is also discussed and found with different activities in hydrogen transfer, dehydrogenation and dihydrogen activation steps in five systems. Our calculated results indicate that the weak Ru–H bond, stronger basicity of hydride and stronger X–H acidity will decrease the barrier of the HT step, and that the polar micro-environment of dihydrogen coordinating with Ru catalysts and short hydrogen transfer distance would be able to facilitate the heterolytic splitting of dihydrogen in the dihydrogen activation step.
Co-reporter:Shi-Lu Chen, Ze-Sheng Li, Wei-Hai Fang
Journal of Inorganic Biochemistry 2012 Volume 111() pp:70-79
Publication Date(Web):June 2012
DOI:10.1016/j.jinorgbio.2012.02.029
Astacin, acting as the prototype of astacin family and of the metzincin superfamily, is a mononuclear zinc enzyme that catalyzes the hydrolysis of polypeptides and proteins. In the present article, the reaction mechanism of astacin has been investigated using density functional theory (DFT) method. Using a model of the active site constructed on the basis of the X-ray crystal structure of astacin, the potential energy surface for catalytic reaction has been mapped and the transition states and intermediates along the reaction pathway are characterized. The calculations give general support to the previously proposed mechanism by experiments, which mainly involve nucleophilic attack on carbonyl group of substrate and C―N bond cleavage, and reveal more detailed mechanistic features. The Glu93 functions as a crucial general base to activate the zinc-bound water and the resulting zinc-bound hydroxide acts as the real nucleophile. It is demonstrated that there exists a “reactant region”, where the interconversion between zinc-bound water and zinc-bound hydroxide occurs rapidly. The rate-limiting step is predicted to be the nucleophilic attack, which leads to an anionic gem-diolate tetrahedral intermediate. During the catalysis, zinc ion provides main catalytic power by stabilizing the developing charge of tetrahedral intermediate, while the Tyr149 residue also partially contributes to the catalysis by stabilizing the anionic intermediate. In addition, it is shown that the Cys64 plays roles in assisting in binding and orientating the substrate via electrostatic interaction.The peptide hydrolysis catalyzed by astacin has been investigated using density functional theory with the B3LYP functional. The calculations give general support to the previously proposed mechanism which mainly involves nucleophilic attack on carbonyl group of substrate and C―N bond cleavage, and reveal more detailed mechanistic features.Highlights► The rate-limiting step is nucleophilic attack. ► Proton transfer to nitrogen should occur prior to C―N bond cleavage. ► Zinc ion provides main catalytic power by stabilizing the developing charge. ► Tyr149 partially contributes to the catalysis by stabilizing anionic intermediate. ► Cys64 plays roles in binding and orientating substrate via electrostatic interaction.
Co-reporter:Qiu Fang;LiNa Ding;WeiHai Fang
Science China Chemistry 2012 Volume 55( Issue 10) pp:2089-2094
Publication Date(Web):2012 October
DOI:10.1007/s11426-012-4735-2
In this work, we report the first CASPT2//CASSCF study of the mechanism of the photodecarboxylation of N-phthaloylglycine. The charge transfer excited state SCT(1ππ*) is initially populated upon irradiation at 266 nm. As a result of a fast internal conversion to the lowest excited singlet state SCT-N(1ππ*), this state becomes a favorable precursor state for proton transfer, which triggers decarboxylation. Actually, the excited state intramolecular proton transfer (ESIPT) and decarboxylation processes proceed in an asynchronous concerted way. The ESIPT process is accomplished in the SCT-N(1ππ*) state, but the CO2 molecule is finally formed in the ground state via the SCT/S0 conical intersection. Azomethine ylide is formed in the ground state as a complex with CO2. A barrier of ∼15 kcal/mol indicates that azomethine ylide is stable in the ground state, which is consistent with the experimental findings. This work provides mechanistic details about the formation of azomethine ylide by photoreaction of N-phthaloylglycine.
Co-reporter:Shu-Feng Chen, Ya-Jun Liu, Isabelle Navizet, Nicolas Ferré, Wei-Hai Fang, and Roland Lindh
Journal of Chemical Theory and Computation 2011 Volume 7(Issue 3) pp:798-803
Publication Date(Web):February 16, 2011
DOI:10.1021/ct200045q
This is a systematic theoretical investigation on all the possible light emitters of firefly using a multireference method. Six chemical forms of oxyluciferin (OxyLH2) molecules/anions were studied by a multistate complete active space second-order perturbation (MS-CASPT2) method in vacuum and dimethyl sulfoxide. The calculated results and subsequent analysis excluded enol-OxyLH2, keto-OxyLH2, and enolate-OxyLH− as possible light emitters. The remaining three candidates, phenolate-enol-OxyLH−, phenolate-keto-OxyLH−, and OxyL2−, were further investigated in protein by a MS-CASPT2/molecular mechanics (MM) study to explain the natural bioluminescence of firefly. By comparison of the MS-CASPT2/MM calculated results of phenolate-enol-OxyLH−, phenolate-keto-OxyLH−, and OxyL2− with the experimental observation and detailed analysis, we concluded that the direct decomposition excited-state product of firefly dioxetanone in vivo and the only light emitter of firefly in natural bioluminescence is the first singlet excited state (S1) of phenolate-keto-OxyLH−.
Co-reporter:Zhenzhen Lin, Yue Chen, Xiaohong Li and Weihai Fang
Analyst 2011 vol. 136(Issue 11) pp:2367-2372
Publication Date(Web):13 Apr 2011
DOI:10.1039/C1AN15080D
Conformational switch from hairpin DNA to G-quadruplex induced by Pb2+ is studied by electrochemical impedance spectroscopy (EIS) in the presence of [Fe(CN)6]3−/4− as the redox probe. In the presence of Pb2+, the G-rich hairpin DNA opens the stem-loop and forms G-quadruplex structure, which gives rise to a sharp increase in the charge-transfer resistance (RCT) of the film reflected by the EIS. This structural change is also confirmed by circular dichroism (CD) measurements and UV-Vis spectroscopic analysis and calculated by density functional theory (DFT). On the basis of this, we develop a label-free electrochemical DNA biosensor for Pb2+ detection. With increasing concentrations of Pb2+, the differences in the charge-transfer resistance RCT before and after the Pb2+ incubation is linearly dependent on the logarithm of Pb2+ concentration within a range from 50 μM to 0.5 nM. The biosensor also exhibits good selectivity for Pb2+ over other metal ions. This is a simple and label-free electrochemical method for Pb2+ detection making use of the G-quadruplex.
Co-reporter:Bingbing Zhang, Jia Xu, Yiming Li, Weihong Du, Weihai Fang
Journal of Inorganic Biochemistry 2011 Volume 105(Issue 7) pp:949-956
Publication Date(Web):July 2011
DOI:10.1016/j.jinorgbio.2011.03.018
Cytoglobin (Cgb), the fourth member of the vertebrate heme globin family, is widely expressed in mammalian tissues, and reversibly binds to CO, O2 and other small ligands. The diverse functions of Cgb may include ligand transport, redox reactions and enzymatic catalysis. Recent studies indicate that Cgb is a potential gene medicine for fibrosis and cancer therapy. In the present work, molecular dynamics (MD) simulations were performed to investigate the functionally related structural properties and dynamic characteristics in carboxy and deoxy human Cgb. The simulation results showed that the loop regions and internal cavities were significantly affected through the binding of an exogenous ligand. The AB, GH and EF loops were found to undergo significant rearrangement and this led to distinct cavity adjustments in Xe2, Xe4 and the distal pocket. In addition, solvent accessibility and torsion angle analyses revealed an interactive distal network comprised of His81(E7), Leu46(B10) and Arg84(E10). The MD study of carboxy and deoxy human Cgb revealed that CO-ligated Cgb modulates the protein conformation primarily by loop and cavity rearrangements rather than the heme sliding mechanism found in neuroglobin (Ngb). The significant differences between Cgb and Ngb in the loop and cavity properties are presumably linked to their various biological functions.MD simulations reveal the functionally related structural dynamic characteristics of carboxy and deoxy human cytoglobin in solution.
Co-reporter:Juan Han; XueBo Chen;Lin Shen;Yue Chen; WeiHai Fang; Haobin Wang
Chemistry - A European Journal 2011 Volume 17( Issue 50) pp:13971-13977
Publication Date(Web):
DOI:10.1002/chem.201102702
Co-reporter:Dr. Ganglong Cui ; Dr. Weihai Fang
ChemPhysChem 2011 Volume 12( Issue 7) pp:1351-1357
Publication Date(Web):
DOI:10.1002/cphc.201000968
Abstract
Herein we report a theoretical study on mechanistic photodissociation of glycolaldehyde, HOCH2CHO. Equilibrium structures, transition states, and intersection structures for the α-CC and -CH bond fissions and the β-CO bond fission in the excited states are determined by the complete active space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations are refined by performing single-point calculations using the multi-state multi-reference CASSCF second order perturbation (MS-MR-CASPT2) method. With a low excitation energy of 280–340 nm, the T1 α-CC and β-CO bond fissions following intersystem crossing from the S1 state are the predominant and comparable channels, whereas the α-CH bond fissions both in the S1 and in the T1 states are nearly prohibited due to the relevant high barriers. The rate constants for the T1 α-CC and β-CO bond fissions are also calculated by RRKM theory. Furthermore, the S0 reactions can occur as a consequence of intersystem crossing via T1/S0 intersection points resulting from the T1 CC and CO bond cleavages. This photodissociation mechanism is consistent with recent experimental studies.
Co-reporter:Dr. Yue-jie Ai;Guangjun Tian;Dr. Rong-zhen Liao;Qiong Zhang; Dr. Wei-hai Fang; Yi Luo
ChemPhysChem 2011 Volume 12( Issue 16) pp:2899-2902
Publication Date(Web):
DOI:10.1002/cphc.201100663
Co-reporter:Ganglong Cui and Weihai Fang
The Journal of Physical Chemistry A 2011 Volume 115(Issue 9) pp:1547-1555
Publication Date(Web):February 14, 2011
DOI:10.1021/jp110632g
Cyclopropanone exhibits an intriguing phenomenon that the fluorescence from the S1 state disappears below 365 nm. This is ascribed to the ultrafast S1 → S0 internal conversion process via conical intersection, which deprives opportunity of the fluorescence emission. In this work, we have used ab initio based surface hopping dynamics method to study vibrational-mode-dependent S1 → S0 internal conversion of cyclopropanone. A new conical intersection between the S1 and S0 states is determined by the state-averaged CASSCF/cc-pVDZ calculations, which is confirmed to play a critical role in the ultrafast S1 → S0 internal conversion by the nonadiabatic dynamics simulations. It is found that the internal conversion occurs more efficiently when the initial kinetic energies are distributed in the four vibrational modes related to the C═O group, especially in the C−O stretching and the O−C−C−C out-of-plane torsional modes. Meanwhile, the S1 lifetime and the time scale of the S1 → S0 internal conversion are estimated by the ab initio based dynamics simulations, which is consistent with the ultrafast S1 → S0 internal conversion and provides further evidence that the ultrafast internal conversion is responsible for the fluorescence disappearance of cyclopropanone.
Co-reporter:Lihong Liu, Shuai Yuan, and Wei-Hai Fang and Yong Zhang
The Journal of Physical Chemistry A 2011 Volume 115(Issue 35) pp:10027-10034
Publication Date(Web):July 25, 2011
DOI:10.1021/jp203704x
Mechanism of phototriggered isomerization of azobenzene and its derivatives is of broad interest. In this paper, the S0 and S1 potential energy surfaces of the ethylene-bridged azobenzene (1) that was recently reported to have highly efficient photoisomerization were determined by ab initio electronic structure calculations at different levels and further investigated by a semiclassical dynamics simulation. Unlike azobenzene, the cis isomer of 1 was found to be more stable than the trans isomer, consistent with the experimental observation. The thermal isomerization between cis and trans isomers proceeds via an inversion mechanism with a high barrier. Interestingly, only one minimum-energy conical intersection was determined between the S0 and S1 states (CI) for both cis → trans and trans → cis photoisomerization processes and confirmed to act as the S1 → S0 decay funnel. The S1 state lifetime is ∼30 fs for the trans isomer, while that for the cis isomer is much longer, due to a redistribution of the initial excitation energies. The S1 relaxation dynamics investigated here provides a good account for the higher efficiency observed experimentally for the trans → cis photoisomerization than the reverse process. Once the system decays to the S0 state via CI, formation of the trans product occurs as the downhill motion on the S0 surface, while formation of the cis isomer needs to overcome small barriers on the pathways of the azo-moiety isomerization and rotation of the phenyl ring. These features support the larger experimental quantum yield for the cis → trans photoisomerization than the trans → cis process.
Co-reporter:Ganglong Cui, Zhigang Sun, and Weihai Fang
The Journal of Physical Chemistry A 2011 Volume 115(Issue 36) pp:10146-10153
Publication Date(Web):August 8, 2011
DOI:10.1021/jp2053025
One of the fundamental photoreactions for ketones is Norrish type I reaction, which has been extensively studied both experimentally and theoretically. Its α bond-cleavage mechanisms are usually explained in an adiabatic picture based on the involved excited-state potential energy surfaces, but scarcely investigated in terms of a nonadiabatic picture. In this work, the S1 α bond-cleavage reactions of CH3OC(O)Cl have been investigated by using the CASSCF and MRCI-SD calculations, and the ab initio based time-dependent quantum wavepacket simulation. The numerical results indicate that the photoinduced dissociation dynamics of CH3OC(O)Cl could exhibit strong nonadiabatic bond-fission characteristics for the S1 α C–Cl bond cleavage, while the dynamics of the S1 α C–O bond cleavage is mainly of adiabatic characteristics. This nonadiabatic mechanism for Norrish type I reaction of CH3OC(O)Cl is uncovered for the first time. The quantum wavepacket dynamics, based on the reduced-dimensional coupled potential energy surfaces, to some extent illustrates the significance of the nonadiabatic effect in the transition-state region on the dynamics of Norrish type I reaction.
Co-reporter:Ganglong Cui and Weihai Fang
The Journal of Physical Chemistry A 2011 Volume 115(Issue 42) pp:11544-11550
Publication Date(Web):September 19, 2011
DOI:10.1021/jp206893n
The ultrafast S1(1ππ*) → S0 deactivation process of thiophene in the gas phase has been simulated with the complete active space self-consistent field (CASSCF) based fewest switch surface hopping method. It was found that most of the calculated trajectories (∼80%) decay to the ground state (S0) with an averaged time constant of 65 ± 5 fs. This is in good agreement with the experimental value of about 80 fs. Two conical intersections were determined to be responsible for the ultrafast S1(1ππ*) → S0 internal conversion process. After thiophene is excited to the S1(1ππ*) state in the Franck–Condon region, it quickly relaxes to the minimum of the S1(1ππ*) state, then overcomes a small barrier near the conical intersection (CI(1ππ*/1πσ*)), and eventually arrives at the minimum of one C–S bond fission (S1(1πσ*)). In the vicinity of this minimum, the conical intersection (CI(1πσ*/S0)) funnels the electron population to the ground state (S0), completing the ultrafast S1(1ππ*) → S0 internal conversion process. This decay mechanism matches well with previous experimental and theoretical studies.
Co-reporter:Shuai Yuan, Wenying Zhang, Lihong Liu, Yusheng Dou, Weihai Fang, and Glenn V. Lo
The Journal of Physical Chemistry A 2011 Volume 115(Issue 46) pp:13291-13297
Publication Date(Web):October 11, 2011
DOI:10.1021/jp207550a
Semiclassical dynamics simulation is used to study dimerization of two stacked cytosine molecules following excitation by ultrashort laser pulses (25 fs fwhm, Gaussian, 4.1 eV photon energy). The initial excited state was found to form an ultrashort exciton state, which eventually leads to the formation of an excimer state by charge transfer. When the interbase distance, defined as an average value of C5–C5′ and C6–C6′, becomes less than 3 Å, charge recombination occurs due to strong intermolecular interaction, eventually leading to an avoided crossing within 20–30 fs. Geometries at the avoided crossing, with average intermolecular distance of about 2.1 Å, are in accord with CASSCF/CASPT2 calculations. Results indicate that the C2–N1–C6–C5 and C2′–N1′–C6′–C5′ dihedral angles' bending vibrations play a significant role in the vibronic coupling between the HOMO and LUMO, which leads to a nonadiabatic transition to the electronic ground state.
Co-reporter:Xuebo Chen, Chensheng Ma, David Lee Phillips, and Wei-Hai Fang
Organic Letters 2010 Volume 12(Issue 22) pp:5108-5111
Publication Date(Web):October 14, 2010
DOI:10.1021/ol102208s
A downhill ladder reaction pathway for the bichromophoric phototrigger 3′,5′-dimethoxybenzoin acetate was mapped using ab initio multiconfigurational methods. These computational results explicitly describe a case of fast photocyclization that overcomes two small barriers (<5.0 kcal/mol) and undergoes three internal conversions (ICs) via efficient nonadiabatic relay of conical intersections among long and short distance charge transfer excited states as well as the nπ* excited and ground states. This novel reaction pathway is a consequence of the interaction of the two chromophores.
Co-reporter:Guofu Zi, Furen Zhang, Li Xiang, Yue Chen, Weihai Fang and Haibin Song
Dalton Transactions 2010 vol. 39(Issue 17) pp:4048-4061
Publication Date(Web):23 Feb 2010
DOI:10.1039/B923457H
A new series of titanium(IV) and zirconium(IV) amides have been prepared from the reaction between M(NMe2)4 (M = Ti, Zr) and chiral ligands, (R)-2,2′-bis(p-toluenesulfonylamino)-1,1′-binaphthyl (1H2), (R)-2,2′-bis(diphenylphosphinoylamino)-1,1′-binaphthyl (2H2), (R)-2,2′-bis(mesitoylamino)-1,1′-binaphthyl (3H2), (R)-5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(pyrrol-2-ylmethyleneamino)-1,1′-binaphthyl (4H2), (R)-5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(mesitoylamino)-1,1′-binaphthyl (5H2), and (R)-5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(mesitylenesulfonylamino)-1,1′-binaphthyl (6H2), which are derived from (R)-2,2′-diamino-1,1′-binaphthyl. Reaction of M(NMe2)4 with 1 equiv of arylsulfonylamides 1H2 and 6H2, diphenylphosphoramide 2H2, mesitoylamides 3H2 and 5H2, or Schiff base ligand 4H2 at room temperature gives, after recrystallization from a benzene, toluene or n-hexane solution, the chiral titanium amides (1)Ti(NMe2)2·3C6H6 (7·3C6H6), (4)Ti(NMe2)2 (11), (5)Ti(NMe2)2 (13) and (6)Ti(NMe2)2 (15), and zirconium amides (1)Zr(NMe2)2 (8), (2)Zr(NMe2)2 (9), (3)Zr(NMe2)2 (10), (4)Zr(NMe2)2 (12), (5)Zr(NMe2)2 (14) and (6)Zr(NMe2)2·C7H8 (16·C7H8) respectively, in good yields. These amides are stable below 90 °C in toluene solution, but they degrade via ligand redistribution at a higher temperature. For example, treatment of (1)Zr(NMe2)2 (8) or (5)Zr(NMe2)2 (14) in refluxing toluene for three days leads to the isolation of the complexes (1)2Zr·C7H8 (17·C7H8) and (5)2Zr·3C7H8 (18·3C7H8) respectively, in moderate yields. These new compounds have been characterized by various spectroscopic techniques, and elemental analyses. The solid-state structures of compounds 7–9, 11–13, and 15–18 have further been confirmed by X-ray diffraction analyses. The titanium amide 13 and all the zirconium amides are active catalysts for the asymmetric hydroamination/cyclization of aminoalkenes, affording cyclic amines in moderate to excellent yields with moderate to excellent ee values (up to 93%). Theoretical studies reveal the interaction between the carbon chain of the substrate and the sterically demanding ligand groups plays a key role in the stereodirection of the enantioselection during the ZrN bond approaches to the CC bond.
Co-reporter:Yue Chen and Wei-Hai Fang
The Journal of Physical Chemistry A 2010 Volume 114(Issue 37) pp:10334-10338
Publication Date(Web):August 30, 2010
DOI:10.1021/jp1065105
The density functional theory (DFT) method was used to explore the light-induced O2 formation from H2O promoted by Ru(II) PNN complex in the present work. The elimination of H2O2 was found to be highly endothermic, which is not in competition with the H2O elimination and hydrogen transfer. The calculated results reported here do not support the mechanism proposed in a recent experiment, where H2O2 was suggested as an important intermediate for formation of O2. We proposed a new mechanism for formation of the triplet O2 molecule, which contains the two steps of the concerted hydrogen transfer and dehydration. The light-induced O2 evolution from water promoted by the Ru(II) complex was found to be a nonadiabatic process. The O−O bond is formed along the T1 pathway as a result of the efficient S1 → T1 intersystem crossing. All experimental findings on the light-induced O2 evolution can be explained by the mechanism proposed in the present work.
Co-reporter:Qiu Fang, Juan Han, Jieling Jiang, Xuebo Chen and Weihai Fang
The Journal of Physical Chemistry A 2010 Volume 114(Issue 13) pp:4601-4608
Publication Date(Web):March 17, 2010
DOI:10.1021/jp911455r
In the present work, we report a quantitative understanding on how to generate hydroxyl radicals from NO2 and H2O in the troposphere upon photoexcitation at 410 nm by using multiconfigurational perturbation theory and density functional theory. The conical intersections dominate the nonadiabatic relaxation processes after NO2 irradiated at ∼410 nm in the troposphere and further control the generation of OH radical by means of hydrogen abstraction. In agreement with two-component fluorescence observed by laser techniques, there are two different photophysical relaxation channels along decreasing and increasing O−N−O angle of NO2. In the former case, the conical intersection between B̃2B1 and Ã2B2 (CI (2B2/2B1) first funnels NO2 out of the Franck−Condon region of B̃2B1 and relaxes to the Ã2B2 surface. Following the primary relaxation, the conical intersection between Ã2B2 and X̃2A1 (CI(2B2/2A1)) drives NO2 to decay into highly vibrationally excited X̃2A1 state that is more than 20 000 cm−1 above zeroth-order |n1,n2,n3 = 0⟩ vibrational level. In the latter case, increasing the O−N−O angle leads NO2 to relax to a minimum of B̃2B1 with a linear O−N−O arrangement. This minimum point is also funnel region between B̃2B1 and X̃2A1 (CI(2B1/2A1)) and leads NO2 to relax into a highly vibrationally excited X̃2A1 state. The high energetic level of vibrationally excited state has enough energy to overcome the barrier of hydrogen abstraction (40−50 kcal/mol) from water vapor, producing OH (2Π3/2) radicals. The collision between NO2 and H2O molecules not only is a precondition of hydrogen abstraction but induces the faster internal conversion (CIIC) via conical intersections. The faster internal conversion favors more energy transfer from electronically excited states into highly vibrationally excited X̃2A1 states. The collision (i.e., the heat motion of molecules) functions as the trigger and accelerator in the generation of OH radicals from NO2 and H2O in the troposphere.
Co-reporter:Feng Zhang, Yue-Jie Ai, Yi Luo and Wei-Hai Fang
The Journal of Physical Chemistry A 2010 Volume 114(Issue 4) pp:1980-1984
Publication Date(Web):January 5, 2010
DOI:10.1021/jp909887d
In the present work, density functional theory and canonical nonadiabatic Monte Carlo transition state theory have been used to investigate the histidine dissociation process from hexacoordinate heme in Ngb protein. The potential energy surfaces (PES) of the lowest singlet, triplet, and quintet states are calculated by stepwise optimization along with the histidine dissociation pathway. Based on the calculated two-dimensional PES, the histidine dissociation rates for the spin-forbidden processes via singlet to triplet and singlet to quintet transitions have been calculated by the nonadiabatic Monte Carlo transition state theory in canonical ensemble. The present study provides a quantitative description on spin-forbidden histidine dissociation processes.
Co-reporter:Xuebo Chen and Weihai Fang
The Journal of Physical Chemistry A 2010 Volume 114(Issue 30) pp:8017-8017
Publication Date(Web):July 13, 2010
DOI:10.1021/jp1048937
Co-reporter:Xuebo Chen, Lianghui Gao, Weihai Fang and David Lee Phillips
The Journal of Physical Chemistry B 2010 Volume 114(Issue 15) pp:5206-5214
Publication Date(Web):March 29, 2010
DOI:10.1021/jp1003616
We report the photoinduced peptide bond (C−N) of an amide unit and S−S bond fission mechanisms of the cyclic tetrapeptide [cyclo(Boc-Cys-Pro-Aib-Cys-OMe)] in methanol solvent by using high-level CASSCF/CASPT2/Amber quantum mechanical/molecular mechanical (QM/MM) calculations. The subsequent energy transport and unfolding−refolding events are characterized by using a semiempirical QM/MM molecular dynamics (MD) simulation methodology that is developed in the present work. In the case of high-energy excitation with <193 nm light, the tetrapeptide molecule in the 1nπ* surface overcomes two barriers with ∼10.0 kcal/mol, respectively, and uses energy consumption for breaking the hydrogen bond as well as the N−C bond in the amide unit, ultimately leading to the ground state via a conical intersection of CI (SNP/S0) by structural changes of an increased N−C distance and a O−C−C angle in the amide unit (a two-dimensional model of the reaction coordinates). Following this point, relaxation to a hot molecule with its original structure in the ground state is the predominant decay channel. A large amount of heat (∼110.0 kcal/mol) is initially accumulated in the region of the targeted point of the photoexcitation, and more than 60% of the heat is rapidly dissipated into the solvent on the femtosecond time scale. The relatively slower propagation of heat along the peptide backbone reaches a phase of equilibration within 3 ps. A 300 nm photon of light initiates the relaxation along the repulsive Sσσ(1σσ*) state and this decays to the CI (Sσσ/S0) in concomitance with the separation of the disulfide bond. Once cysteinyl radicals are generated, the polar solvent of methanol molecules rapidly diffuses around the radicals, forming a solvent cage and reducing the possibility of close contact in a physical sense. The fast unfolding−refolding event is triggered by S−S bond fission and powered by dramatic thermal motion of the methanol solvent that benefits from heat dissipation. The β-turn opening (unfolding) can be achieved in about 120 ps without the inclusion of the time associated with the photochemical steps and eventually relaxes to a 310-helix structural architecture (refolding) within 200 ps.
Co-reporter:Yue-Jie Ai, Feng Zhang, Shu-Feng Chen, Yi Luo and Wei-Hai Fang
The Journal of Physical Chemistry Letters 2010 Volume 1(Issue 4) pp:743-747
Publication Date(Web):January 29, 2010
DOI:10.1021/jz900434z
The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this Letter that the often used model system, a lumiflavin (7,8-dimethy-10-methylisoalloxazine), cannot correctly describe geometrical and electronic structures of FADH− in DNA photolyase. The intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is found to play a significant role in controlling photochemical properties of FADH− in DNA photolyase.Keywords (keywords): excited states; flavin; intramolecular hydrogen bonding;
Co-reporter:Yue-Jie Ai, Rong-zhen Liao, Shu-feng Chen, Yi Luo, and Wei-Hai Fang
The Journal of Physical Chemistry B 2010 Volume 114(Issue 44) pp:14096-14102
Publication Date(Web):October 20, 2010
DOI:10.1021/jp107873w
The (6−4) photoproduct ((6−4) PP) is one of the main lesions in UV-induced DNA damage. The (6−4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6−4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (CI) points play a crucial role in the photoisomerization reaction between the (6−4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S2 (1ππ*) and the S0 states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the “dark” excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
Co-reporter:Isabelle Navizet ; Ya-Jun Liu ; Nicolas Ferré ; Hong-Yan Xiao ; Wei-Hai Fang ;Roland Lindh
Journal of the American Chemical Society 2009 Volume 132(Issue 2) pp:706-712
Publication Date(Web):December 16, 2009
DOI:10.1021/ja908051h
This is the first report on a multiconfigurational reference second-order perturbation theory−molecular mechanics study of the color modulation of the observed bioluminescence of the oxyluciferin−luciferase complex of the Japanese genji-botaru firefly using structures according to recent X-ray data. Our theoretical results do not support the experimentally deduced conclusion that the color modulation of the emitted light primarily depends on the size of the compact luciferase protein cavity embedding the excited oxyluciferin molecule. Rather, we find, in agreement with recent experimental observations, that the wavelength of the emitted light depends on the polarity of the microenvironment at the phenol/phenolate terminal of the benzothiazole fragment in oxyluciferin.
Co-reporter:Lina Ding, Xuebo Chen and Wei-Hai Fang
Organic Letters 2009 Volume 11(Issue 7) pp:1495-1498
Publication Date(Web):March 2, 2009
DOI:10.1021/ol9001043
Photodecarboxylation was found to be an ultrafast process for o-acetylphenylacetic acid, which is triggered by excited-state intramolecular proton transfer. The reaction starts from the charge-transfer ππ* singlet state and passes through the conical intersection to the ground state. Subsequent electron transfer and proton transfer in the ground state lead to formation of the final products. This represents a completely new mechanism of photoinduced decarboxylation for various arylcarboxylic acids.
Co-reporter:Shi-Lu Chen, Wei-Hai Fang, Fahmi Himo
Journal of Inorganic Biochemistry 2009 Volume 103(Issue 2) pp:274-281
Publication Date(Web):February 2009
DOI:10.1016/j.jinorgbio.2008.10.016
The glyoxalase system catalyzes the conversion of toxic methylglyoxal to nontoxic d-lactic acid using glutathione (GSH) as a coenzyme. Glyoxalase II (GlxII) is a binuclear Zn enzyme that catalyzes the second step of this conversion, namely the hydrolysis of S-d-lactoylglutathione, which is the product of the Glyoxalase I (GlxI) reaction. In this paper we use density functional theory method to investigate the reaction mechanism of GlxII. A model of the active site is constructed on the basis of the X-ray crystal structure of the native enzyme. Stationary points along the reaction pathway are optimized and the potential energy surface for the reaction is calculated. The calculations give strong support to the previously proposed mechanism. It is found that the bridging hydroxide is capable of performing nucleophilic attack at the substrate carbonyl to form a tetrahedral intermediate. This step is followed by a proton transfer from the bridging oxygen to Asp58 and finally C–S bond cleavage. The roles of the two zinc ions in the reaction mechanism are analyzed. Zn2 is found to stabilize the charge of tetrahedral intermediate thereby lowering the barrier for the nucleophilic attack, while Zn1 stabilizes the charge of the thiolate product, thereby facilitating the C–S bond cleavage. Finally, the energies involved in the product release and active-site regeneration are estimated and a new possible mechanism is suggested.
Co-reporter:Feng Zhang;WeiHai Fang;Yi Luo;RuoZhuang Liu
Science China Chemistry 2009 Volume 52( Issue 11) pp:
Publication Date(Web):2009 November
DOI:10.1007/s11426-009-0259-9
A general formula for the multi-dimensional Monte Carlo microcanonical nonadiabatic rate constant expressed in configuration space is applied to calculate the rate of intersystem crossing (ISC) between the ground (S0) and first excited triplet (T1) states for isocyanic acid. One-, two- and three-dimensional potential energy surfaces are constructed by coupled-cluster single-double CCSD calculations, which are used for Monte Carlo sampling. The calculated S0→T1 ISC rate is in good agreement with experimental findings, which gives us a reason to believe that the multi-dimensional Monte Carlo microcanonical nonadiabatic rate theory is a very effective method for calculating nonadiabatic transition rate of a polyatomic molecule.
Co-reporter:Yue Chen, Yanhui Tang, Shubin Liu, Ming Lei and Weihai Fang
Organometallics 2009 Volume 28(Issue 7) pp:2078-2084
Publication Date(Web):March 18, 2009
DOI:10.1021/om8012212
Density functional theory calculations have been performed to study the hydrogenation of ketones catalyzed by a η6-arene ruthenium(II) complex in an acidic conditions. Six possible dihydrogen activation (DA) pathways were investigated in this work. The direct DA (path 1) and alcohol-assisted DA (path 2), which will occur in basic/neutral conditions, have higher energy barriers, 19.9 and 18.7 kcal/mol, respectively. If an acid participates in DA in the other three paths (paths 4, 5, and 6), the barrier will substantially decrease to about 3.7, 7.1, and 7.8 kcal/mol, respectively. Compared with paths 1 and 2, the acid-assisted pathways are more favorable. In path 1 and path 2, molecular hydrogen is unable to coordinate with Ru to form a stable η2-H2 ruthenium(II) complex, leading to the increase of the free energy barrier of DA. On the contrary, dihydrogen forms a stable η2-H2 ruthenium(II) complex with Ru in paths 4, 5, and 6. These results indicate that the coordination of dihydrogen with Ru plays an important role in the conversion of H2-hydrogenation in acidic conditions.
Co-reporter:Wei-Hai Fang
Accounts of Chemical Research 2008 Volume 41(Issue 3) pp:452
Publication Date(Web):February 6, 2008
DOI:10.1021/ar700205f
Mechanistic photodissociation of a polyatomic molecule has long been regarded as an intellectually challenging area of chemical physics, the results of which are relevant to atmospheric chemistry, biological systems, and many application fields. Carbonyl compounds play a unique role in the development of our understanding of the spectroscopy, photochemistry, and photophysics of polyatomic molecules and their photodissociation has been the subject of numerous studies over many decades. Upon irradiation, a molecule can undergo internal conversion (IC) and intersystem crossing (ISC) processes, besides photochemical and other photophysical processes. Transient intermediates formed in the IC and ISC radiationless processes, which are termed “dark”, are not amenable to detection by conventional light absorption or emission. However, these dark intermediates play critical roles in IC and ISC processes and thus are essential to understanding mechanistic photochemistry of a polyatomic molecule. We have applied the multiconfiguration complete active space self-consistent field (CASSCF) method to determine the dark transient structures involved in radiationless processes for acetophenone and the related aromatic carbonyl compounds. The electronic and geometric structures predicted for the dark states are in a good agreement with those determined by ultrafast electron diffraction experiments. Intersection structure of different electronic states provides a very efficient “funnel” for the IC or ISC process. However, experimental determination of the intersection structure involved in radiationless transitions of a polyatomic molecule is impossible at present. We have discovered a minimum energy crossing point among the three potential energy surfaces (S1, T1, and T2) that appears to be common to a wide variety of aromatic carbonyl compounds with a constant structure. This new type of crossing point holds the key to understanding much about radiationless processes after photoexcitation of aromatic carbonyl compounds. The importance of ab initio determination of transient structures in the photodissociation dynamics has been demonstrated for the case of the aromatic carbonyl compounds. In addition, the detailed knowledge of mechanistic photochemistry for aromatic carbonyl compounds forms the basis for further investigating photodissociation dynamics of a polyatomic molecule.
Co-reporter:Juan Li, Yue-Jie Ai, Zhi-Zhong Xie and Wei-Hai Fang
The Journal of Physical Chemistry B 2008 Volume 112(Issue 29) pp:8715-8723
Publication Date(Web):June 26, 2008
DOI:10.1021/jp711919f
In the present work, density functional theory (DFT) has been used to investigate CO binding to the hexacoordinated heme in neuroglobin (Ngb) protein. Structural relaxation of the selected model system in the protein environment has been fully included by the alternative quantum and molecular mechanical optimizations. The polarized continuum model (PCM) was used to simulate interaction between the model system and the protein environment. The CO binding could take place in a concerted way and a barrier of 17.9 kcal mol−1 was predicted on the concerted singlet pathway, which is not favorable in energy. The adiabatically sequential pathway requires an energy of 14.5 kcal mol−1 for formation of the singlet intermediate. There exist two nonadiabatic sequential pathways for the CO binding, which involves the triplet and quintet states of intermediate. Both the singlet/triplet and singlet/quintet intersections play an important role in nonadiabatic sequential processes, which enhance the probability that the processes occur. The nonadiabatic processes that involve the triplet and quintet states of intermediate are the most probable pathways for the CO binding to the hexacoordinated heme in Ngb to form the product complex.
Co-reporter:Weihong Du, Ling Wang, Juan Li, Baohuai Wang, Zhifen Li, Weihai Fang
Thermochimica Acta 2007 Volume 452(Issue 1) pp:31-35
Publication Date(Web):1 January 2007
DOI:10.1016/j.tca.2006.10.011
The present work carried out a study on the interactions between Actinomycin D (ActD) and some single-stranded DNA oligomers, which contain double GTC triplets separated by TTT sequence. The interactions of drugs with DNA oligomers were investigated by UV, circular dichroism (CD) spectroscopy and isothermal titration calorimetry (ITC). The results indicate that ActD binds to the single stranded DNA oligomers in the fold back binding model as supported by added A/T base at DNA strand terminal which facilitates the formation of hairpin. The apparent binding constant Kb, the apparent binding molar enthalpy ΔH0 and other thermodynamic data were obtained. The binding affinities are sequence dependent and related to the length of DNA strand. And the higher molar binding enthalpy indicates that the binding process is enthalpy driven.
Co-reporter:Jun Cao;Ya-Jun Liu
Chinese Journal of Chemistry 2007 Volume 25(Issue 2) pp:
Publication Date(Web):7 FEB 2007
DOI:10.1002/cjoc.200790029
The photodissociation mechanism of benzyl chloride (BzCl) under 248 nm has been investigated by the complete active space SCF (CASSCF) method by calculating the geometries of the ground (S0) and lower excited states, the vertical (Tv) and adiabatic (T0) excitation energies of the lower states, and the dissociation reaction pathways on the potential energy surfaces (PES) of S1, T1 and T2 states. The calculated results clearly elucidated the photodissociation mechanism of BzCl, and indicated that the photodissociation on the PES of T1 state is the most favorable.
Co-reporter:Ya-Jun Liu Dr. ;Luca De Vico Dr.;Rol Lindh and
ChemPhysChem 2007 Volume 8(Issue 6) pp:890-898
Publication Date(Web):12 MAR 2007
DOI:10.1002/cphc.200600737
The UV photodissociation (<5 eV) of diiodomethane (CH2I2) is investigated by spin-orbit ab initio calculations. The experimentally observed photodissociation channels in the gas and condensed phases are clearly assigned by multi-state second-order multiconfigurational perturbation theory in conjunction with spin-orbit interaction through complete active space-state interaction potential energy curves. The calculated results indicate that the fast dissociations of the first two singlet states of CH2I2 and CH2II lead to geminate-radical products, CH2I .+I(2P3/2) or CH2I .+ I*(2P1/2). The recombination process from CH2II to CH2I2 is explained by an isomerization process and a secondary photodissociation reaction of CH2II. Finally, the study reveals that spin-orbits effects are significant in the quantitative analysis of the electronic spectrum of the CH2II species.
Co-reporter:Wei-Hai Fang Dr.;David Lee Phillips Dr.
ChemPhysChem 2002 Volume 3(Issue 10) pp:
Publication Date(Web):14 OCT 2002
DOI:10.1002/1439-7641(20021018)3:10<889::AID-CPHC889>3.0.CO;2-U
Where shall we three meet again? A minimum energy crossing point among the three potential energy surfaces (S1, T1, and T2) is found in a wide variety of aromatic ketones with a common structure. This new type of crossing point holds the key to understanding much of the relaxation dynamics and mechanistic photochemistry (nπ* excitation) of aromatic carbonyl compounds.
Co-reporter:Xin Zhang, Xiaojia Guo, Yue Chen, Yanhui Tang, Ming Lei and Weihai Fang
Physical Chemistry Chemical Physics 2012 - vol. 14(Issue 17) pp:NaN6012-6012
Publication Date(Web):2012/03/06
DOI:10.1039/C2CP23936A
In this paper, the mechanism of ketone hydrogenation catalyzed by five Ru bifunctional catalysts with different structural frameworks was studied in detail using density functional theory (DFT). This mechanism contains hydrogen transfer, dehydrogenation of alcohol, and dihydrogen activation fundamental reactions. The involvement of alcohol is also discussed and found with different activities in hydrogen transfer, dehydrogenation and dihydrogen activation steps in five systems. Our calculated results indicate that the weak Ru–H bond, stronger basicity of hydride and stronger X–H acidity will decrease the barrier of the HT step, and that the polar micro-environment of dihydrogen coordinating with Ru catalysts and short hydrogen transfer distance would be able to facilitate the heterolytic splitting of dihydrogen in the dihydrogen activation step.
Co-reporter:Liu Yang, Weihai Fang and Yong Zhang
Chemical Communications 2012 - vol. 48(Issue 32) pp:NaN3844-3844
Publication Date(Web):2012/02/27
DOI:10.1039/C2CC31016C
HNO binds to many different metals in organometallic and bioinorganic chemistry. To help understand experimentally observed metal centre effects, a quantum chemical investigation was performed, revealing clear general binding trends with respect to metal centre characteristics and the electronic origin for the first time.
Co-reporter:Guofu Zi, Furen Zhang, Li Xiang, Yue Chen, Weihai Fang and Haibin Song
Dalton Transactions 2010 - vol. 39(Issue 17) pp:NaN4061-4061
Publication Date(Web):2010/02/23
DOI:10.1039/B923457H
A new series of titanium(IV) and zirconium(IV) amides have been prepared from the reaction between M(NMe2)4 (M = Ti, Zr) and chiral ligands, (R)-2,2′-bis(p-toluenesulfonylamino)-1,1′-binaphthyl (1H2), (R)-2,2′-bis(diphenylphosphinoylamino)-1,1′-binaphthyl (2H2), (R)-2,2′-bis(mesitoylamino)-1,1′-binaphthyl (3H2), (R)-5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(pyrrol-2-ylmethyleneamino)-1,1′-binaphthyl (4H2), (R)-5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(mesitoylamino)-1,1′-binaphthyl (5H2), and (R)-5,5′,6,6′,7,7′,8,8′-octahydro-2,2′-bis(mesitylenesulfonylamino)-1,1′-binaphthyl (6H2), which are derived from (R)-2,2′-diamino-1,1′-binaphthyl. Reaction of M(NMe2)4 with 1 equiv of arylsulfonylamides 1H2 and 6H2, diphenylphosphoramide 2H2, mesitoylamides 3H2 and 5H2, or Schiff base ligand 4H2 at room temperature gives, after recrystallization from a benzene, toluene or n-hexane solution, the chiral titanium amides (1)Ti(NMe2)2·3C6H6 (7·3C6H6), (4)Ti(NMe2)2 (11), (5)Ti(NMe2)2 (13) and (6)Ti(NMe2)2 (15), and zirconium amides (1)Zr(NMe2)2 (8), (2)Zr(NMe2)2 (9), (3)Zr(NMe2)2 (10), (4)Zr(NMe2)2 (12), (5)Zr(NMe2)2 (14) and (6)Zr(NMe2)2·C7H8 (16·C7H8) respectively, in good yields. These amides are stable below 90 °C in toluene solution, but they degrade via ligand redistribution at a higher temperature. For example, treatment of (1)Zr(NMe2)2 (8) or (5)Zr(NMe2)2 (14) in refluxing toluene for three days leads to the isolation of the complexes (1)2Zr·C7H8 (17·C7H8) and (5)2Zr·3C7H8 (18·3C7H8) respectively, in moderate yields. These new compounds have been characterized by various spectroscopic techniques, and elemental analyses. The solid-state structures of compounds 7–9, 11–13, and 15–18 have further been confirmed by X-ray diffraction analyses. The titanium amide 13 and all the zirconium amides are active catalysts for the asymmetric hydroamination/cyclization of aminoalkenes, affording cyclic amines in moderate to excellent yields with moderate to excellent ee values (up to 93%). Theoretical studies reveal the interaction between the carbon chain of the substrate and the sterically demanding ligand groups plays a key role in the stereodirection of the enantioselection during the ZrN bond approaches to the CC bond.
Co-reporter:Juan Han, Lin Shen, Xuebo Chen and Weihai Fang
Journal of Materials Chemistry A 2013 - vol. 1(Issue 27) pp:NaN4235-4235
Publication Date(Web):2013/05/02
DOI:10.1039/C3TC30692E
A comprehensive theoretical model of electron exchange-induced energy transfer combined with the CASPT2//CASSCF theory is first applied to explore the mechanism of tunable emission for the single-dopant WOLED of FPt and the related photophysical processes. The monomer-like bluish emission is demonstrated to depend on the efficiency of direction-specific charge transfer along O1 → Pt → pyridinyl ring, while the dimer-like reddish emission from the TLC state is dominated by the electron exchange that takes place between the TMLCTx and TLC states via the ground state. The strategy of molecular design is proposed to improve the efficiency of emission for the analogous C⁁NPt(O⁁O) complex on the basis of accurate electronic structure calculations and quantitative rates of Dexter energy transfer as well as comparisons with the case of Pt-4.
Co-reporter:Hongjuan Wang, Xuebo Chen and Weihai Fang
Physical Chemistry Chemical Physics 2014 - vol. 16(Issue 46) pp:
Publication Date(Web):
DOI:10.1039/C4CP04130E
