Excitation energy transfer pathways in light‐harvesting proteins: Modeling with PyFREC

Excitation energy transfer (EET) determines the fate of sunlight energy absorbed by light‐harvesting proteins in natural photosynthetic systems and photovoltaic cells. As previously reported (D. Kosenkov, J. Comput. Chem. 2016, 37(19), 1847), PyFREC software enables computation of electronic couplings between organic molecules with a molecular fragmentation approach. The present work reports implementation of direct fragmentation‐based computation of the electronic couplings and EET rates in pigment–protein complexes within the Förster theory in PyFREC. The new feature enables assessment of EET pathways in a wide range of photosynthetic complexes, as well as artificial molecular architectures that include light‐harvesting proteins or tagged fluorescent biomolecules. The developed methodology has been tested analyzing EET in the Fenna–Matthews–Olson (FMO) pigment–protein complex. The pathways of excitation energy transfer in FMO have been identified based on the kinetics studies. © 2017 Wiley Periodicals, Inc.     

The ground state of TiC revisited

The ground state of TiC is ³⁺, as predicted by previous configuration interaction calculations. It is shown that there are two low-lying ¹⁺ states and that the density functional theory solution corresponds to the higher of the two ¹⁺ states.Contribution to the Björn Roos Honorary Issue     

Parallel pseudospectral electronic structure: II. Localized Møller–Plesset calculations

We have developed a parallel version of our pseudospectral localized Møller–Plesset electronic structure code. We present timings for molecules up to 1010 basis functions and parallel speedup for molecules in the range of 260–658 basis functions. We demonstrate that the code is scalable; that is, a larger number of nodes can be efficiently utilized as the size of the molecule increases. By taking advantage of the available distributed memory and disk space of a scalable parallel computer, the parallel code can calculate LMP2 energies of molecules too large to be done on workstations. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1030–1038, 1998     

Ab initio conformational analysis of cyclooctane molecule

The potential energy surface (PES) for the cyclooctane molecule was comprehensively investigated at the Hartree–Fock (HF) level of theory employing the 3–21G, 6–31G, and 6–31G* basis sets. Six distinct true minimum energy structures (named B, BB, BC, CROWN, TBC, and TCC₁), characterized through harmonic frequency analysis, were located on the multidimensional PES. Two transition state structures were also located on the PES for the cyclooctane molecule. Electron correlation effects were accounted for using the Møller–Plesset second-order perturbation theory (MP2) approach. The predicted global minimum energy structure on the ab initio PES for the cyclooctane molecule is the BC conformer. A gas phase electron diffraction study at 300 K suggested a conformational mixture while an NMR study in solution at 161.5 K predicted the BC conformer as the predominant form. The equilibrium constants reported in the present study, which were evaluated from the ab initio calculated total Gibbs free energy change values, were in good agreement with both experimental investigations. The ab initio results showed that the low temperature condition significantly favored the BC conformer while above room temperature both BC and CROWN structures can coexist. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 524–534, 1998     

A theoretical study of radical-only and combined radical/carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Prostaglandin H synthase catalyzes the oxygenation of arachidonic acid into the cyclic endoperoxide, prostaglandin G₂ (PGG₂), and the subsequent reduction of PGG₂ to the corresponding alcohol, prostaglandin H₂ (PGH₂), the precursor of all prostaglandins and thromboxanes. Both radical abstraction by a neighboring tyrosyl radical and combined radical/carbocationic models have been proposed to explain the cyclooxygenase part of this reaction. We have used density functional theory calculations to study the mechanism of the formation of the cyclooxygenated product PGG₂. We found an activation free energy for the initial hydrogen abstraction by the tyrosine radical of 15.6 kcal/mol, and of 14.5 kcal/mol for peroxo bridge formation, in remarkable agreement with the experimental value of 15.0 kcal/mol. Subsequent steps of the radical-based mechanism were found to happen with smaller barriers. A combined radical/carbocation mechanism proceeding through a sigmatropic hydrogen shift was ruled out, owing to its much larger activation free energy of 36.5 kcal/mol. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00214-003-0476-9. Electronic Supplementary MaterialSupplementary material is available in the online version of this article at Electronic Supplementary Material: Supplementary material is available in the online version of this article at     

Ab initio and density functional studies on the structure and vibrational spectra of 2-hydroxy-1,4-naphthoquinone-1-oxime derivatives

Structure and vibrational frequencies of lawsoneoxime and its C₃-substituted (R=CH₃, NH₂, Cl, NO₂) derivatives in keto and nitrosophenol forms have been obtained employing the Hartree–Fock and density functional methods. Charge distributions in different conformers have been studied using the molecular electrostatic potential topography as a tool. For all these derivatives except for nitrolawsoneoxime the amphi conformer in the keto form is predicted to be of lowest energy, which can partly be attributed to hydrogen bonding through the oximino nitrogen. In the nitro derivative, however, the preference to form a six membered ring owing to O–H–O hydrogen-bonded interactions makes the anti conformer (keto) the stablest. Further one of the nitrosophenol conformers of nitrolawsoneoxime turns out to be very close in energy (0.21 kJ mol^–1 higher) to this anti conformer. The consequences of hydrogen bonding on charge distribution and vibrational spectra are discussed.     

Integral transformation with low-order scaling for large local second-order Møller–Plesset calculations

An algorithm is presented for the four-index transformation of electron repulsion integrals to a localized molecular orbital (MO) basis. Unlike in most programs, the first two indices are transformed in a single step. This and the localization of the orbitals allows the efficient neglect of small contributions at several points in the algorithm, leading to significant time savings. Thresholds are applied to the following quantities: distant orbital pairs, the virtual space before and after the orthogonalizing projection to the occupied space, and small contributions in the transformation. A series of calculations on medium-sized molecules has been used to determine appropriate thresholds that keep the truncation errors small (below 0.01% of the correlation energy in most cases). Benchmarks for local second-order Møller–Plesset perturbation theory (MP2; i.e., MP2 with a localized MO basis in the occupied subspace) are presented for several large molecules with no symmetry, up to 975 contracted basis functions, and 60 atoms. These are among the largest MP2 calculations performed on a single processor. The computational time (with constant basis set) scales with a somewhat lower than cubic power of the molecular size, and the memory demand is moderate even for large molecules, making calculations that require a supercomputer for the traditional MP2 feasible on workstations. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1241–1254, 1998     

Unusual NH Activation of 2‐Aminopyrimidine: Supramolecular Assembly into an AgI Metal–Organic Framework

A rare example of coordination at the amino group of NH₂pym (2‐aminopyrimidine) relevant to N? H activation is described that leads to a novel Ag^I–imide 3D metal–organic framework (MOF). The coordination of Ag^I to NH₂pym produced an electron‐withdrawing effect and thus increased its acidity, which facilitated the N? H activation and the subsequent formation of the Ag–imide bond. A cooperative metalation/deprotonation process for the N? H activation of NH₂pym is suggested. Interestingly, photoluminescence of 1 is switched on at the low temperature of 77 K.     

Systematic convergence of energies with respect to basis set and treatment of electron correlation: focal-point conformational analysis of methanol

A practical means of overcoming the limitation in accuracy of conformational analysis due to incompleteness of basis sets used in ab initio calculations involves calculating the energy with a series of systematically improving basis sets and extrapolating to the basis set limit. We report here a focal-point conformational analysis for methanol. The Hartree–Fock energy converges exponentially to the basis set limit, while the convergence of second-order correlation energy is well described by the formula . This formula also describes well the convergence of fourth-order correlation energy. The height of the rotational barrier at the Hartree–Fock level can be obtained reliably by taking the difference of the extrapolated energies of the two conformations and correcting the difference for correlation effects. Electron correlation has only a small decreasing effect on the height of the rotational barrier in methanol. The focal-point value for the torsional barrier in methanol is 0.999±0.007 kcal/mol. Acknowledgement.This project was supported by Provost Funds at University of California, Santa Barbara (UCSB). The computational resources were provided partially by the National Computational Science Alliance and UCSBs Supercomputer Facility. We also acknowledge the Horgan Award (University of Missouri-Columbia) to K. K., which made possible the purchase of additional computational resources. We thank Robert Gdanitz and Bernie Kirtman for valuable discussions and Jozef Noga for providing us with a copy of the DIRCCR12-OS program.     

Formulation of unrestricted and restricted Hartree–Fock–Bogoliubov equations

The Hartree–Fock–Bogoliubov (HFB) method, dealing with Bogoliubov orbitals, which consist of particle and hole part, can provide states with pair correlations associated with Cooper pairs. The dimension of HFB Fock matrices can be reduced by restrictions of spin states of Bogoliubov orbitals similarly to ordinary Hartree–Fock (HF) equations such as restricted HF (RHF), unrestricted HF (UHF), and generalized HF (GHF). However, there are few studies of moderate restricted HFB equations such as UHF‐based HFB equations. In this article, formulation and calculations of restricted HFB equations are described. The solutions of general and restricted HFB equations are compared. Pair correlations taking account of restricted and general HFB equations are discussed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

New structural parameters of fullerenes for principal component analysis

The Kekulé structure count and the permanent of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q, r, q/p and r/p, where p is the number of edges common to two pentagons, q is the number of vertices common to three pentagons and r is the number of pairs of nonadjacent pentagons adjacent to another common pentagon. The cluster analysis of the structural parameters allows classification these parameters. Principal component analysis (PCA) of the structural parameters and the cluster analyses of the fullerenes permit their classification. PCA clearly distinguishes five classes of fullerenes. The cluster analysis of fullerenes is in agreement with PCA classification. Cluster analysis shows greatest similarity for the q–q/p and r–r/p pairs. PCA provides five orthogonal factors F ₁–F ₅. The use of F ₁ gives an error of 28%. The inclusion of F ₂ decreases the error to 2%.From the Proceedings of the 28th Congreso de Químicos Teóricos de Expresión Latina (QUITEL 2002)     

Effect of nitrogen on mechanical,oxidation and structural behaviour of Ti–Si–B–C–N nanocomposite hard coatings deposited by DC sputtering

Ti–Si–B–C–N film was deposited by DC magnetron sputtering at different argon and nitrogen ratios such as N₂/Ar = 1 : 5, 2 : 4, 3 : 3, 4 : 1 and 5 : 0. The formation of TiN and TiB phases was observed because of incorporation of nitrogen. The hardness, modulus, microstructure, structure and bond formation with different nitrogen contents during the deposition were studied by nanoindentation, scanning electron microscope, X‐ray diffraction and X‐ray photoelectron spectroscopy, respectively. The oxidation kinetics of Ti–Si–B–C–N was investigated. The nitrogen incorporation during deposition influences different properties of the coating. Hardness and modulus decreased, and microstructure showed very fine grain presence, and film changes to fully amorphous because of incorporation of nitrogen in the film. Copyright © 2016 John Wiley & Sons, Ltd.     

SiIV Incorporation into a [28]Hexaphyrin That Triggered Formation of Möbius Aromatic Molecules

Incorporation of Si^IV into an expanded porphyrin has been achieved for the first time. Treatment of [28]hexaphyrin 1 with CH₃SiCl₃ and N,N‐diisopropylethylamine gave Si^IV complex 2 and its N‐fused product 4 that both have Möbius aromatic nature. In both complexes, the coordinated Si atom is satisfied in a typical trigonal bipyramidal coordination. Si^IV incorporation induces conformational rigidification and redshifted absorption profiles due to σ–π conjugation between the Si atom and hexaphyrin macrocycle. Tamao–Fleming oxidation of 2 with H₂O₂ gave β‐hydroxy [28]hexaphyrin 5 , which exists as a ruffled rectangular shape in the solid state, yet it has been revealed to exist predominantly as a twisted Möbius aromatic conformer in CH₂Cl₂.     

Strong and Confined Acids Control Five Stereogenic Centers in Catalytic Asymmetric Diels–Alder Reactions of Cyclohexadienones with Cyclopentadiene

We describe a highly enantioselective Diels–Alder reaction of cross‐conjugated cyclohexadienones with cyclopentadiene, in which five stereocenters are effectively controlled by a strongly acidic and confined imidodiphosphorimidate catalyst. Our approach provides tricyclic products in excellent stereoselectivity. We also report methods to convert the obtained products into useful intermediates and a computational study that aids in gaining deeper insight into the reaction mechanism and origin of stereoselectivity.     

Revised state diagram of Laponite dispersions

We propose a state diagram of charged disk-like mineral particle (Laponite) dispersions as a function of the Laponite concentration (C) and the concentration of added salt (C(s)), based on simple observation and light-scattering measurements. At low C or high C(s) the dispersions separate into two domains due to sedimentation of Laponite aggregates, while at high C and low C(s) they form homogeneous gels that do not flow upon tube reversal. The aggregation rate and the structure factor of the Laponite dispersions is determined with light scattering as a function of C and C(s). We discuss in detail the controversy on the origin of gelation of Laponite dispersions in the absence of added salt. We argue that aggregation rather than glass formation causes gelation.     

The curvature of the Arrhenius plots predicted by conventional canonical transition-state theory in the absence of tunneling

The reasons for the nonlinearity of the Arrhenius plots of gas-phase reactions are analyzed in detail within the frame of conventional canonical transition-state theory and in the absence of tunneling effects. The purpose is to show how the vibrational normal mode frequencies of reactants and the transition state determine the curvature of an Arrhenius plot. Conventional canonical transition-state theory without tunneling corrections predicts curved Arrhenius plots with an inflexion point that separates the concave (high-temperature range) and convex region (at low temperatures). The frequencies of the transitional modes at the transition-state structure determine the temperature at which an Arrhenius plot presents upward curvature. AcknowledgementsWe are grateful for financial support from the Spanish Ministerio de Ciencia y Tecnología and the Fondo Europeo de Desarrollo Regional through project no. BQU2002–00301, and the use of the computational facilities of the CESCA.     

The performance of density functional theory for LnF (Ln=Nd,Eu, Gd,Yb) and YbH

Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue     

Electric properties of hydrogen iodide: Reexamination of correlation and relativistic effects

The electric dipole moment and the static dipole polarizability of the hydrogen iodide molecule were studied using sophisticated correlated and relativistic methods. Both scalar and spin–orbit relativistic effects were carefully accounted for. We conclude that the large differences between the theoretical and experimental dipole moment, the dipole moment derivative and the polarizability cannot be reconciled by improved account of electron correlation and relativistic effects. The most striking difference between theory and experiment is observed for the polarizability anisotropy. We believe that experimental data, namely the experimental dipole moment (the most recent value is 0.176 au as compared to our best theoretical estimate, 0.154±0.003 au), the parallel polarizability (44.4 and 38.47±0.05 au) and the anisotropy (11.4 and 2.33±0.05 au) must be inaccurate. Experimental and theoretical perpendicular polarizability components (33.0 and 36.14±0.05 au,) and the mean polarizability (36.8 and 36.92±0.05 au) agree better. Our vibrationally corrected relativistic CCSD(T) results represent the most sophisticated predictions of electric properties of HI obtained so far.Contribution to the Björn Roos Honorary Issue