PHYSICAL AND CHEMICAL PROPERTIES OF CHLOROPHYLL RCI EXTRACTED FROM PHOTOSYSTEM I OF SPINACH LEAVES AND FROM GREEN ALGAE

Abstract— A new chlorophyll, designated chlorophyll RCI (Chi RCI), with absorption and fluorescence properties different to other known chlorophylls, has been extracted from photosystem I (PSI) sub-chloroplast particles of the green alga Scenedesmus obliquus; it was suggested that this chlorophyll is either the chromophore ofP–700 or the chromophore of another holochrome associated in a 1:1 molar ratio withP–700. We now report the extraction and isolation of a chlorophyll from PSI particle preparations from spinach leaves with properties identical to those of Chi RCI from Scenedesmus. Its molar ratio toP–700 measured in vivo is again approximately 1:1. Chlorophyll RCI is further characterized by its fluorescence characteristics and redox behaviour. Molecular weight determinations show that Chi RCI has a mol wt 35 units higher than that of chlorophyll a (Chi a).     

Evolutionary algorithm based configuration interaction approach

A new evolutionary algorithm for stochastic configuration interaction (CI) method designed as an affordable approximation to full configuration interaction (FCI) has been described here. The key components of the algorithm are initiation, propagation, and termination steps taking inspiration from the genetic algorithm. The propagation step is performed with cloning (retention of a Slater determinant without change), mutation (single excitation/de‐excitation), and crossover (exchange of α and β strings between two Slater determinants) and termination is selection of few Slater determinants based on certain fitness function (measure of importance of a determinant in the CI space) and rejection of the rest. We find that the absolute value of the CI coefficients is a suitable fitness function when combined with a fixed selection scheme. We have tested its accuracy in 1D Hubbard problem and ground state potential energy surface (PES) has also been constructed for symmetric bond breaking of water molecule, where the errors are found to be around 10 mE_h with low non‐parallelity error, when retaining only a small fraction of the total number of Slater determinants in the final population. This shows that this method has the ability to capture both static and dynamic correlation. Performance and convergence properties of the algorithm are also tested for N₂ triple bond breaking problem. The algorithm opens up a promising way for stochastic sampling of the important determinants in the full Hilbert space.     

Relative stability of the 3A2, 1A2, and 1A1 states of phenylnitrene: A difference-dedicated configuration interaction calculation

The relative stability of the ³A₂, ¹A₂, and ¹A₁ states of phenylnitrene is evaluated by means of ab initio calculations followed by difference-dedicated configuration interaction (DDCI). This approach is based on effective Hamiltonian theory at a low order of perturbation to select rationally the determinants which contribute to the energy difference. The CI space built on this criterion is then treated variationally. The method allows a considerable reduction of the CI space compared with a complete CAS*SDCI calculation (where CAS stands for complete active space). Depending on the concerned energy difference, different model spaces may be chosen, as illustrated in the ³A₂ → ¹A₂ and the ³A₂ → ¹A₁ transitions in phenylnitrene. Since the CI space may reach considerable dimensions, a direct CI algorithm for selected CI spaces, the SCIEL algorithm, has been used to perform the calculations. The results are in excellent agreement with previous calculations and with available experimental data. © 1996 by John Wiley & Sons, Inc.     

A flexible correlation group table (CGT) method for the relativistic configuration interaction wavefunctions

A generalized correlation group table (CGT) method is described for the relativistic configuration interaction (RCI) wavefunctions of molecules containing heavy atoms. In this method first four keywords are defined and two properties are discussed in terms of spectroscopic states and double group theory. These definitions and properties are then used to summarize six principles to stipulate the relationship among relativistic states, nonrelativistic states, as well as RCI configurations. The definitions, properties, and principles comprise the generalized CGT method, which facilitates the classification and assignment of the RCI wavefunctions, and thus, provide a general technique for complex systems containing several open shells. Finally, the techniques are exemplified with a few computational models.     

A multireference configuration interaction method based on the separated electron pair wave functions

A multireference configurational interaction method based on the separated electron pair (SEP) wave functions, SEP‐CI approach, has been developed as an approximation to the traditional CASSCF method. It differs from the CASSCF method in that active orbitals are obtained from the SEP wave function without further optimization in the subsequent CI calculations, and the active space is automatically constructed according to the occupation coefficients of SEP natural orbitals. These features make the present SEP‐CI method computationally much less demanding than the CASSCF method. The applicability of the SEP‐CI method is illustrated with sample calculations on the insertion reaction of BeH₂ and dissociation energies of LiH, BH, FH, H₂O, and N₂. © 2005 Wiley Periodicals, Inc. J Comput Chem 27: 39–47, 2006     

A quantum chemical calculation on Fe(CO)5 revealing the operation of the Dewar–Chatt–Duncanson model

A nonstandard computational scheme has been applied to calculate Fe(CO)₅ with the aim to illustrate the operation of the Dewar–Chatt–Duncanson model by computation. A full configuration interaction (CI) calculation in an active space has been performed. The active space is built from naturally localized molecular orbitals (NLMOs) localized in bond regions or forming lone pairs. For selecting this active space, Weinhold's perturbation theory formulated in the natural bond orbital (NBO) space has been applied. Bonding, lone pair, and antibond NBOs exhibiting large interaction energies serve to define the active space. The actually applied active space, however, comprises NLMOs that are close in shape to the NBOs indicated by perturbation theory. Thus, a CI calculation with localized orbitals has been performed meeting the classical reasoning of chemists that is often based on local bonding concepts. The computational scheme yields the Lewis structure for Fe(CO)₅ whose energy is identical to the Hartree–Fock energy. The Lewis energy comprises CO → Fe σ‐electron transfer (ET) and CO ← Fe electron back donation (BD). This Lewis energy gets lowered by localized correlation energy contributions caused by ET processes where electrons are back donated from the Fe d‐lone pairs into the CO ligands. Thus, electron correlation within the selected active space is dominated by electron BD. Energies and electron populations of the NBOs support the notion that electrons are preferentially back donated into the equatorial CO ligands. Weights of local Slater determinants, determining the correlation energy, also point to a predominant BD into the equatorial CO ligands. Correlation energy increments resulting from electron BD into single antibond orbitals of the CO ligands have been calculated. These energy quantities also demonstrate that BD into the equatorial CO ligands is more energy lowering than BD into the axial CO ligands. © 2012 Wiley Periodicals, Inc.     

Selected excitation for CAS-SDCI calculations

A new selected-configuration interaction method is proposed, based on the use of local orbitals. A corresponding code has been written, which is devoted to CI calculations of rather large systems (about 50-100 carbon-like atoms). Taking advantage of the locality, and then of the fact that interactions vanish when the distance is large, the dimension of the CI space is largely reduced. The determinants that would be created by long range excitations are expected to have a small weight in the wave function and are therefore eliminated. This selected excitation CI space is particularly suited for large molecules. It is tested on large polyene chains and on a transition metal complex. For large enough systems, the CPU time saving is important and, what is more noticeable, calculations that were impossible to perform without selection are feasible in this approach.     

On multireference superdirect configuration interaction in third order

The superdirect configuration interaction (Sup-CI ) method has the usual versatility and stability of the CI methods with computational efficiency typical to that of the many-body methods, such as the many-body perturbation theory (MBPT ). The Hamilton operator is projected into a space of a few trial vectors, such as Krylov, Nesbet, or Møller–Plesset correction vectors. In this space, Hamiltonian matrix elements may be directly computed in the many-body fashion, as weighted sums of integral products over orbital indices. The variation-perturbation method based on the first-order wave function is equivalent to the Sup-CI method with a single correction vector of the Møller–Plesset type. Different points of view on the superdirect CI method are discussed and a version in which third-order contributions are computed for a relatively small (10–100) space of reference and correction vectors is tested. Selection of the best “effective first-order spaces” and size-extensivity corrections in Sup-CI are briefly discussed. Møoller–Plesset, Epstein–Nesbet, and other correction vectors are included in the model calculations on the symmetric stretch of bonds in water, acetylene, and the NH₂ molecule. Errors are almost independent of molecular geometry and the method appears to be superior than the multireference second-order perturbation methods. © 1994 John Wiley & Sons, Inc.     

The ground-state potential curve for F2

The ground-state potential curve for F₂ has been obtained using large-scale MC SCF and CI methods. MC SCF curves were obtained with the CAS SCF method using a variety of sets of active orbitals. The main conclusion from the CAS SCF calculations is that the 2π_u orbital is important. CI curves were obtained using the contracted CI method. The largest calculations contained 312000 configurations proper spin and space (d_2h) symmetry. The main conclusions from the CI calculations are that the configuration XXX are important, otherwise errors in D_e of 0.3 eV and in r_e of 0.02 Å are found. The remaining errors at the CI level are 0.08 eV for D_e, 0.005 Å for r_e and less than 10 cm^?1 for the lowest vibrational levels.     

Symmetry simplifications of space types in configuration interaction induced by orbital degeneracy

Symmetry simplifications are introduced in configuration interaction (CI ) by reducing the number of symmetry-allowed space types if there is degeneracy in some of the molecular orbitals by constructing the unique space types. A new symmetry group which we call the configuration symmetry group is defined and is shown to be expressible as a generalized wreath product group. Generating functions are derived for enumerating the equivalence classes of space types. A double coset method is expounded which constructs the representatives of all equivalence classes of space types using the cycle index of generalized wreath product and the double cosets of label subgroup with generalized wreath product in the symmetric group S_n, if n is twice the number of occupied and virtual orbitals. Method is illustrated with CI using the localized orbitals of polyenes, CI in benzene, and atomic CI for several reference states.     

The electronic structure of protonated forms of azaindoles

The Pariser-Parr-Pople (PPP) method has been applied to protonated 4-, 5-, 6-, and 7-azaindoles, and the results are compared with published ones [1] for indole and azaindoles. These show that protonation and solvation at the N in the six-membered ring can play a major part in the chemical behavior of the azaindoles. The differences between the compounds are due to induction rather than to differences in the structure of the -system. The method of restricted configuration interaction (RCI) has been used to calculate the energies of the lowest - transitions.We are indebted to L. N. Yakhontov and M. Ya. Uritskaya for numerous discussions.     

On the choice of active space orbitals in MCSCF calculations

We describe a procedure which may be used to aid selection of the active space in multiconfigurational self-consistent field (MCSCF) calculations for general chemical systems. Starting from a restricted Hartree-Fock calculation, we define a hierarchy of interacting virtual orbitals for every occupied orbital. The most strongly interacting orbitals are then taken to constitute the active space in a configuration interaction (CI) calculation. The natural orbital occupation numbers obtained from the CI calculation are then used to choose the active space to be used in a subsequent MCSCF calculation. We illustrate our method on a number of systems (Li₂, B₂, C₂, carbonyl oxide and the transition state for oxidation of H₂S by dioxirane). In all these cases, ‘intuitive’ active spaces are inadequate, as are active spaces derived from the natural orbitals of unrestricted Hartree-Fock calculations.     

AM1/CI, CNDO/S and ZINDO/S computations of absorption bands and their intensities in the UV spectra of some 4(3H)-quinazolinones

A detailed analysis of both frontier MOs and electronic transitions in UV spectra of 16 4-quinazolinone derivatives has been carried out in MO terms, by semiempirical methods AM1/CI, CNDO/S and ZINDO/S. On the basis of experimental and theoretical investigations by the ZINDO/S and CNDO/S methods the long-wavelength bands of 4(3H)-quinazolinone and its derivatives have been assigned to n-->pi(*) transition of the CO fragment and to the transition caused by intramolecular charge transfer from Ph and NCN fragments to CO group. It was shown that theoretically obtained electronic transitions applying method AM1/CI are not in agreement with experimental data observed for the 4(3H)-quinazolinone and 2,4(1H,3H)-quinazolinedione. Good correlation of theoretical and experimental data has been obtained by the method ZINDO/S for the wavelengths and the molar extinction coefficients of the compounds studied. Satisfactory correlation of theoretical and experimental data has also been obtained by the method CNDO/S with singly and doubly excited configurations, for the wavelengths only. Such correlations on experimental and theoretical wavelength and molar absorption coefficients of 4-quinazolinone derivatives are carried out for the first time.     

Configuration interaction spaces with arbitrary restrictions on orbital occupancies

Configuration interaction (CI) spaces obtained from the full CI space by imposing arbitrary restrictions on the occupancies of molecular orbital (MO) groups are studied. It is proved that such restricted spaces are in a certain sense “closed.” Namely, in the course of the Hamiltonian matrix construction the excitations out of the chosen restricted CI space may be easily replaced by the excitations within this space. © 1996 John Wiley & Sons, Inc.     

Real space Hartree-Fock configuration interaction method for complex lateral quantum dot molecules

We present unrestricted Hartree-Fock method coupled with configuration interaction (CI) method (URHF-CI) suitable for the calculation of ground and excited states of large number of electrons localized by complex gate potentials in quasi-two-dimensional quantum dot molecules. The method employs real space finite difference method, incorporating strong magnetic field, for calculating single particle states. The Hartree-Fock method is employed for the calculation of direct and exchange interaction contributions to the ground state energy. The effects of correlations are included in energies and directly in the many-particle wave functions via CI method using a limited set of excitations above the Fermi level. The URHF-CI method and its performance are illustrated on the example of ten electrons confined in a two-dimensional quantum dot molecule.     

Selected configuration interaction with truncation energy error and application to the Ne atom

Selected configuration interaction (SCI) for atomic and molecular electronic structure calculations is reformulated in a general framework encompassing all CI methods. The linked cluster expansion is used as an intermediate device to approximate CI coefficients B(K) of disconnected configurations (those that can be expressed as products of combinations of singly and doubly excited ones) in terms of CI coefficients of lower-excited configurations where each K is a linear combination of configuration-state-functions (CSFs) over all degenerate elements of K. Disconnected configurations up to sextuply excited ones are selected by Brown's energy formula, Delta E(K) = (E-H(KK))B(K)2/(1-B(K)2), with B(K) determined from coefficients of singly and doubly excited configurations. The truncation energy error from disconnected configurations, Delta E(dis), is approximated by the sum of Delta E(K)s of all discarded Ks. The remaining (connected) configurations are selected by thresholds based on natural orbital concepts. Given a model CI space M, a usual upper bound E(S) is computed by CI in a selected space S, and E(M) = E(S) + Delta E(dis) + delta E, where delta E is a residual error which can be calculated by well-defined sensitivity analyses. An SCI calculation on Ne ground state featuring 1077 orbitals is presented. Convergence to within near spectroscopic accuracy (0.5 cm(-1)) is achieved in a model space M of 1.4 x 10(9) CSFs (1.1 x 10(12) determinants) containing up to quadruply excited CSFs. Accurate energy contributions of quintuples and sextuples in a model space of 6.5 x 10(12) CSFs are obtained. The impact of SCI on various orbital methods is discussed. Since Delta E(dis) can readily be calculated for very large basis sets without the need of a CI calculation, it can be used to estimate the orbital basis incompleteness error. A method for precise and efficient evaluation of E(S) is taken up in a companion paper.     

Do-it-yourself microelectrophoresis chips with integrated sample recovery

We present a microelectrophoresis chip that is simple to fabricate using the microfluidic tectonics (microFT) platform (Beebe, D. J. et al., Proc. Natl. Acad. Sci. USA 2000, 97, 13488-13493; Agarwal, A. K. et al.,. J. Micromech. Microeng. 2006, 16, 332-340). The device contains a removable capillary insert (RCI) for easy sample collection after separation (Atencia, J. et al.,. Lab Chip 2006, DOI: 10. 1039/b514068d). Device construction is accomplished in less than 20 min without specialized equipment traditionally associated with microelectrophoresis chip construction. microFT was used to build a PAGE device utilizing two orthogonal microchannels. One channel performs standard separations, while the second channel serves as an access point to remove bands of interest from the chip via the RCI. The RCI contains an integrated electrode that facilitates the removal of bands using electrokinetic techniques. The device was characterized using prestained proteins (Pierce BlueRanger and TriChromRanger). Samples were loaded into the microelectrophoresis device via a standard micropipette. An electrical field of 40 V/cm was used to separate and collect the proteins. The microPAGE device is simple to fabricate, benefits from microscale analysis, and includes an on-chip collection scheme that interfaces the macroworld with the microworld.     

Configuration selection as a route towards efficient vibrational configuration interaction calculations

A configuration selective vibrational configuration interaction (CI) approach is presented that efficiently reduces the variational space and thus leads to significant speedups in comparison to standard vibrational CI implementations. Deviations with respect to reference calculations are well below the accuracy of the underlying electronic structure calculations for the potential and hence are essentially negligible. Parallel implementations of the presented configuration selective vibrational CI approaches lead to further significant time savings. Benchmark calculations based on potential energy surfaces of coupled-cluster quality are presented for the fundamental modes of cis- and trans-difluoroethylene. The size-consistency error within the vibrational configuration interaction calculations of the difluoroethylene dimer has been studied in dependence on the excitation level.