Quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes

The present review describes the use of quantum chemical methods in estimation of structures and electronic transition energies of photosynthetic pigments in vacuum, in solution and imbedded in proteins. Monomeric Mg-porphyrins, chlorophylls and bacteriochlorophylls and their solvent 1:1 and 1:2 complexes were studied. Calculations were performed for Mg-porphyrin, Mg-chlorin, Mg-bacteriochlorin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), d and bacteriochlorophylls a, b, c, d, e, f, g, h, plus several homologues. Geometries were optimised with PM3, PM3/CISD, PM5, ab initio HF (6-31G*/6-311G**) and density functional B3LYP (6-31G*/6-311G**) methods. Spectroscopic transition energies were calculated with ZINDO/S CIS, PM3 CIS, PM3 CISD, ab initio CIS, time-dependent HF and time-dependent B3LYP methods. Estimates for experimental transition energies were obtained from linear correlations of the calculated transition energies of 1:1 solvent complexes against experimentally recorded solution energies (scaling). According to the calculations in five-coordinated solvent complexes the magnesium atom lies out of the porphyrin plane, while in six-coordinated complexes the porphyrin is nearly planar. Charge densities on magnesium and nitrogen atoms were strongly dependent on the computational method deployed. Several dark states of low oscillator strength below the main Soret band were predicted for solvent complexes and chlorophylls and bacteriochlorophylls in protein environment. Such states, though not yet identified experimentally, might serve as intermediate states for excitation energy transfer in photosynthetic complexes. Q(y), Q(x) and Soret transition energies were found to depend on the orientation of the acetyl group and external pressure. A method to estimate site energies and dimeric interaction energies and to simulate absorption and CD spectra of photosynthetic complexes is described. Simulations for the light harvesting complexes Rhodospirillum molischianum, chlorosomes of Chlorobium tepidum and Chloroflexus aurantiacus, and LHC-II of Spinacia oleracea are presented as examples.     

Trees and Ehrenfeucht–Fraïssé games

Trees are natural generalizations of ordinals and this is especially apparent when one tries to find an uncountable analogue of the concept of the Scott-rank of a countable structure. The purpose of this paper is to introduce new methods in the study of an ordering between trees whose analogue is the usual ordering between ordinals. For example, one of the methods is the tree-analogue of the successor operation on the ordinals.     

New Heteroaromatic Complexing Agents and Luminescence of Their Europium(III) and Terbium(III) Chelates

Twelve heteroaromatic complexing agents 9a–I were synthesized with the purpose to develop suitable labels for time-resolved luminescence-based bioaffinity assays. The relative luminescence yields, excitation maxima, and emission decay constants of their europium(III) and terbium(III) chelates were determined. According to these results, 2,2′,2″,2?-[(2,2′-bipyridine-6,6′-diyl)bis(methylenenitrilo)]tetrakis (acetic acid) ( 9e ) and 2,2′,2″,2?-[(2,2′:6′,2″-terpyridine-6,6″-diyl)bis(methylenenitrilo)] tetrakis(acetic acid) ( 91 ) are the most promising agents.     

Fast screening method for the analysis of total flavonoid content in plants and foodstuffs by high-performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry with polarity switching

A liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) method based on time-of-flight (TOF) MS with polarity switching and continuous exact mass measurement using a LockSpray ion source was developed for fast evaluation of the total flavonoid content in plants and foodstuffs. No complicated sample preparation was needed, but only a dilution of the extracts. A fast generic gradient elution and wide mass range acquisition was used with good sensitivity. The total analysis time was only 23 min. The ion chromatograms for flavonoid compounds were automatically extracted, and the fragmentation patterns obtained using positive ion mode and exact mass data for both polarities were used for the tentative identification of compounds. Software-based automated searching of molecular ions for flavonoids and their glycosides (xylosides/arabinosides, rhamnosides, glucosides/galactosides) from total ion chromatograms was used. The compounds were quantified using quercetin, quercitrin, rutin and kuromanine as external standards and dextromethorphan as an internal standard. The detection limits ranged from 0.01-0.04 microg/mL, while the quantitation ranges obtained were 0.2-10 microg/mL for anthocyanins and 0.2-4 microg/mL for the other flavonoids. The accuracies within these ranges varied between 80-120% and precision was in the range 0-14% (relative standard deviation). Flavonoid contents of two medicinal plants (Hypericum perforatum and Rhodiola rosea), two grape red wines, two orange juices and two green teas were evaluated using the method, and the results obtained were in good agreement with those published previously.     

Determination of cobalt, copper, iron, nickel and zinc in cemented tungsten carbides with cobalt as a binder by FAAS: Matrix effect control by multivariate technique

A new approach for the determination of cobalt, copper, iron, nickel and zinc in cemented tungsten carbides with cobalt as a binder by flame atomic absorption spectrophotometry (FAAS) is reported. Real samples were dissolved in phosphoric, hydrochloric and nitric acid. PTFE bomb or alternatively small amounts of HF were used for the enhancement of the recovery of the elements investigated. Synthetic samples were used for interference studies. Multiple linear regression was applied for the control of matrix effects and it proved to be very effective in the search for interfering elements. Using simple acid based standards, all investigated elements could be determined sequentially in a complex matrix by using an appropriate method of calculation. The method described has been succesfully applied to real type commercial samples. Results were compared with those obtained by inductively coupled plasma atomic emission spectrometry (ICP-AES) and X-ray fluorescence spectrometry (XRF), being in good agreement with each other and having relative standard deviations better than 5%.     

Self-termination rate of para-substituted benzyl radicals in aqueous solutions: a time-resolved study

The self-termination rates of the benzyl radical (C₆H₅---CH₂^√) and para-substituted benzyl radicals (X---C₆H₄---CH₂^√) were studied in aqueous solutions. The Arrhenius parameters and activation energies were determined in the temperature range 275.5–328 K. The kinetic activation energies of these radicals were close to the dynamic activation energy of the solvent, indicating that the termination rate is controlled by diffusion. The values for the rate constants (2k_t (10⁹ dm³ mol⁻¹ s⁻¹)) and the activation energies (E (kJ mol⁻¹)) were 5.94±0.52 and 14.69±0.61 for CH₃O---C₆H₄---CH₂^√, 4.52±0.2 and 17.65±1.16 for CH₃7z.sbnd;C₆H₄---CH₂^√, 3.07±0.45 and 17.58±0.97 for H---C₆H₄---CH₂^√, 4.13±0.81 and 19.10±1.20 for Cl---C₆H₄---CH₂^√ and 4.17±0.44 and 14.62±0.52 for NO₂---C₆H₄---CH₂^√.     

Synthesis of novel optical isomers of α-methylpolyamines

Earlier unknown (R)- and (S)-α-methylspermidine, (R)- and (S)-α-methylspermine, (R,R)-, (S,S)-, and (R,S)-α,ω-dimethylspermine were synthesized in gram scale from readily available (R)- and (S)-2-aminopropanols in high overall yields.     

Channel selective scanning tunneling spectroscopy

In this paper we simulate STM and STS experiments for CO monomers and dimers on Cu(1 1 1) surface. We show that the contrast of STM images can be attributed to interference effects between tunneling channels, and suggest that functionalizing the microscope tip improves the channel selectivity of STM. Furthermore, we show that voltage and position dependent tunneling spectra also reflect the same interference effects, but adds the energy resolution to the channel analysis. Especially in the case of nonresonant tunneling, STS measures local density of states only indirectly. The present study suggests that STS in constant height mode can be used in investigating the phase and energy sensitivity of tunneling channels in adsorbate molecules and nanostructures.     

Variational principles and linked-cluster exp S expansions for static and dynamic many-body problems

The exp S formalism for the ground state of a many-body system is derived from a variational principle. An energy functional is constructed using certain n-body linked-cluster amplitudes with respect to which the functional is required to be stationary. By using two different sets of amplitudes one either recovers the normal exp S method or obtains a new scheme called the extended exp S method. The same functional can be used also to obtain the average values of any operators as well as the linear response to static perturbations. The theory is extended to treat dynamical phenomena by introducing time dependence to the cluster amplitudes. This allows the calculation of both nonlinear dynamical behaviour and of dynamical linear response and Green's functions. Practical approximation schemes are considered. In a SUB n approximation the m-body amplitudes are restricted to the order $\text{m ? n}$ and the energy functional is a finite-order multinomial in the amplitudes to be variationally determined. It is shown that the solution corresponds to summing well-defined subsets of Goldstone diagrams. These subsets are conveniently specificed in terms of tree structures, the normal or extended generalized time ordering g.t.o. trees. The extended exp S method is in the SUB n approximation able to sum, in addition to the normal SUB n diagrams, a set which contains m-body cluster amplitudes of arbitrarily high order (m > n) in the ordinary sense. The article also discusses how the SUB n truncation schemes must be modified to be able to treat a system with a strong repulsive core in the two-body interaction. The method is formulated for the general cases of Bose and Fermi systems which may or may not conserve total particle number. It is shown that the simplest approximation, SUB 1, in the extended exp S method agrees with the mean field theory, which is the coherent-state approximation in the boson case or the Hartree-Fock approximation in the fermion case. It is argued that the extended exp S method already in low-order approximations can realistically treat a great variety of diverse many-body problems, even including systems which may undergo ground-state phase transitions. A few applications are described in more detail. The Bose liquid is treated in the extended SUB 2 approximation. It is shown that the ground-state results in the uniform limit are exact and agree with the hypernetted-chain approximation. The modifications due to hard-core interactions and the non-linear equations of motion are also discussed in this case. For Fermi systems it is shown that the supercondictive phase transition of the BCS model Hamiltonian and the deformation phase transition of the Lipkin model are properly obtained by the extended exp S method in a low-order approximation.     

Association of tert-butyl alcohol: a matrix infrared study

Infrared spectra of (CH₃) ₃COH, (CH₃)₃COD, (CD₃)₃COH and (CD₃)₃COD have been studied in the liquid and solid states, in CCl₄ and CS₂ solutions, and in argon, krypton and nitrogen matrices. The Raman spectra of the solids and of CCl₄, and H₂O solutions have been recorded. The matrix infrared results show that in the matrices tert-butyl alcohol has two well-defined dimer associates, both of which seem to have an open-chain structure. A network is proposed for the higher associates. The relative strengths of the protium and deuterium bonds are discussed in terms of the monomer hydroxyl-stretching frequencies and the Δv shifts. Association characteristics of the most important fundamental bands in several spectra are given.