[Show abstract][Hide abstract] ABSTRACT: We report a theoretical study to ascertain dye regeneration in dye sensitized solar cells (DSSCs) with the TiO2-dye-electrolyte model. Oxidized 3-(5-(4-(diphenylamino)styryl)thiophen-2-yl)-2-cyanoacrylic acid (L2) dye, three electrolyte main components (I-, I2, I3-) and (TiO2)9 cluster has been selected in this model. The calculated results show that the combination capability of electrolyte to L2+@TiO2 is according to the order of I- > I3- > I2. Furthermore, oxidized dye together with electrolyte can get good performance of absorption in visible light region. Specifically, I- may accelerate the electronic transition and injection by participating in the positive charge transfer. I2 may lead to the opposite transition and I3- ions seem to be a mixed result of both effects. In this study, the charge transfer pathway during dye regeneration process has been found. It can be predicted that the charge transfer of dye regeneration may contribute to the absorption in UV-vis region of DSSC.
[Show abstract][Hide abstract] ABSTRACT: TvMyb2, one of the Myb-like transcriptional factors in Trichomonas vaginalis, binds to two closely spaced promoter sites, MRE-1/MRE-2r and MRE-2f, on the ap65-1 gene. However, detailed dynamical structural characteristics of the tvMyb2-ap65-1 complex and a detailed study of the protein in the complex have not been done. Focused on a specific tvMyb2-MRE-2-13 complex (PDB code: ) and a series of mutants K51A, R84A and R87A, we applied molecular dynamics (MD) simulation and molecular mechanics generalized Born surface area (MM-GBSA) free energy calculations to examine the role of the tvMyb2 protein in recognition interaction. The simulation results indicate that tvMyb2 becomes stable when it binds the DNA duplex. A series of mutants, K51A, R84A and R87A, have been followed, and the results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on recognition and binding to ap65-1 DNA. Our work gives important information to understand the interactions of tvMyb2 with ap65-1.
[Show abstract][Hide abstract] ABSTRACT: Focal adhesion kinase is an important target for the treatment of many kinds of cancers. Inhibitors of FAK are proposed to be the anticancer agent for multiple tumors. The interaction characteristic between FAK and its inhibitors is crucial to develop new inhibitors. In the present article, we used Molecular Dynamic (MD) simulation method to explore the characteristic of interaction between FAK and three inhibitors (PHM16, TAE226, and ligand3). The MD simulation results together with MM-GB/SA calculations show that the combinations are enthalpy-driven process. Cys502 and Asp564 are both essential residues due to the hydrogen bond interactions with inhibitors, which was in good agreement with experimental data. Glu500 can form a non-classical hydrogen bond with each inhibitor. Arg426 can form electrostatic interactions with PHM16 and ligand3, while weaker with TAE226. The electronic static potential was employed, and we found that the ortho-position methoxy of TAE226 has a weaker negative charge than the meta-position one in PHM16 or ligand3. Ile428, Val436, Ala452, Val484, Leu501, Glu505, Glu506, Leu553, Gly563 Leu567, Ser568 are all crucial residues in hydrophobic interactions. The key residues in this work will be available for further inhibitor design of FAK and also give assistance to further research of cancer.
[Show abstract][Hide abstract] ABSTRACT: The local electric field formed between dye sensitizers and semiconductor interface is one of key factors to determine the overall performance of dye-sensitized solar cells (DSSCs). Herein, a strategy has been proposed to explore the influence of the local electric field on the functionality of DSSCs of YD2-O-C8 dye via calculating the relevant properties in various electric field strengths. The YD2-O-C8 dye has been systemically studied with density functional theory (DFT) and time-dependent DFT (TD-DFT) for its electronic structure and optical properties in tetrahydrofuran (THF) solution. The absorption spectra are gradually narrowing and blue-shifting while increasing the electric field strength. Two key parameters of the light harvesting efficiency (LHE) and the TiO2 conduction band shift (ΔEcb) have been examined for the YD2-O-C8 sensitized TiO2 system. It is found that it is of great importance to reduce the charge accumulation on the TiO2 film, which lowers the electric field strength and shows the best performance of DSSCs. This study is expected to deepen our understanding of the function of local electric field and the operational principles of the DSSCs for further optimization.
[Show abstract][Hide abstract] ABSTRACT: Two types of detoxification routes, N-demethylation to form 4-phenyl-1,2,3,6-tetrahydropyridine (PTP) and aromatic hydroxylation to generate 4-(4'-hydroxyphenyl)-1-methyl-1,2,3,6-tetrahydropyridine (MPTP-OH), for 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mediated by Compound I (Cpd I) of cytochrome P450 are investigated theoretically using hybrid density functional calculations. Quantum chemical results reveal that for the N-demethylation, the initial C-H bond activation is achieved via a hydrogen atom transfer (HAT) mechanism. This is followed by a subsequent O-rebound to yield the carbinolamine intermediate. Due to the nature of pericyclic reaction, the generated carbinolamine decomposes in a non-enzymatic aqueous environment with the assistance of water molecules, forming amine and hydrated formaldehyde. For the aromatic hydroxylation, an initial addition of Cpd I to the substrate occurs mainly through a side-on approach with a subsequent proton shuttle to form the phenol product. A comparison of the energy barriers for both routes indicates that the N-demethylation (7.5/5.7kcal/mol for the quartet/doublet state in solvent) is thermodynamically more favorable than the aromatic hydroxylation process (14.9/14.8kcal/mol for the quartet/doublet state in solvent). This trend is in good agreement with the experimental product distribution, viz., the N-demethylation product PTP is more than the aromatic hydroxylation product MPTP-OH. Taken together, these observations not only enrich our knowledge on the mechanistic details of the N-dealkylation and the aromatic hydroxylation by P450s, but also provide certain insights into the metabolism of other analogous toxins.
[Show abstract][Hide abstract] ABSTRACT: In this work, we report performed a high level ab initio study on the low-lying electronic states of C6H5OO, utilizing complete active space self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) method, and the contracted ANO-L basis set have been taken into account. The potential energy curves for the four lowest states associated with the lowest dissociation limit of C6H5OO radical. The calculated results clearly assigned the experimentally observed photodissociation channels leading to C6H5O (X2A, 22A) + O(3Pg) and C6H5 (X2A) + O2(X3Σg−, 11Δg, 11Σg+).
[Show abstract][Hide abstract] ABSTRACT: Based on titanium dioxide model and LJBs sensitizers (triphenylamine as the donor, 3,4-ethylene dioxy thiophene plus various functionalized phenylenes as the π-spacer, and cyanoacrylic acid as the anchoring group) with different connection types on TiO2 substrate, the reasonable dye-TiO2 connection has been located. The results show that the dissociative adsorption of LJBs is more thermodynamically favorable than the neutral molecule bound configurations. LJBs adsorb onto TiO2 via interaction between 3d orbital of surface Ti atom and 2p orbital of N/O atoms in the acceptors. This result is confirmed in both neutral and dissociation forms of LJBs molecules. According to our calculations, adding a meta-fluorine substituent to the phenyl group of cyanoacrylic acid (LJB-Fm) may damage the planarity and conjugation. Consequently, the light harvesting efficiency decreased, and that is particularly unfavorable for the DSSCs application. The Ortho F-substituted dye (LJB-Fo), however, exhibited enhanced light absorption and more efficient intra-molecular charge transport. The bigger Jsc, Voc values of LJB-Fo system predicts its superior DSSC performance. Additionally, LJBs anchored on TiO2 surface via group –COO (LJB-H and LJB-Fo) lead to an indirect mechanism for electron injection. While LJB-Fm preferred to direct electron injection mechanism due to the strong orbital-coupling between sensitizer and the TiO2 substrate.
[Show abstract][Hide abstract] ABSTRACT: Understanding of reaction and structural property of diuranium(III) complexes of a single ligand is essential to advancing their experimental synthesis and exploring promising applications in small molecule activation chemistry. In this work, we theoretically examined a series of diuranium(III) complexes building on the reaction of [UI3(THF)4] and octadentate polypyrrolic ligands (H4L1 and H4L2). At the relativistic density functional theory level, 11.2 kcal/mol energy is required to form the Pacman-like [(UI)2(μ2-I)(L1)]- (1) in THF solution, while only 0.5 kcal/mol for its non-classic Pacman isomer 1n. These agree with their analogues that have been experimentally proposed. A variety of chemical modification has been made for 1. The addition of one THF solvent or one iodine ion raises reaction energy by 6.8∼14.5 kcal/mol, while two or more are significantly endoergic. Smaller energies of 1.4 and 7.4 kcal/mol are required when varying bridged atom (from the iodine of 1 into the THF of 2 [(UI)2(μ2-THF)(L1)]) and lengthening ligand linker size (from ortho-phenylene of H4L1 of 1 into anthracene of H4L2 of 3 [(UI)2(μ2-I)(L2)]-), respectively. Eleven diuranium(III) complexes were optimized to be energetically stable. The U-U distances of 4.13 and 4.08 Å were calculated for 1 and 2, respectively, compared with the long one of 5.90 Å for 3.
[Show abstract][Hide abstract] ABSTRACT: BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assemble the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.
[Show abstract][Hide abstract] ABSTRACT: The equation of state (EOS) from virial expansion (VE) is used in this work to pave the way for determining the fugacity coefficients of the hydrogen fluid at arbitrary temperature and pressure. The fugacity coefficients from our VE method have more physical meanings than the empirical values. In this way, the hydrogen storage capacity of a novel material model can be estimated by using few density functional theory (DFT) calculations with the aid of a continuum model. The efficient continuum model can provide a more accurate estimation of the hydrogen storage capacity than the pure DFT calculations. Furthermore, the expensive grand canonical ensemble (mNT) simulations combining with the quantum mechanics methods (i.e., QM/MD-mNT) are unnecessary within this method. The hydrogen fluid can be handled with our VE method at the temperature in the range of 160e773 K. The hydrogen storage capacity and the detailed thermodynamic information of a designed novel material can thereby be estimated by using this method with relatively high accuracy and low computing cost. As an example, the hydrogen storage capacities of the expanded bilayer graphene systems are presented. Our theoretical results agree with the experimental values very well.
International Journal of Hydrogen Energy 07/2015; DOI:10.1016/j.ijhydene.2015.07.005 · 3.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The photophysical properties of 2,2′-bis-(4-alkoxyphenyl)-bi-1,3,4-oxadiazole (BOXD-n), have been studied by a combination of spectroscopic techniques and theoretical calculations. Interestingly, strong fluorescence red-shift in polar solvents was observed in this highly symmetric molecule, which indicates an efficient charge transfer (CT) occurred in the excited state. The change of molecular dipole moment between the ground state and CT excited state was calculated to be 9.9 D. Theoretical calculations at Density Functional Theory level revealed that the first singlet excited state of BOXD-n shows both π-π∗and CT characters. Clear evidence for charge transfer from alkoxy benzene to the central bi-1,3,4-oxadiazole group can be observed by analysing the atomic charge and electron density change, though it is not significant. Since BOXD-1 retained a planar conformation and became more quinoid-like in the excited state, a planar intramolecular charge transfer is assigned for it. By further comparing these results with the half molecule terminated by CH3 group (2-tetradecyloxyphenyl, 5-methyl-1,3,4-oxadiazole), it could be concluded that intramolecular charge transfer property was enhanced in this DAAD arrangement of BOXD-n.
[Show abstract][Hide abstract] ABSTRACT: Cytochrome P450 (CYP) 3A7 plays a crucial role in the biotransformation of the metabolized endogenous and exogenous steroids. To compare the metabolic capabilities of CYP3A7-ligands complexes, three endogenous ligands were selected, namely, dehydroepiandrosterone (DHEA), estrone and estradiol. In this study, a three-dimensional model of CYP3A7 was constructed by homology modeling using the crystal structure of CYP3A4 as the template and refined by molecular dynamics simulation (MD). The docking method was adopted, combined with MD simulation and the Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) method, to probe the ligand selectivity of CYP3A7. These results demonstrate that DHEA has the highest binding affinity, and the results of the binding free energy were in accordance with the experimental conclusion that estrone is better than estradiol. Moreover, several key residues responsible for substrate specificity were identified on the enzyme. Arg372 may be the most important residue as the low interaction energies and the existence of hydrogen bond with DHEA throughout simulation. In addition, a cluster of Phe residues provides a hydrophobic environment to stabilize ligands. The present study provides insights into the structural features of CYP3A7, which could contribute to further understanding of related protein structures and dynamics.
[Show abstract][Hide abstract] ABSTRACT: The molecular aggregation structure of three D-A cocrystal complexes based on substituted distyrylbenzenes (DSB) was studied by density functional theory calculation. The influence of molecular stacking on molecular interactions, frontier molecular orbitals, charge transport and photophysical properties have been investigated in depth, by comparison of D1-A1, D2-A2 and D2-A2’ pairs with different substituents in D and A monomers. Our results provide not only better understanding of the relationship of D-A configuration and electrical/optical properties, but also the theoretical prediction of novel organic semiconductor materials for the mixed-stack D−A charge-transfer crystal. In particular, the charge-transfer complexes of D1-A1 have been demonstrated as good ambipolar material, while the complexes of D2-A2 and D2-A2’ should conduct as better n-type organic semiconductor materials.
[Show abstract][Hide abstract] ABSTRACT: Dye regeneration was a key process to influence lifetime and open-circuit voltage of dye-sensitized solar cells. In order to explore the mechanism of dye regeneration, the intermediate forms of this reaction were searched by first principle calculations in this study. The possible intermediat forms were obtained by analyzing the reactivity of four organic dyes with different donors and two electrolyte ions (I- and Br-). Then camparing their structures,interaction energy and reaction free energy, most appropraite intermediate forms were screened out. Throughout the comparison between I- and Br-, we found that Br-/Br3- could be a good redox couple if the redox potential matched with the energy gap of dye. In particular, steric-hindrance was likely the most infuential factor in determining the intermediate forms. It is suggested that triphenylamine homologues as donor groups may both interact with electrolyte easily and accordingly keep off the electrolyte from semiconductor effectively.
Dyes and Pigments 04/2015; 120. DOI:10.1016/j.dyepig.2015.03.026 · 3.97 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Ruthenium(II) complexes, as the dye sensitizer in the solar cell system, has attracted great interests. In the present study, based on the ruthenium(II) complex N749, new sensitizers have been designed theoretically to increase the stability and the efficiency of dye-sensitized solar cell (DSSC). By investigating the ground state geometries, electronic structures, and spectroscopic properties by density functional theory (DFT) and time-dependent DFT, the orbital components and absorption transition have been obtained. The effect of tripyrrin ligand in the designed new sensitizers can be demonstrated from our results. The results show that the absorption spectra are systematically broadened and red-shifted with the increase sizes of the pyrrole ligands. The important unoccupied orbitals referred to charge transfer are mainly from di/tripyrrin derivative groups. Consequently, the charge transfer to the di/tripyrrin derivative groups has been strengthened. According to our study, the di/tripyrrin derivative ligand is more efficient than the NCS− ligand in absorbing visible light. The calculation results also indicate that the electronic structures of the N749 derived sensitizers are significantly influenced by the different substituted positions of the thienyl groups on di/tripyrrin ligands. Thus, the efficiency of DSSCs would be different. Our research predicted that the Ru(II) complexes containing 5,10-(2-thienyl)-4,6,9,11-tripyrrin ligand may enhance the visible light absorption of DSSC. This is in accordance with the corresponding experiment. These results are expected to assist the molecular design for new dyes in future DSSCs.
[Show abstract][Hide abstract] ABSTRACT: The dye sensitizers play an important role in dye-sensitized solar cell (DSSC). Owing to the synthetic challenge and cost of precious metal-complex dyes, increasing researches have been focused on the organic molecule dyes, porphyrin and light metal porphyrins dyes. In this paper, three natural porphyrin derivatives as dyes with TiO2 nanoparticulate model are studied theoretically using density functional theory (DFT) approaches to explore their spectroscopic properties and application future in DSSC. The detailed orbital components and absorption transitions of thses porphyrin derivatives are analyzed from the calculated results. Key parameters of the short-circuit current density (Jsc) including light harvesting efficiency (LHE), electron injection driving force (ΔGinject) and nonlinear optical properties (NLO) were discussed. In addition, the calculated values of open circuit photovoltage (Voc) for these dyes were also presented. The tetrapyrrole macrocycle of porphyrin with central metals Mg or Zn can enrich the absorption strength greatly. Our research reveals that the Zn-porphyrin sensitizer can be used as potential sensitizer for DSSCs due to its best electronic and optical properties and good photovoltaic parameters. This study is expected to understand natural dye sensitizers and assist the molecular design of new dyes for the further DSSC improvement.
[Show abstract][Hide abstract] ABSTRACT: The global minimum structures of Mgn clusters have been determined using the so-called "kick method". With the improved DFT method of B3PW91 functional and Grimme's dispersion correction, a series of the most stable structure of Mgn have been found and a novel Mg9 structure has been located. Subsequently, the chemisorption of hydrogen onto Mg clusters was systemically studied. Considering the average adsorption energies and the ratio of Mg and H, we developed a function that can describe the relation between average adsorption energy and number of Mg and H atoms. Our result may be helpful in developing further to other gas chemisorption material.
The Journal of Physical Chemistry A 03/2015; 119(15). DOI:10.1021/acs.jpca.5b01474 · 2.69 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In this work, the effect of regulated host and auxiliary ligand π-conjugation on photophysical properties of a series of Ir(III) carbene complexes are examined by using the start-of-the-art theoretical methods. According to our results, all of the lowest-lying and strongest absorptions can be assigned as a mixed ligand-to-ligand/metal-to-ligand charge transfer (LLCT/MLCT) character, but the different ways of the introduced phenyl have a great effect on the absorption wavelength variation. In addition, the charge transfer characters of lowest-lying emission have some minute differences. What is more, when the extension of π-conjugation is broken, the emission wavelength can be effectively retained due to the similar emission charge transfer related electronic density distribution of occupied molecular orbital and unoccupied molecular orbital. However, the larger π-conjugation can give rise to the remarkably blue-shifted emission. This blue-shifted emission can be attributed to the alteration of transition character from intense interaction between nearly degenerated unoccupied molecular orbitals. Through the evaluation of the spin-orbit coupling (SOC) effect, we can gain the deeply understanding concerning the radiative decay rate processes. These results reveal that the larger π-conjugation can also lead to the higher quantum efficiency due to the larger radiative decay and smaller nonradiative decay rate. Our theoretical studies highlight the role of π-conjugation of host and auxiliary ligand, thus, can pave the way for the design of novel and efficient blue phosphorescence materials.