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Probing the electronic structure and conformational flexibility of individual light-harvesting 3 complexes by optical single-molecule spectroscopy.

We present fluorescence-excitation spectra of individual light-harvesting 3 (LH3 or B800-820) complexes of Rhodopseudomonas acidophila at 1.2 K. The optical single-molecule studies were employed to investigate the electronic structure as well as the conformational flexibility of the individual pigment-protein complexes. The optical spectra resemble those of individual light-harvesting 2 (LH2) complexes, in agreement with the structural similarity of both types of complexes. Although variations among the LH3 spectra are large, there is a distinct difference in the spectral features of the 800 and 820 nm region that appears in all the complexes studied. In the B800 region 4-6 narrow bands are present whereas in the B820 region a limited number of relatively broad bands are observed. These observations can generally be interpreted in terms of localized excitations in the 800 nm region and delocalized excitations in the 820 nm region. The observed heterogeneous spectral behavior, especially in the B820 band, indicates that the B820 pigments of LH3 are sensitive to light-induced local conformational changes. It is suggested that a rotation of the C(3)-acetyl chain of a BChl a pigment bound to the beta-subunit of the light-harvesting complex is the origin of the conformational flexibility and affects the optical properties of the whole pigment-protein complex.

Biophysics↗

[Spin-dependent electronic structure near the iron atom in rubredoxin].

The fine structure of X-ray absorption spectrum of Fe in rubredoxin was interpreted on the basis of the multiple scattering theory and the results of calculations of the self-consistent potential. For biological molecules, such calculations were made for the first time. It was found that the Fe-S interaction is the main factor, which determines the electronic structure of the protein active center. The changes in spectrum shape are mostly due to the spin configuration of 3d-electrons. It was shown that the dipole transition element significantly changes near the absorption edge; therefore, it is impossible to determine the distribution of unoccupied electronic p-states directly from experiment. However, the results of calculations obtained in this work are consistent with the corresponding experimental data, indicating the adequacy of the calculated densities of free electronic states.

Electron Probe Microanalysis↗

Electronic structure, vibrational stability, and predicted infrared-Raman spectra of the As20, As @ Ni12, and As @ Ni12 @ As20 clusters.

Recently an inorganic fullerine-like [As@Ni(12)@As(20)](3-) onion with near-perfect icosahedral symmetry in the crystalline phase was reported [M. J. Moses, J. C. Fettinger, and B. W. Eichhorn, Science 300, 778 (2003)]. This paper presents a detailed computational study in the framework of density functional theory on various aspects of this molecule. The electronic structure of the As@Ni(12)@As(20) is investigated in its neutral as well as -3 charged state together with its subunits As(20) and As@Ni(12) by the all electron linear combination of Gaussian-type orbitals method. The bonding is studied by examining the integrated charge within atomic sphere, the electron localization function, changes in the electron density distribution, and from vibrational modes. We find that strong covalent As-As bonds seen in isolated As(20) become weaker in the As@Ni(12)@As(20) and strong covalent As-Ni bonds are formed. The structural stability of all four clusters is examined by analyzing the energetics and by calculating the vibrational frequencies. Further, the infrared and Raman spectra is predicted for both the neutral and charged As@Ni(12)@As(20) clusters. Finally, the energy barrier for removal of a single arsenic atom is calculated for the neutral As@Ni(12)@As(20) cluster.

Journal Article↗

Electronic structures and properties of eight-coordinate metal-polyarsenic complexes MAs8n- (M = V, Nb, Ta, Cr, Mo, W, Mn, Tc, Re).

The eight-coordinate early transition metal polyarsenic complexes, MAs(8)3- (M = V, Nb, Ta), MAs(8)2- (M = Cr, Mo, W), and MAs8- (M = Mn, Tc, Re), have been studied using density functional theory (DFT). The geometry optimizations of these complexes indicate that in the most stable structures the transition metal atoms are trapped in a crownlike cavity consisting of a zigzag eight-membered ring of As8 cluster. The scalar-relativistic effects and spin-orbit coupling effects on the electronic structures and energy levels were taken into account. The stabilities of gas-phase MAs8n- ions and bonding between the As8 ring and early transition metals are discussed on the basis of population analysis, atomization energies, and decomposition reaction energies. All these complex ions are found to be diamagnetic with notable HOMO-LUMO energy gaps. The vibrational frequencies and infrared absorption intensities of the MAs8n- series are predicted theoretically. Brief theoretical calculations of the similar MoA(8)2- pnictide ions indicate that the analogous P, Sb, and even Bi complexes are likely to be stable, whereas the crownlike MoN(8)2- is not a stable complex.

Journal Article↗

Variation of the electronic structure in systematically synthesized Sr2MO4 (M = Ti, V, Cr, Mn, and Co).

We have systematically synthesized single-crystalline thin films of layered perovskites Sr2MO4 (M = Ti, V, Cr, Mn, and Co) which cannot be obtained in a form of bulk crystal apart from M = Mn. The two-dimensional electronic structure of these M4+ oxides, ranging from a correlated insulator to a ferromagnetic metal, has been investigated by using their optical conductivity spectra with polarizations E is perpendicular to c and E is parallel to c, which reveal systematic variation of the correlated charge gap, Mott-Hubbard gap, or charge-transfer gap. Temperature dependence of the gap-transition spectra is argued in the light of possible spin and/or orbital ordering.

Journal Article↗

One-Dimensional Electronic Structure and Suppression of d-Wave Node State in (La(1.28)Nd(0.6)Sr(0.12))CuO(4).

Angle-resolved photoemission spectroscopy was carried out on (La(1.28)Nd(0.6) Sr(0.12))CuO(4), a model system of the charge- and spin-ordered state, or stripe phase. The electronic structure contains characteristic features consistent with other cuprates, such as the flat band at low energy near the Brillouin zone face. However, the low-energy excitation near the expected d-wave node region is strongly suppressed. The frequency-integrated spectral weight is confined inside one-dimensional segments in the momentum space (defined by horizontal momenta &cjs3539;k(x)&cjs3539; = pi/4 and vertical momenta &cjs3539;k(y)&cjs3539; = pi/4), deviating strongly from the more rounded Fermi surface expected from band calculations. This departure from the two-dimensional Fermi surface persists to a very high energy scale. These results provide important information for establishing a theory to understand the charge and spin ordering in cuprates and their relation with high-temperature superconductivity.

Journal Article↗

[Electronic structures of organometallic complexes of f elements. Part 54. Electronic Raman and f-f transitions in the low temperature vibrational spectra of Cp3Ce(NCCH3)2].

A comparison of the low temperature Raman spectra of Cp(3)Ce(NCCH(3))(2) (1), Cp(3)La(NCCH(3))(2) (2), Cp(3)La(NCCH(3))(2):Pr(3+) (3), Cp(3)La x NCCH(3) (4), Cp(3)Ce x NCCH(3) (5) and Cp(3)Tb x NCCH(3) (6) shows that the former compound exhibits three additional bands at 320, 2129 and 2154 cm(-1), which we ascribe to electronic Raman transitions. The two latter signals also appear in the low temperature IR spectrum of complex 1, but not in those of compounds 2-6. By performing crystal field (CF) calculations, the terminal states of the observed electronic Raman transitions could be identified. On the basis of both experimental and calculated CF energies as well as calculated wave functions the observed temperature dependence of mu(2)(eff) of complex 1 could be simulated in a satisfactory manner. A comparison of the low temperature Raman spectrum of compound 1 with the low temperature FIR spectrum of complex 2 shows that the selection rules for trigonal-bipyramidal coordination do not hold strictly for the skeletal vibrations. If the additional criterion of allowed vibronic side bands is applied to the transitions Gamma(1)-->Gamma(1, 4, 5, 6) of compound 3, the observed vibrational energies may be partly classified according to their symmetry.

Cerium↗

Molecular and electronic structures of iron complexes containing N,S-coordinated, open-shell o-iminothionebenzosemiquinonate(1-) pi radicals.

The reaction of the dinuclear species (mu-NH,NH)[Fe(III)(L(IP))(L(AP))](2) dissolved in CH(2)Cl(2) with dioxygen affords black microcrystals of diamagnetic (mu-S,S)[Fe(III)(L(IP))(L(ISQ))](2).n-hexane (6) upon the addition of n-hexane, where (L(IP))(2)(-) represents the dianion of 4,6-di-tert-butyl-2-aminothiophenol, (L(AP))(-) is the corresponding monoanion, and (L(ISQ))(-) is the corresponding o-iminothionebenzosemiquinonate(1-) pi radical monoanion; similarly, the dianion ('H(2)N(2)S(2)')(2)(-) is derived from 1,2-ethanediamine-N,N'-bis(2-benzenethiol), and ('N(2)S(2)(*)')(3)(-) is its monoradical trianion. The above reaction in a CH(2)Cl(2)/CH(3)OH (1:1) mixture yields the diamagnetic isomer (mu-NH,NH)[Fe(III)(L(IP))(L(ISQ))](2).5CH(3)OH (7), whereas air oxidation of (mu-S,S)[Fe(II)('H(2)N(2)S(2)')](2) in CH(3)CN yields diamagnetic (mu-S,S)[Fe(III)('N(2)S(2)(*)')](2) (8). Complexes 6 and 8 were shown to undergo addition reactions with phosphines, phosphites, or cyanide affording the following complexes: trans-[Fe(II)(L(ISQ))(2)(P(OPh)(3))] (9; S(t) = 0) and [N(n-Bu)(4)][Fe(II)(L(ISQ))(2)(CN)] (S(t) = 0). Oxidation of 6 in CH(2)Cl(2) with iodine, bromine, and chlorine respectively yields black microcrystals of [Fe(III)(L(ISQ))(2)X] (X = I, Br, or Cl) with S(t) = (1)/(2). The structures of complexes 6-9 have been determined by X-ray crystallography at 100 K. The oxidation level of the ligands and iron ions in all complexes has been unequivocally established, as indicated by crystallography; electron paramagnetic resonance, UV-vis, and Mössbauer spectroscopies; and magnetic-susceptibility measurements. The N,S-coordinated o-iminothionebenzosemiquinonate(1-) pi radicals have been identified in all new complexes. The electronic structures of the new complexes have been determined, and it is shown that no evidence for iron oxidation states >III is found in this chemistry.

Journal Article↗

Electronic structures of intermolecular charge-transfer states in fast electron transfers with tetrathiafulvalene donor. Thermal and photoactivation of [2 + 4] cycloaddition to o-chloranil acceptor.

Tetrathiafulvalene (TTF) spontaneously forms a series of unusual charge-transfer complexes with various quinonoid acceptors such as o-chloranil (CA) that show pronounced near-IR absorption (lambda(CT) = 1100 nm). The successful isolation of the corresponding [1 : 1] donor-acceptor complex from solution and X-ray crystallographic analysis at low temperatures reveal the polarized charge-transfer state: [TTF(q+),CA(q-)] with high degree of charge-transfer (q = 0.6), which is spectrally and crystallographically distinguished from the separate redox (ion-pair) state: [TTF(+*) + CA(-*) ]. The unique interconversion of charge-transfer and electron-transfer states is theoretically well-accommodated by Mulliken theory using semi-empirical valence-bond and molecular-orbital methodologies. Mechanistic implications are discussed of both the thermally activated and the photochemically promoted processes via fast (intracomplex) electron transfer followed by collapse of the adiabatic and the non-adiabatic (vibrationally-excited) ion-pairs, respectively, to the [2 + 4] cycloadduct of tetrathiafulvalene and o-chloranil.

Journal Article↗

Electronic structures and charge transport properties of the organic semiconductor bis[1,2,5]thiadiazolo-p-quinobis(1,3-dithiole), BTQBT, and its derivatives.

We analyze the correlation between crystal and film structures and charge transport of an important organic semiconductor, bis[1,2,5]thiadiazolo-p-quinobis(1,3-dithiole) (BTQBT), and its derivatives 4,8-bis(1,3-dithiol-2-ylidene)-4H,8H-[1,2, 5]selenadiazolo[3,4-f]-2,1,3-benzothiadiazole, 4,8-bis(1,3-diselenol-2-ylidene)-4H,8H-benzo[1,2-c:4,5-c']bis[1,2,5]thiadiazole, and tetramethyl-BTQBT. We present first-principles density functional theory (DFT) calculations that agree well with earlier angle-resolved photoelectron spectroscopy (ARPES) experiments on BTQBT films, strongly supporting that the BTQBT films adopt the same layered structure as in the single crystals. Qualitative charge transport properties based on presented DFT results agree with experiments regarding the sign of the charge carriers and the unusually small anisotropy of conductivity. These agreements indicate that accurate electronic structure calculations, when coupled with ARPES, help establish the correlation between intermolecular packing and charge transport, which is one of the central but elusive aspects of organic molecular materials. Predictions are made for derivatives of BTQBT, and calculations agree with available experimental information on the conductivities. Comparisons are made with pentacene, one of the most widely studied organic molecular materials.

Journal Article↗

Structures, electronic states, photoluminescence, and carrier transport properties of 1,1-disubstituted 2,3,4,5-tetraphenylsiloles.

The excellent electroluminescent (EL) properties of 1,1-disubstituted 2,3,4,5-tetraphenylsiloles, 1-methyl-1,2,3,4,5-pentaphenylsilole (MPPS), and 1,1,2,3,4,5-hexaphenylsilole (HPS) have been found. Despite some studies devoted to these materials, very little is known about the real origin of their unique EL properties. Therefore, we investigated the structures, photoluminescence (PL), and charge carrier transport properties of 1,1-disubstituted 2,3,4,5-tetraphenylsiloles as well as the effect of substituents on these characteristics. The single crystals of the three siloles involving 1,1-dimethyl-2,3,4,5-tetraphenylsilole (DMTPS), MPPS, and HPS were grown and their crystal structures were determined by X-ray diffraction. Three siloles have nonplanar molecular structures. The substituents at 1,1-positions enhance the steric hindrance and have predominant influence on the twisted degree of phenyl groups at ring carbons. This nonplanar structure reduces the intermolecular interaction and the likelihood of excimer formation, and increases PL efficiency in the solid state. The silole films show high fluorescence quantum yields (75-85%), whereas their dilute solutions exhibit a faint emission. The electronic structures of the three siloles were investigated using quantum chemical calculations. The highest occupied molecular orbitals (HOMOs) and the lowest unoccupied molecular orbitals (LUMOs) are mainly localized on the silole ring and two phenyl groups at 2,5-positions in all cases, while the LUMOs have a significant orbital density at two exocyclic Si-C bonds. The extremely theoretical studies of luminescent properties were carried out. We calculated the nonradiative decay rate of the first excited state as well as the radiative one. It is found that the faint emission of DMTPS in solutions mainly results from the huge nonradiative decay rate. In solid states, molecular packing can remarkably restrict the intramolecular rotation of the peripheral side phenyl ring, which has a large contribution to the nonradiative transition process. This explains why the 1,1-disubstituted 2,3,4,5-tetraphenylsiloles in the thin films exhibit high fluorescence quantum yields. The charge carrier mobilities of the MPPS and HPS films were measured using a transient EL technique. We obtained a mobility of 2.1 x 10(-)(6) cm(2)/V.s in the MPPS film at an electric field of 1.2 x 10(6) V/cm. This mobility is comparable to that of Alq(3), which is one of the most extensively used electron transport materials in organic light-emitting diodes (LEDs), at the same electric field. The electron mobility of the HPS film is about approximately 1.5 times higher than that of the MPPS film. To the best of our knowledge, this kind of material is one of the most excellent emissive materials that possess both high charge carrier mobility and high PL efficiency in the solid states simultaneously. The excellent EL performances of MPPS and HPS are presumably ascribed to these characteristics.

Journal Article↗

[EPR studies and the role of the electron structure of the heterocycle in the metabolic denitrosation of 5-nitrofuran].

The ESR method revealed that the reduction of 5-nitrofuran and nitrobenzene in liver homogenate is accomplished by the appearance of the nitro anion radicals. ESR spectrum of nitroxyl radical for nitrobenzene was recorded. Metabolic denitrosation in liver homogenate and the formation of hemoprotein nitrosyl complexes were present for 5-nitrofuran and were absent for nitro- and nitrosobenzene. Quantum chemical calculations of the electron structure for the molecules of 5-nitrosofuran and nitrosobenzene showed that the electronegative oxygen atom in the aromatic system turns to increase the positive charge of C atom bonded to NO group. The process of denitrosation in the molecules of 5-nitrosofuran and 5-N-furylhydroxylamine was proposed to include the reaction of nucleophilic NO group substitution.

Animals↗

A simple theoretical model to study the voltage dependence of the electronic structure of phenyl ethylene oligomers.

Although very few measurements have appeared in the open literature and there seems to be a controversy about the existence of the NDR phenomenon in molecules, the prospects of building such systems have attracted significant attention. In the work reported in this paper we used a model based on DFT calculations of the electronic structure of the 2'-amino-4,4'-di(ethynylphenyl)-5'-nitro-1-benzenethiolate molecule (previously reported to exhibit NDR behavior) in a capacitor-like electric field that mimics the potential spatial profile of the junction. Our results suggest that in these systems, there seems to be a correlation between a substantial charge density rearrangement of the neutral bridge at a threshold voltage and the NDR behavior observed in previous experiments. Our results highlight the importance of inclusion of the field in the study of electrified interfaces. We applied this model to a fluorine-substituted conjugated diethynylphenyl molecule and found that these calculations predict similar behavior. Results based on extended system calculations, including electrode-molecule interactions, confirm the validity of the model based on the isolated molecule and suggest the use of these simple models to rationally design molecular devices with similar switching characteristics.

Algorithms↗

Numerical performance and throughput benchmark for electronic structure calculations in PC-Linux systems with new architectures, updated compilers, and libraries.

A number of recently released numerical libraries including Automatically Tuned Linear Algebra Subroutines (ATLAS) library, Intel Math Kernel Library (MKL), GOTO numerical library, and AMD Core Math Library (ACML) for AMD Opteron processors, are linked against the executables of the Gaussian 98 electronic structure calculation package, which is compiled by updated versions of Fortran compilers such as Intel Fortran compiler (ifc/efc) 7.1 and PGI Fortran compiler (pgf77/pgf90) 5.0. The ifc 7.1 delivers about 3% of improvement on 32-bit machines compared to the former version 6.0. Performance improved from pgf77 3.3 to 5.0 is also around 3% when utilizing the original unmodified optimization options of the compiler enclosed in the software. Nevertheless, if extensive compiler tuning options are used, the speed can be further accelerated to about 25%. The performances of these fully optimized numerical libraries are similar. The double-precision floating-point (FP) instruction sets (SSE2) are also functional on AMD Opteron processors operated in 32-bit compilation, and Intel Fortran compiler has performed better optimization. Hardware-level tuning is able to improve memory bandwidth by adjusting the DRAM timing, and the efficiency in the CL2 mode is further accelerated by 2.6% compared to that of the CL2.5 mode. The FP throughput is measured by simultaneous execution of two identical copies of each of the test jobs. Resultant performance impact suggests that IA64 and AMD64 architectures are able to fulfill significantly higher throughput than the IA32, which is consistent with the SpecFPrate2000 benchmarks.

Journal Article↗

The synthesis and electronic structure of a novel [NiS4Fe2(CO)6] radical cluster: implications for the active site of the [NiFe] hydrogenases.

A novel [NiS4Fe2(CO)6]cluster (1: 'S(4)'=(CH(3)C(6)H(3)S(2))(2)(CH(2))(3)) has been synthesised, structurally characterised and has been shown to undergo a chemically reversible reduction process at -1.31 V versus Fc(+)/Fc to generate the EPR-active monoanion 1(-). Multifrequency Q-, X- and S-band EPR spectra of (61)Ni-enriched 1(-) show a well-resolved quartet hyperfine splitting in the low-field region due to the interaction with a single (61)Ni (I=3/2) nucleus. Simulations of the EPR spectra require the introduction of a single angle of non-coincidence between g(1) and A(1), and g(3) and A(3) to reproduce all of the features in the S- and X-band spectra. This behaviour provides a rare example of the detection and measurement of non-coincidence effects from frozen-solution EPR spectra without the need for single-crystal measurements, and in which the S-band experiment is sensitive to the non-coincidence. An analysis of the EPR spectra of 1(-) reveals a 24 % Ni contribution to the SOMO in 1(-), supporting a delocalisation of the spin-density across the NiFe(2) cluster. This observation is supported by IR spectroscopic results which show that the CO stretching frequencies, nu(CO), shift to lower frequency by about 70 cm(-1) when 1 is reduced to 1(-). Density functional calculations provide a framework for the interpretation of the spectroscopic properties of 1(-) and suggest that the SOMO is delocalised over the whole cluster, but with little S-centre participation. This electronic structure contrasts with that of the Ni-A, -B, -C and -L forms of [NiFe] hydrogenase in which there is considerable S participation in the SOMO.

Binding Sites↗