Quantum chemical investigations aimed at modeling highly efficient zinc porphyrin dye sensitized solar cells

Zinc tetraphenylporphyrin (ZnTPP) was modified by a push-pull strategy and then density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were performed for the resulting derivatives. The smallest HOMO-LUMO energy gaps were found in ZnTPP-6 and ZnTPP-7, which had nitro substituents and a conjugated chain, while the largest was observed for ZnTPP-5. The energy gaps of all of the systems designed in this work were smaller than that of ZnTPP. Clear intramolecular charge transfer was observed from donor to acceptor in ZnTPP-6 and ZnTPP-7, which had nitro groups at positions R8, R9, and R10, as well as in ZnTPP-3 and ZnTPP-4, which had cyano groups at those positions. The narrow band gaps (compared to that of ZnTPP) of these designed systems, where the LUMO is above the conduction band of TiO(2) and the HOMO is below the redox couple, indicate that they are efficient sensitizers. The B bands of these newly designed derivatives, except for ZnTPP-5, are redshifted compared with the B band of ZnTPP.     

Why is the crystal shape of TATB is so similar to its molecular shape? Understanding by only its root molecule

We present an understanding of the quasi-regular or regular hexagonal enlargement of 1,3,5-triamino-2,4,6 (TATB) from its root molecule to its bulk crystal, by only its root molecule. That is, the mechanism of regular hexagonal TATB molecules stacking to a quasi-regular or regular hexagonal TATB crystal was discussed using a combined method of a density functional theory BLYP and Dreiding forcefield, and a series of static scanning calculations. As a result, we found that there are two styles of forming the most energetically favored TATB dimers: a hydrogen bonding along the molecular plane and an offset π-stacking vertical to the plane, just leading to the outspread and the thickening of the regular hexagon during the crystal growth, respectively. At the same time, it was found that the rotation of one TATB layer in any parallel stacked double-layer should overcome a very high energy barrier. It suggests that the TATB molecules or layers are arranged on the crystal face always along the special orientation of a regular hexagon and other orientations are strongly thermodynamically forbidden, resulting in a hexagonal crystal bulk.     

Charge-transfer processes in bipyrazine and bi-(N-methylpyridine): A semiempirical MO study

In the present paper, the bipyrazine and bi-(N-methylpyridine) dication systems are studied. Charge distributions and occupied and unoccupied molecular orbitals, obtained from semiempirical MNDO calculations, are reported as functions of the length of the -chain connecting the pyrazine/pyridine fragments. Single CI calculations, using ZINDO, are performed, and the transition energies and oscillator strengths for various vertical excitations from the ground state, along with the excited state dipole moments, are reported. The concepts of broken symmetry and localized excitations, to enhance the charge transfer in this class of compounds, are discussed. Comparison with theoretical and experimental studies of core photoionization and valence-excitation in nitrogen-containing molecules is made.     

Theoretical evaluation of the order of reactivity of transfer agents utilized in RAFT polymerization: group Z

In the present study we report theoretical calculations, by means of density functional theory (DFT), for 28 transfer agents used in reversible addition-fragmentation chain transfer (RAFT) polymerization. Functional PBE1PBE and 3–21G* theory levels with Gaussian 03 software were used to determine the order of reactivity of RAFT agents through the evaluation of reactivity parameters such as global softness, global hardness and global philicity. It was found that the global softness of the agent was more favored when it contained benzyl or phenyl groups as the Z group, than in RAFT agents with Z groups based on oxygen, nitrogen, or sulfur. On the one hand, when the Z group is based on oxygen or nitrogen, the tendency to form zwitterionic bonds with the adjacent radical center is very high, causing reactivity reduction in these kinds of compounds (e.g., dithiocarbamates) in comparison with compounds that do not experience this type of event; on the other hand, with Z groups based on sulfur, two fragmentation paths are possible, which reduces the fragmentation rate since both Z and R can function as leaving groups. With this investigation we contribute to the understanding of RAFT-mediated polymerization mechanisms by proposing an order of reactivity based on evaluating the importance of the Z group.     

Theoretical insights into the stabilities,detonation performance,and electrostatic potentials of cocrystals containing α- or β-HMX and TATB,FOX-7, NTO,or DMF in various molar ratios

A molecular dynamics method was employed to study the binding energies associated with the cocrystallization (at selected crystal planes) of either 1,3,5-triamino-2,4,6-trinitro-benzene (TATB), 1,1-diamino-2,2-dinitroethylene, 3-nitro-1,2,4-triazol-5-one (TATB, FOX-7, and NTO, respectively, all of which are explosives), or N,N-dimethylformamide (DMF, a nonenergetic solvent) in various molar ratios with 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane in its α and β conformations (α-HMX and β-HMX, respectively). The results showed that the cocrystals with low molar ratios (2:1, 1:1, 1:2, and 1:3) were the most stable. The binding energies of HMX/NTO and HMX/DMF were larger than those of HMX/TATB and HMX/FOX-7. According to the calculated stabilities, HMX prefers to adopt its α form in HMX/TATB and its β form in HMX/NTO, whereas the two forms coexist in HMX/FOX-7. For HMX/TATB, HMX/NTO, and α-HMX/FOX-7, increasing the proportion of the cocrystal component with the highest detonation heat (HMX in the first two cases, FOX-7 in the latter) increases the detonation heat, velocity, and pressure of the cocrystal. However, increasing the proportion of the component with the highest detonation heat in β-HMX/FOX-7 and γ-CL-20/FOX-7 increases the detonation heat of the cocrystal but decreases its detonation velocity. An investigation of the surface electrostatic potential revealed how the sensitivity changes upon cocrystal formation.

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Graphical Abstract Surface electrostatic potential of HMX/TATB

     

Electronic structure theory based study of proline interacting with gold nano clusters

Interaction between metal nanoparticles and biomolecules is important from the view point of developing and designing biosensors. Studies on proline tagged with gold nanoclusters are reported here using density functional theory (DFT) calculations for its structural, electronic and bonding properties. Geometries of the complexes are optimized using the PBE1PBE functional and mixed basis set, i. e., 6-311++G for the amino acid and SDD for the gold clusters. Equilibrium configurations are analyzed in terms of interaction energies, molecular orbitals and charge density. The complexes associated with cluster composed of an odd number of Au atoms show higher stability. Marked decrease in the HOMO-LUMO gaps is observed on complexation. Major components of interaction between the two moieties are: the anchoring N-Au and O-Au bond; and the non covalent interactions between Au and N-H or O-H bonds. The electron affinities and vertical ionization potentials for all complexes are calculated. They show an increased value of electron affinity and ionization potential on complexation. Natural bond orbital (NBO) analysis reveals a charge transfer between the donor (proline) and acceptor (gold cluster). The results indicate that the nature of interaction between the two moieties is partially covalent. Our results will be useful for further experimental studies and may be important for future applications.     

Predicted melt curve and liquid-state transport properties of TATB from molecular dynamics simulations

The melt curve and the liquid-state transport properties shear viscosity, self-diffusion coefficient and thermal conductivity of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) were predicted using all-atom molecular dynamics simulations. The TATB melt curve was obtained using solid–liquid coexistence simulations and is in good accord with the Simon–Glatzel equation. The temperature dependencies of the shear viscosity and self-diffusion coefficient are predicted to obey Arrhenius behaviour for pressures up to P = 20 kbar. The thermal conductivity has a linear temperature dependence for P < 15 kbar and a linear density (ρ) dependence for ρ > 1200 kg m^?3. At similar densities the shear viscosity of liquid TATB is close to the predictions for liquid nitromethane [58] but lower than the predictions for liquid HMX [24] and RDX [59]. The self-diffusion coefficient for TATB is predicted to be higher than predictions for nitromethane, HMX and RDX at similar densities. The conductivity of TATB is ≈20% greater than the conductivity of liquid HMX at a given density.     

Density functional calculations for a high energy density compound of formula C6H6?n (NO2) n

A series of polynitroprismanes, C(6)H(6-n )(NO(2))(n) (n?=?1-6) intended for use as high energy density compounds (HEDCs) were designed computationally. Their electronic structures, heats of formation, interactions between nitro groups, specific enthalpies of combustion, bond dissociation energies, and explosive performances (detonation velocities and detonation pressures) were calculated using density functional theory (DFT) with the 6-311 G** basis set. The results showed that all of the polynitroprismanes had high positive heats of formation that increased with the number of substitutions for the prismane derivatives, while the specific enthalpy of combustion decreased as the number of nitro groups increased. In addition, the range of enthalpy of combustion reducing is getting smaller. Interactions between ortho (vicinal) groups deviate from the group additivity rule and decrease as the number of nitro groups increases. In terms of thermodynamic stability, all of the polynitroprismanes had higher bond dissociation energies (BDEs) than RDX and HMX. Detonation velocities and detonation pressures were estimated using modified Kamlet-Jacobs equations based on the heat of detonation (Q) and the theoretical density of the molecule (ρ). It was found that ρ, D, and P are strongly linearly related to the number of nitro groups. Taking both their energetic properties and thermal stabilities into account, pentanitroprismane and hexanitroprismane are potential candidate HEDCs.     

Theoretical studies on the structures and detonation properties of nitramine explosives containing benzene ring

The nitramine compounds containing benzene ring were optimized to obtain their molecular geometries and electronic structures at DFT-B3LYP/6-31+G(d) level. The theoretical molecular density (ρ), heat of formation (HOF), energy gap (ΔE(LUMO-HOMO)), charge on the nitro group (-Q(NO2)), detonation velocity (D) and detonation pressure (P), estimated using Kamlet-Jacobs equations, showed that the detonation properties of these compounds were excellent. It is found that there are good linear relationships between density, heat of formation, detonation velocity, detonation pressure and the number of nitro group. The simulation results reveal that molecule G performs similarly to famous explosive HMX, and molecule H outperforms HMX. According to the quantitative standard of energetics as an HEDC (high energy density compound), molecule H essentially satisfies this requirement. These results provide basic information for molecular design of novel high energetic density compounds.     

Molecular dynamics simulation of primary detonation process of TATB crystal under shock loading

Molecular dynamics simulations were performed to gain fundamental insights into the mechanisms for the primary detonation process of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) under shock wave loading using self-consistent charge density-functional tight binding(SCC-DFTB) calculations combined with the multiscale shock technique (MSST). The primary process starts with shock loading and ends with the formation of dynamically stable heterocyclic clusters, which could inhibit the reactivity of TATB. The results show that the initial step of shocked TATB decomposition is the N–O bond cleavage; then carbon rings aggregate and connect by N atoms to form clusters; after the carbon rings open, heterocyclic clusters with nitrogen are formed, and persist throughout the simulation. This is a new mechanism for the primary processes of shocked TATB and this initiation mechanism is independent of the initial shock speeds.     

Computational study of proton and methyl cation affinities of imidazole-based highly energetic ionic liquids

The present study deals with the evaluation of gas phase proton and methyl cation affinities for alkyl- and nitrosubstituted imidazoles using DFT (B3LYP)/6-31 + G(d) and MP2 methods in the Gaussian 03 software package. The extent of charge delocalization of these cations is correlated with proton affinity. The study reveals that weakly electron-donating alkyl groups at position 1 of the imidazole enhance its proton affinity, which also increases with increasing alkyl chain length. This is expected to result in an increased tendency to form salts. In contrast, the presence of strongly electron-withdrawing nitro groups lowers proton affinity, which decreases as the number of nitro groups on the ring increases. The same trend is observed for the methyl cation affinity, but to a lower degree. These trends in the proton and methyl cation affinities were analyzed to study the effects of these substituents on the basicity of the energetic imidazole moieties and their tendency to form salts. This, in turn, should aid searches for better highly energetic ionic liquids. In addition, calculations performed on different isomers of mono and dinitroimidazoles show that 5-nitro-1H-imidazole and 2,4-dinitro-1H-imidazole are more stable than the other isomers. Amongst the many nitro derivatives of imidazoles considered in the present study, cations resulting from these two would be the best choice for creating highly energetic ionic liquids when coupled with appropriate energetic anions.     

Potential energy barriers to ion transport within lipid bilayers. Studies with tetraphenylborate.

Tetraphenylborate-induced current transients were studied in lipid bilayers formed from bacterial phosphatidylethanolamine in decane. This ion movement was essentially confined to the membrane in terior during the current transients. Charge movement through the interior of the membrane during the current transients was studied as a function of the applied potential. The transferred charge approached an upper limit with increasing potential, which is interpreted to be the amount of charge due to tetraphenylborate ions absorbed into the boundary regions of the bilayer. A further analysis of the charge transfer as a function of potential indicates that the movement of tetraphenylborate ions is only influenced by a certain farction of the applied potential. For bacterial phosphatidylethanolamine bilayers the effective potential is 77 +/- 4% of the applied potential. The initial conductance and the time constant of the current transients were studied as a function of the applied potential using a Nernst-Planck electrodiffusion regime. It was found that an image-force potential energy barrier gave a good prediction of the observed behavior, provided that the effective potential was used in the calculations. We could not get a satisfactory prediction of the observed behavior with an Eyring rate theory model or a trapezoidal potential energy barrier.     

Theoretical investigation of the enzymatic phosphoryl transfer of β-phosphoglucomutase: revisiting both steps of the catalytic cycle

Enzyme catalyzed phosphate transfer is a part of almost all metabolic processes. Such reactions are of central importance for the energy balance in all organisms and play important roles in cellular control at all levels. Mutases transfer a phosphoryl group while nucleases cleave the phosphodiester linkages between two nucleotides. The subject of our present study is the Lactococcus lactis β-phosphoglucomutase (β-PGM), which effectively catalyzes the interconversion of β-D-glucose-1-phosphate (β-G1P) to β-D-glucose-6-phosphate (β-G6P) and vice versa via stabile intermediate β-D-glucose-1,6-(bis)phosphate (β-G1,6diP) in the presence of Mg(2+). In this paper we revisited the reaction mechanism of the phosphoryl transfer starting from the bisphosphate β-G1,6diP in both directions (toward β-G1P and β-G6P) combining docking techniques and QM/MM theoretical method at the DFT/PBE0 level of theory. In addition we performed NEB (nudged elastic band) and free energy calculations to optimize the path and to identify the transition states and the energies involved in the catalytic cycle. Our calculations reveal that both steps proceed via dissociative pentacoordinated phosphorane, which is not a stabile intermediate but rather a transition state. In addition to the Mg(2+) ion, Ser114 and Lys145 also play important roles in stabilizing the large negative charge on the phosphate through strong coordination with the phosphate oxygens and guiding the phosphate group throughout the catalytic process. The calculated energy barrier of the reaction for the β-G1P to β-G1,6diP step is only slightly higher than for the β-G1,6diP to β-G6P step (16.10 kcal mol(-1) versus 15.10 kcal mol(-1)) and is in excellent agreement with experimental findings (14.65 kcal mol(-1)).     

Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA

The flavoenzyme medium-chain acyl-CoA dehydrogenase (MCAD) eliminates the alpha-proton of the substrate analog, 3-thiaoctanoyl-CoA (3S-C8-CoA), to form a charge-transfer complex with deprotonated 3S-C8-CoA. This complex can simulate the metastable reaction intermediate immediately after the alpha-proton elimination of a substrate and before the beta-hydrogen transfer as a hydride, and is therefore regarded as a transition-state analog. The crystalline complex was obtained by co-crystallizing MCAD in the oxidized form with 3S-C8-CoA. The three-dimensional structure of the complex was solved by X-ray crystallography. The deprotonated 3S-C8-CoA was clearly located within the active-site cleft of the enzyme. The arrangement between the flavin ring and deprotonated 3S-C8-CoA is consistent with a charge transfer interaction with the negatively charged acyl-chain of 3S-C8-CoA as an electron donor stacking on the pyrimidine moiety of the flavin ring as an electron acceptor. The structure of the model complex between lumiflavin and the deprotonated ethylthioester of 3-thiabutanoic acid was optimized by molecular orbital calculations. The obtained theoretical structure was essentially the same as that of the corresponding region of the X-ray structure. A considerable amount of negative charge is transferred to the flavin ring system to stabilize the complex by 9.2 kcal/mol. The large stabilization energy by charge transfer probably plays an important role in determining the alignment of the flavin ring with 3S-C8-CoA. The structure of the highest occupied molecular orbital of the complex revealed the electron flow pathway from a substrate to the flavin ring.     

Charge Compensation Mechanism of a Na+-coupled, Secondary Active Glutamate Transporter

Forward glutamate transport by the excitatory amino acid carrier EAAC1 is coupled to the inward movement of three Na(+) and one proton and the subsequent outward movement of one K(+) in a separate step. Based on indirect evidence, it was speculated that the cation binding sites bear a negative charge. However, little is known about the electrostatics of the transport process. Valences calculated using the Poisson-Boltzmann equation indicate that negative charge is transferred across the membrane when only one cation is bound. Consistently, transient currents were observed in response to voltage jumps when K(+) was the only cation on both sides of the membrane. Furthermore, rapid extracellular K(+) application to EAAC1 under single turnover conditions (K(+) inside) resulted in outward transient current. We propose a charge compensation mechanism, in which the C-terminal transport domain bears an overall negative charge of -1.23. Charge compensation, together with distribution of charge movement over many steps in the transport cycle, as well as defocusing of the membrane electric field, may be combined strategies used by Na(+)-coupled transporters to avoid prohibitive activation barriers for charge translocation.     

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase is a redox-driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a membrane proton gradient. The structure of the enzyme has been solved; however, the mechanism of proton pumping is still poorly understood. Recent calculations from this group indicate that one of the histidine ligands of enzyme's CuB center, His291, may play the role of the pumping element. In this paper, we report on the results of calculations that combined first principles DFT and continuum electrostatics to evaluate the energetics of the key energy generating step of the model-the transfer of the chemical proton to the binuclear center of the enzyme, where the hydroxyl group is converted to water, and the concerted expulsion of the proton from delta-nitrogen of His291 ligand of CuB center. We show that the energy generated in this step is sufficient to push a proton against an electrochemical membrane gradient of about 200 mV. We have also re-calculated the pKa of His291 for an extended model in which the whole Fe(a3)-CuB center with their ligands is treated by DFT. Two different DFT functionals (B3LYP and PBE0), and various dielectric models of the protein have been used in an attempt to estimate potential errors of the calculations. Although current methods of calculations do not allow unambiguous predictions of energetics in proteins within few pKa units, as required in this case, the present calculation provides further support for the proposed His291 model of CcO pump and makes a specific prediction that could be targeted in the experimental test.     

Structures of the neutral and positively charged forms of the 4,4′,4″-tris(<Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer,and charge localization in the corresponding cationic species

The structures of the 4,4′,4″-tris(N,N-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer in their neutral and positively charged forms were studied by performing quantum-chemical calculations at the Hartree?Fock (HF) and density functional theory (DFT) levels of theory using several exchange-correlation functionals (PBE, PBE0, BHANDHLYP, and M06-HF) with different percentages of HF exchange. It was found that there are at least four possible isomeric structures of m-MTDATA with different (planar or perpendicular) arrangements of the peripheral diphenylamino groups. The charge localization in the monomeric and dimeric cationic species was also determined. The results indicated that the charge on the dimeric cation is localized on the central region or on the side fragment of the cationic part of the dimer, depending on the dimer structure. DFT calculations showed a tendency to overestimate the charge delocalization over the molecule, irrespective of the percentage of HF exchange applied.

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Graphical abstract Structure of an m-MTDATA dimer cation.

     

Charge transfer and optoelectronic properties in the triarylamine-based donor–π bridge–acceptor dyes for dye-sensitised solar cells

The triarylamine–based donor–π bridge–acceptor dyes (namely, Ds-3, Ds-5 and Ds-6), with the higher conversion efficiency of sunlight to electricity, have been studied with quantum chemistry methods. The geometrical structure, frontier molecular orbital and electronic vertical excitation energies were calculated by using the density functional theory (DFT) and the time-dependent DFT with the Cam-B3LYP and PBE0 functional. From the calculated results, we perform a three-dimensional real-space analysis, which demonstrates that the lowest energy excited state of the triarylamine-based dye is a charge transfer (CT) excited state and electrons shift from triarylamine to cyanoacrylic acid group. The excited-state oxidation potentials and driving force energy are identified as the essential parameters to study the electron injection ability of the excited dyes. The evaluation of photochemical parameter and the visualised study of CT process provide the important information for revealing the relationship between structure and photochemical property of the triarylamine-based dyes.