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.     

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     

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     

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     

Bond length alternation in ground and HOMO→LUMO excited states in polyenes. Dynamic Stokes shift?

Complete-active-space self-consistent-field calculation of the reorganisation energy, , corresponding to the strongly allowed HOMOLUMO transition in planar polyenes in the trans form (C _{2 h} symmetry), gives >0.5 eV. This large depends on the fact that the short and long bond lengths of the excited ¹B _u (or ³B _u ) state compared to the ¹A _g ground state are almost cancelled. The emission redshift (Stokes shift) in molecules with the same type of system is quite small, however, which suggests that the Stokes shift may be dynamic, owing to the presence of another excited state at lower or about the same energy. Acknowledgement.We congratulate Björn on his birthday and at the same time thank him for the CASSCF method and for many years of collaboration and help from him and his collaborators to make this wonderful method work in our laboratory.Contribution to the Björn Roos Honorary Issue     

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.     

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     

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.     

Modeling water exchange on monomeric and dimeric Mn centers

Water exchange on Mn centers in proteins has been modeled with density functional theory using the B3LYP functional. The reaction barrier for dissociative water exchange on [Mn^IV(H₂O)₂(OH)₄] is only 9.6 kcal mol^–1, corresponding to a rate of 6×10⁵ s^–1. It has also been investigated how modifications of the model complex change the exchange rate. Three cases of water exchange on Mn dimers have been modeled. The reaction barrier for dissociative exchange of a terminal water ligand on [(H₂O)₂(OH)₂Mn^IV(-O)₂Mn^IV(H₂O)₂(OH)₂] is 8.6 kcal mol^–1, while the bridging oxo group exchange with a ring-opening mechanism has a barrier of 19.2 kcal mol^–1. These results are intended for interpretations of measurements of water exchange for the oxygen evolving complex of photosystem II. Finally, a tautomerization mechanism for exchange of a terminal oxyl radical has been modeled for the synthetic O₂ catalyst [(terpy)(H₂O)Mn^IV(-O)₂Mn^IV(O)(terpy)]³⁺ (terpy=2,2:6,2-terpyridine). The calculated reaction barrier is 14.7 kcal mol^–1.Contribution to the Björn Roos Honorary Issue     

Semidirect parallel self-consistent field: the load balancing problem in the input/output intensive self-consistent field iterations

The full capacity of contemporary parallel computers can, in the context of iterative ab initio procedures like, for example, self-consistent field (SCF) and multiconfigurational SCF, only be utilized if the disk and input/output (I/O) capacity are fully exploited before the implementation turns to an integral direct strategy. In a recent report on parallel semidirect SCF http://www.tc.cornell.edu/er/media/1996/collabrate.html, http://www.fp.mcs.anl.gd/grand-challenges/chem/nondirect/index.html it was demonstrated that super-linear speedups are achievable for algorithms that exploit scalable parallel I/O. In the I/O-intensive SCF iterations of this implementation a static load balancing, however, was employed, dictated by the initial iteration in which integral evaluation dominates the central processing unit activity and thus determines the load balancing. In the present paper we present the first implementation in which load balancing is achieved throughout the whole SCF procedure, i.e. also in subsequent iterations. The improved scalability of our new algorithm is demonstrated in some test calculations, for example, for 63-node calculation a speedup of 104 was observed in the computation of the two-electron integral contribution to the Fock matrix.Contribution to the Björn Roos Honorary Issue Acknowledgement.We thank J. Nieplocha for valuable help and making the toolkit (including ChemIO) available to us. R.L. acknowledges the Intelligent Modeling Laboratory and the University of Tokyo for financial support during his stay in Japan.     

Correlation factor approach to the correlation energy functional

A global survey of the correlation factor energy functionals and its application to atomic and molecular properties is made. Its performances are compared with those of the density functional theory (DFT) correlation energy functionals, and some interesting conclusions from previous publications are reinforced here; namely, after removing the one-Slater-determinant hypothesis from the Kohn–Sham method, all DFT correlation functionals are able to provide reasonable results in any circumstance, with an additional restriction, for systems having a quasi-degenerate wave function, the DFT correlation functionals must depend explicitly on the on-top density. Acknowledgement.This work has been done under the support of the Spain DGICYT, project n⁰ BQU2001-0883.     

Ab initio and density functional theory based studies on collagen triplets

An understanding of the amino acid sequence dependent stability of polypeptides is of renowned interest to biophysicists and biochemists, in order to identify the nature of forces that stabilize the three-dimensional structure of proteins. In this study, the role of various collagen triplets influencing the stability of collagen has been addressed. It is found from this study that proline can stabilize the collagen triplet only when other residues are also in the polyproline II conformation. Solvation studies of various triplets indicate that the presence of polar residues increases the free energy of solvation. Especially the triplets containing arginine residues displays a higher solvation free energy. The chemical hardness of all the triplets in collagen-like conformation has been found to be higher than that in the extended conformation. Studies on Gly–X–Y, Gly–X–Hyp, and Gly–Pro–Y triplets confirm that there will be local variations in the stability of collagen along the entire sequence.     

Valence ab initio calculation of the potential-energy curves for the Ca<Subscript>2</Subscript> dimer

The electronic structure of the Ca₂ molecule has been investigated by use of a two-valence-electron semiempirical pseudopotential and applying the internally contracted multireference configuration interaction method with complete-active-space self-consistent-field reference wave functions. Core–valence correlation effects have been accounted for by adding a core-polarization potential to the Hamiltonian. The ground-state properties of the Ca₂ and Ca₂⁺ dimers have also been studied at the single-reference coupled-cluster level with single and double excitations including a perturbative treatment of triple excitations. Good agreement with experiment has been obtained for the ground-state potential curve and the only experimentally known A¹_u⁺ excited state of Ca₂. The spectroscopic parameters D_e and R_e deduced from the calculated potential curves for other states are also reported. In addition, spin–orbit coupling between the singlet and triplet molecular states correlating, respectively, with the (4p)¹P and (4p)³P Ca terms has been investigated using a semi-empirical two-electron spin–orbit pseudopotential. Acknowledgement.This work was supported by grant 5 P03B 082 21 from the Polish State Committee for Scientific Research (KBN).     

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.     

Test study on the excitation spectra of the N<Subscript>2</Subscript>–He van der Waals molecule

We have performed ab initio fourth-order Møller–Plesset perturbation theory calculations in the framework of the supermolecule approach on the vertical excitation spectra of the weakly bound van der Waals N₂–He dimer. They indicate a ``T-shaped' stablest ground N<sub>2</sub>(X<sup>1</sup><sub>g</sub><sup>+</sup>)–He(<sup>1</sup>S) electronic state with a well depth, D<sub>e</sub>, of 21.63 cm<sup>–1</sup> at a minimum distance, R<sub>e</sub>, of 3.44 Å and zero-point vibration correction, D<sub>o</sub>, of 7.07 cm<sup>–1</sup>. They also indicate a ``T-shaped' stablest excited conformer with R_e=3.25 Å, D_e=36.85 cm^–1 and D_o=17.06 cm^–1 for the N₂(B³_g)–He(¹S) triplet electronic level. In order to investigate the use of less-demanding correlation methods, test density functional theory calculations using the mPW1PW exchange–correlation functional are also presented for comparison.     

Determination of selected polycyclic aromatic hydrocarbons and oxygenated polycyclic aromatic hydrocarbons in aerosol samples by high-performance liquid chromatography and liquid chromatography–tandem mass spectrometry

Fine and ultrafine particles are probably responsible for numerous health effects, but it is still unclear whether and to what extent the particle itself or organic compounds adsorbed or condensed on the particle are responsible for the effects observed. One important class of particle-bound substances are the polycyclic aromatic hydrocarbons (PAH) and their oxygenated derivatives. To improve the tools used for chemical characterization of particulate matter analytical methods for the determination of PAH and oxygenated PAH in aerosol samples of different origin have been developed and optimized. PAH on high-volume filters and on soot aerosols were analyzed by using accelerated solvent extraction for extraction and high-performance liquid chromatography with fluorescence detection for separation and quantification. Total PAH concentrations were in the range 0.3–9.3 ng m^–3. For analysis of selected oxygenated PAH on high-volume filters a liquid chromatography–tandem mass spectrometric method was developed and optimized. Preliminary investigations showed that oxygenated PAH at pg m^–3 concentrations can be determined.     

Electronic coupling in electron transfer and the influence of nuclear modes: theoretical and computational probes

Long-range electronic coupling of local donor and acceptor sites is formulated in the context of thermal and optical electron transfer and then illustrated with examples based on electronic structure calculations. The relationship of the calculated results to available experimental kinetic and optical data is discussed in detail. The influence of nuclear modes on the magnitude of the coupling (i.e., departures from the Condon approximation) is investigated in terms of both discrete molecular modes and solvent modes, and a general expression is presented for the modulation of the superexchange tunneling gap by motion along the electron transfer reaction coordinate. AcknowledgementsThe author is grateful to R.J. Cave and M. Rust for making available molecular coordinates for acridinium derivatives, and to R.J. Cave for several valuable discussions. This work was supported by the Division of Chemical Sciences, US Department of Energy, under grant DE-AC02-98CH10886.