A DFT/TDDFT interpretation of the ground and excited states of porphyrin and porphyrazine complexes

A comprehensive treatment is given of the electronic excitation spectra of Mg, Zn and Ni complexes of porphyrin and porphyrazine using time-dependent density functional theory (TDDFT). It is emphasized that the Kohn–Sham (KS) molecular orbital (MO) method, which is the basis for the TDDFT calculations, affords a MO interpretation of the ground state electronic structure and of the nature of the excitations. This implies that a direct connection can be made to many previous MO treatments of the title compounds. We discuss in particular, how the original explanations of the intensity distribution over the lowest excitations (the Q and B bands) in terms of a cyclic polyene model, or even a free-electron model, can be reconciled with the actual molecular and electronic structure of these compounds being much more complicated than these simple models. A fragment approach is used, building the porphyrin ring from pyrrole rings and CH or N bridges. This leads directly to a simple interpretation of the orbitals of Gouterman's four-orbital model, which are responsible for the Q and B bands. It also leads to additional occupied π-orbitals which are absent in the cyclic polyene model and which need to be invoked to understand other features of the electronic spectra such as the origin of the N, L and M bands. Considerable attention is given to the intensities of the various transitions, explaining why the transitions within the so-called four-orbital model of Gouterman have large transition dipoles, why transitions from additional occupied π-orbitals have relatively small transition dipoles.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center of Rps.viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteria Rhodopseudomonas (Rps.) viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises the ELUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease the ELUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacterioc     

Modeling and computations of the intramolecular electron transfer process in the two-heme protein cytochrome c(4)

The di-heme protein Pseudomonas stutzeri cytochrome c(4) (cyt c(4)) has emerged as a useful model for studying long-range protein electron transfer (ET). Recent experimental observations have shown a dramatically different pattern of intramolecular ET between the two heme groups in different local environments. Intramolecular ET in homogeneous solution is too slow (>10 s) to be detected but fast (ms-μs) intramolecular ET in an electrochemical environment has recently been achieved by controlling the molecular orientation of the protein assembled on a gold electrode surface. In this work we have performed computational modeling of the intramolecular ET process by a combination of density functional theory (DFT) and quantum mechanical charge transfer theory to disclose reasons for this difference. We first address the electronic structures of the model heme core with histidine and methionine axial ligands in both low- and high-spin states by structure-optimized DFT. The computations enable estimating the intramolecular reorganization energy of the ET process for different combinations of low- and high-spin heme couples. Environmental reorganization free energies, work terms ("gating") and driving force were determined using dielectric continuum models. We then calculated the electronic transmission coefficient of the intramolecular ET rate using perturbation theory combined with the electronic wave functions determined by the DFT calculations for different heme group orientations and Fe-Fe separations. The reactivity of low- and high-spin heme groups was notably different. The ET rate is exceedingly low for the crystallographic equilibrium orientation but increases by several orders of magnitude for thermally accessible non-equilibrium configurations. Deprotonation of the propionate carboxyl group was also found to enhance the ET rate significantly. The results are discussed in relation to the observed surface immobilization effect and support the notion of conformationally gated ET.     

Effect of mono-CDNP substitution of lysine residues on the redox reaction of cytochrome c electrostatically adsorbed on a mercaptoheptanoic acid modified Au(111) surface

The effect of charge-inverting modification of single surface lysine residue on the electron transfer (ET) reaction of horse heart cytochrome c (cyt c) is examined for 12 different types of mono-4-chloro-2,5-dinitrobenzoic acid substituted cyt c (mCDNPc) adsorbed on a Au(111) electrode modified with a self-assembled monolayer (SAM) of 7-mercapto-heptanoic acid (MHA). A negative shift in the redox potential by 10-35 mV as compared to that of native cyt c and a monolayer coverage in the range of 13-17 pmol cm(-2) are observed for electroactive mCDNPc's. The magnitude of the decrease in the ET rate constant (k(et)) of mCDNPc's compared with that of native cyt c depends on the position of the CDNP substitution. For mCDNPc's in which the modified lysine residue is outside of the interaction domain of cyt c with the SAM, the ratio of the k(et) of mCDNPc to that of native cyt c is correlated to the change in the dipole moment vector of cyt c due to the CDNP modification. This correlation suggests that the dipole moment of cyt c determines its orientation of adsorption on the SAM of MHA and significantly affects the rate of the ET. The CDNP modification of lysine residues at the interaction domain significantly decreases the rate, demonstrating the importance of the local charge environment in determining the rate of ET.     

Theoretical studies on the influence of molecular interactions on the mechanism of electron transfer in photosynthetic reaction center ofRps. viridis

Based on the QM/MM optimized X-ray crystal structure of the photosynthetic reaction center (PRC) of purple bacteriaRhodopseudomonas (Rps.)viridis, quantum chemistry density functional method (DFT, B3LYP/6-31G) has been performed to study the interactions between the pigment molecules and either the surrounded amino acid residues or water molecules that are either axially coordinated or hydrogen bonded with the pigment molecules, leading to an explanation of the mechanism of the primary electron-transfer (ET) reactions in the PRC. Results show that the axial coordination of amino acid residues greatly raises theE _LUMO of pigment molecules and it is important for the possibility of ET to take place. Different hydrogen bonds between amino acid residues, water molecules and pigment molecules decrease theE _LUMO of the pigment molecules to different extents. It is crucial for the ET taking place from excited P along L branch and sustains that the ET is a one-step reaction without through accessory bacteriochlorophyll (ABChl b). It is insufficient to treat the whole protein surrounding as a homogeneous dielectric medium.     

Spectroscopic and theoretical studies of optically active porphyrin dimers: a system uninterpretable by exciton coupling theory.

The electronic excited states of a meso-meso beta-beta doubly linked bis-porphyrin are comprehensively investigated by measuring its circular dichroism (CD) and magnetic circular dichroism (MCD) spectra. The observed spectroscopic properties are rationalized by DFT calculations. The frontier molecular orbitals (MOs) are constructed by the linear combinations of the constituent monomers' four MOs. Comparison of a theoretical CD spectrum based on time-dependent DFT (TDDFT) with the experimental spectra resulted in the assignment of the helical conformation of the dimer. This assignment is contrary to the previous assignment based on the point-dipole approximation (exciton coupling theory).     

Consequences of Substitution in the Photoelectron Spectra of [2, 2]Paracyclophanes: Separation of ‘through-space’ and ‘through-bond’ interactions as a consequence of fluorosubstitution

The PE. spectra of [2, 2]paracyclophane ( 1 ), 4-amino[2, 2]paracyclophane ( 2 ) and 1, 1, 2, 2, 9, 9, 10, 10-octafluoro[2, 2]paracyclophane ( 3 ) are presented. The bands corresponding to ejection of the photoelectron from the five highest occupied π-orbitals have been assigned. The ‘observed’ orbital energies (i.e. the negative ionization potentials) are discussed in terms of ‘through space’ and ‘through-bond’ interactions between the semi-localized π-orbitals ( e_1g ) of the benzene moieties and the C, C-σ-orbitals of the ethylene bridges. The PE. spectrum of 3 shows that the fluorine-induced lowering of the C, C-σ-orbital energy effectively ‘turns-off’ the ‘through-bond’ interaction. The resulting pattern of the first four bands confirms the assignment given for 1 . Finally the band shifts induced by an amino group in position 4 are again in agreement with this assignment. Attention is drawn to the phenomenon of ‘orbital switching’ as a consequence of substitution in loosely coupled systems such as 1 .     

Intermolecular biological electron transfer: an electrochemical approach.

We investigated the electron transfer (ET) rates between a well-defined gold electrode and cytochrome c immobilized at the carboxylic acid terminus of alkanethiol self-assembled monolayers (SAMs) by using the potential modulated electroreflectance technique. A logarithmic plot of ET rates against the chain length of the alkanethiol is linear with long chain alkanethiols. The ET rates become independent of the chain length with short alkanethiols. It is proposed that the rate-limiting ET step through short alkyl chains results from a configurational rearrangement process preceding the ET event. This "gating" process arises from a rearrangement of the cytochrome c from a thermodynamically stable binding form on the carboxylic acid terminus to a configuration, which facilitates the most efficient ET pathways (surface diffusion process). We propose that the lysine-13 of mammalian cytochrome c facilitates the most efficient ET pathway to the carboxylate terminus and this proposal is supported by the ET reaction rate of a rat cytochrome c mutant (RC9-K13A) [Elektrokhimiya (2001) in press], in which lysine-13 is replaced by alanine. The ET rate of K13A is more than six orders of magnitude smaller than that of the native protein.     

Terms representing the reorganization of bonding within charge‐bond order matrices of reacting molecules

The usual way of obtaining charge‐bond order (CBO) matrices of molecules by summing up the MO LCAO coefficients over occupied molecular orbitals (MOs) is extended to derive terms representing the reorganization of bonding in reacting systems. The CBO matrix of a certain molecule (reactant) under influence of another one (reagent) is expressed in the form of power series with respect to intermolecular interaction. Terms of this series responsible for the internal reorganization of bonding in the reactant are also shown to be representable by sums of MO LCAO coefficients of the relevant isolated compound. As opposed to the case of a single molecule, the new sums embrace all MOs of the reactant and their pairs. This result is conditioned by the fact that the actual occupation numbers of MOs differ from either two or zero in the bimolecular system because of the intermolecular charge transfer, and bond orders arise between pairs of MOs in addition. Partial increments to the final reorganization of bonding related to individual MOs and to their pairs are then studied separately. These increments may be classified on the basis of criteria applied to MOs they originate from. In particular, symmetric and antisymmetric increments are distinguished with respect to any symmetry operation of the isolated reactant lost under influence of an approaching reagent. Increments of the same symmetry are subsequently collected into separate groups representable by specific graphical schemes. Consequently, the final pattern of charge and bond order redistribution in the reactant under influence of an approaching reagent follows from superposition of a few principal schemes. The results are illustrated by consideration of specific examples, in particular of addition of electrophile to the butadiene molecule. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Photoelectrochemical properties of alternating multilayer films composed of titania nanosheets and Zn porphyrin

Alternating multilayer films composed of titania nanosheets and Zn porphyrins were prepared by use of a previously reported Langmuir-Blodgett film-transfer method in order to fabricate photoelectrochemical devices. Closely packed titania nanosheet monolayers on indium tin oxide (ITO), mica, and quartz surfaces strongly adsorbed cationic [5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrinatozinc]4+ (ZnTMPyP4+) by electrostatic interactions. The alternating deposition process afforded nanometer-scale multilayer films with the following structure: solid surface/(titania nanosheet/ZnTMPyP4+)n (n is the number of layers). The multilayer films were characterized by various physical measurements, including AFM, XRD, and UV-visible spectra. The visible-light irradiation of this multilayer film on an ITO electrode in the presence of triethanolamine as an electron donor yielded an anodic photocurrent. The action spectrum was consistent with the absorption spectrum of ZnTMPyP4+, which indicates that the photoexcitation of ZnTMPyP4+ is responsible for the photocurrent generation. However, the photocurrent density decreased with an increasing number of layers, which indicates that the harvesting of photoexcited electrons vertically through the titania nanosheets in the ITO/(titania nanosheet/ZnTMPyP4+)n structure was not efficient. To overcome this problem, the use of a lateral interlayer connection to all of the titania nanosheets with Ag paste was examined. As a result, a dramatic improvement in the photocurrent density was obtained. Thus, for efficient photocurrent generation with the titania nanosheet-ZnTMPyP4+ composite material, the lateral connection to all of the titania nanosheet layers is effective.     

Photochemical and photoelectrochemical behaviour of chlorophyll a-smectite conjugate

Chlorophyll a was adsorbed onto smectite to form chlorophyll-smectite conjugate, which became photostable against light illumination. The chlorophyll-smectite conjugate caused the photoreduction of nitro blue tetrazolium, NBT, through the formation of superoxide anion, and the conjugate retained the photosensitive activity even after 20 hour illumination. Furthermore, the conjugate deposited on SnO₂ electrode caused electron transfer under light illumination. The anodic photocurrent rose at ?200 mV versus Ag/AgCl electrode (KCl saturated) and reached a maximum level at approximately +100 mV. The photocurrent spectrum was in good agreement with the absorption spectrum of chlorophyll-smectite conjugate in an aqueous solution and the quantum efficiency was approximately 1% at 670 nm.     

Using scanning electrochemical microscopy (SECM) to measure the electron-transfer kinetics of cytochrome c immobilized on a COOH-terminated alkanethiol monolayer on a gold electrode

Cytochrome c was electrostatically immobilized onto a COOH-terminated alkanethiol self-assembled monolayer (SAM) on a gold electrode at ionic strengths of less than 40 mM. Scanning electrochemical microscopy (SECM) was used to simultaneously measure the electron transfer (ET) kinetics of the bimolecular ET between a solution-based redox mediator and the immobilized protein and the tunneling ET between the protein and the underlying gold electrode. Approach curves were recorded with ferrocyanide as a mediator at different coverages of cytochrome c and at different substrate potentials, allowing the measurement of k(BI) = 2 x 10(8) mol(-1) cm3 s(-1) for the bimolecular ET and k degrees = 15 s(-1) for the tunneling ET. The kinetics of ET was also found to depend on the immobilization conditions of cytochrome c: covalent attachment gave slightly slower tunneling ET values, and a mixed CH3/COOH-terminated ML gave faster tunneling ET rates. This is consistent with previous studies and is believed to be related to the degree of mobility of cyt c in its binding configuration and its orientation with respect to the underlying electrode surface.     

Photosensing Device Composed of Bilayer Membranes of Polymer-Pendant Ru(bpy)3 2+ and Prussian Blue

A photosensing device was fabricated based on a photochemical electron transfer reaction. A graphite electrode was coated with bilayer membranes of polymer-pendant Ru(bpy)₃ ²⁺ and Prussian Blue (PB) to give a bilayer-coated device. It was irradiated with visible light in an aqueous electrolyte and the induced photocurrent was measured as a function of the applied potential. The excitation of PB was responsible for the anodic photocurrent, while the excitation of the Ru complex mainly induced the cathodic photocurrent by an electron-transfer mechanism.     

Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO-LCMO approach

By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling T(DA) of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate T(DA). Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable T(DA) for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.     

Kernel energy method: Basis functions and quantum methods

The kernel energy method (KEM) has been illustrated with peptides and has been shown to reduce the computational difficulty associated with obtaining ab initio quality quantum chemistry results for large biological compounds. In a recent paper, the method was illustrated by application to 15 different peptides, ranging in size from 4 to 19 amino acid residues, and was found to deliver accurate Hartree–Fock (HF) molecular energies within the model, using Slater‐type orbital (STO)‐3G basis functions. A question arises concerning whether the results obtained from the use of KEM are wholly dependent on the STO‐3G basis functions that were employed, because of their relative simplicity, in the first applications. In the present work, it is shown that the accuracy of KEM does not depend on a particular choice of basis functions. This is done by calculating the ground‐state energy of a representative peptide, ADPGV7B, containing seven amino acid residues, using seven different commonly employed basis function sets, ranging in size from small to medium to large. It is shown that the accuracy of the KEM does not vary in any systematic way with the size or mathematical completeness of the basis set used, and good accuracy is maintained over the entire variety of basis sets that have been tested. Both approximate HF and density functional theory (DFT) calculations are made. We conclude that the accuracy inherent in the KEM is not dependent on a particular choice of basis functions. The first application, to 15 different peptides mentioned above, employed only HF calculations. A second question that arises is whether the results obtained with the use of KEM will be accurate only within the HF approximation. Therefore, in the present work we also study whether KEM is applicable across a variety of quantum computational methods, characterized by differing levels of accuracy. The peptide, Zaib4, containing 74 atoms, was used to calculate its energy at seven different levels of accuracy. These include the semi‐empirical methods, AM1 and PM5, a DFT B3LYP model, and ab initio HF, MP2, CID, and CCSD calculations. KEM was found to be widely applicable across the spectrum of quantum methods tested. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Long-Range Electron Transfer in Rigid 310-Helical Oligopeptides Containing Redox Cyclic a-Amino Acids

Intrahelical photoinduced electron transfer processes (ET) in conformationally restricted oligopeptides have been studied by nanosecond time-resolved transient spectroscopy. The helical peptides were constructed from sterically hindered alpha-aminoisobutyric acid (Aib) and two cyclic alpha-amino acids (Aib class) bearing electron acceptor and donor side chains (DkNap, ThQx). This helical backbone design provides high conformation stability, as previously demonstrated, and yields reliable 3(10)-helical architectures in solution. The forward ET between ThQx and 3DkNap is followed by a slow back ET thus giving rise to an accumulation of the charge-separated ion pairs for hundreds of nanoseconds. We demonstrate the modulation of electronic interactions by the number of intervening Aib residues separating acceptor-donor side chains and propose modifications of the peptide framework by inclusion of a non-Aib amino acid residue. These well-defined and sterically stable frameworks are suited for the precise evaluation of intrahelical electron transfer processes mediated by peptides.     

重氮树脂-聚(4-羧酸苯基)乙炔自组装膜与光电转换

近年来 ,自组装及其形成的多层复合膜已经在导电、生物传感器及非线性光学等领域得到深入研究 ,特别是以聚阴离子与聚阳离子相互作用的静电自组装研究更为深入 .这一技术制备方法简单 ,无需特别的设备 ,对膜层厚度能随意调控 ,并以水作为介质 ,对环境无害 [1～ 3] .共轭高分子 (如聚苯胺、聚吡咯及聚苯亚乙烯等 )通过自组装形成共轭高分子膜 ,对制备具有导电、光电和传输等功能的薄膜半导体器件具有重要意义 .聚乙炔类是最早被发现且理论与应用研究最多的一类共轭高分子材料[4 ,5] .本文以聚 ( 4 -羧酸苯基 )乙炔 ( PCPA)为聚阴离子 ,以重…     

对电极性能对染料敏化太阳电池动力学过程的影响

借助电化学阻抗谱(EIS)和强度调制光电流谱(IMPS)/强度调制光电压谱(IMVS)技术, 采用不同纳米TiO₂多孔薄膜对电极研究了染料敏化太阳电池(DSC)内部2个主要电荷输运过程的内在联系, 并探讨了载Pt材料对DSC界面动力学过程及电池宏观性能的影响机理. 借助等效电路模型分析了基于不同对电极材料电池的填充因子变化原因. 结果表明, 对电极材料的电极电荷交换过程制约光阳极膜内电子传输, 进而影响电池光伏性能; 同时对电极催化反应速率主要与催化剂活性、 载Pt材料电导率和催化反应面积有关.     

Electronic structure of 2,5-dimethylazaferrocene

The electronic structure of 2,5-dimethylazaferrocene has been studied by UV photoelectron spectroscopy (UPS) and high-level DFT methods. UPS data have been used to assign the previously reported spectrum of its radical-cation. We show that aza substitution enhances mixing/interaction between Fe 3d and ligand π-orbitals.     

Dynamic theory of the alternating current response of semiconductor electrodes under illumination

A photoinduced admittance enhancement has been observed on n-GaAs and n-GaP electrodes in the potential range between flatband and stationary photocurrent onset. In order to provide a theoretical evaluation, the alternating current response of a semiconductor electrode under illumination has been investigated on the basis of non-equilibrium treatment of the carrier balance in the semiconductor and of the interfacial charge transfer kinetics. Superposition of an irreversible stationary and small-amplitude periodic rate has been treated for the following cases of charge transfer at the interface: (a) one-step electrochemical process; (b) two-step electrochemical process including an adsorbed intermediate and partial charge transfers; (c) parallel couple of one-step electrochemical and partial charge transfer chemisorption process. Empirical criteria for preference of charge transfer over surface recombination have been considered. In connection with the present development, the general equivalent circuit of a semiconductor electrode has been briefly derived from the dynamical charge balance. The theoretical approach of the stationary photocurrent-voltage curve has been discussed and refined.