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Effect of Stacking Interactions
Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol
Contributors: Bresnahan, C. G.*, Reinhardt, C. R.*, Bartholow, T. *, Rumpel, J. P.*, North, M. A.*, and Bhattacharyya, S.
Where it's published: J. Phys. Chem. A 2015, 119, 172-182
Abstract: The π-π stacking interaction between lumiflavin and a number of π-electron-rich molecules has been studied by density functional theory using several new-generation density functionals. Six known lumiflavin-aromatic adducts were used and the models were evaluated by comparing the geometry and energetics with experimental results. The study found that dispersion-corrected and hybrid functionals with larger (>50%) Hartree-Fock exchanges produced superior results in modeling thermodynamic characteristics of these complexes. The functional producing the best energetics for these model systems was used to study the stacking interactions of lumiflavin with biologically relevant aromatic groups. Additionally, the reduction of flavin-in the presence of both a hydride donor and a nondonor π-electronic system was also studied. Weak interactions were observed in the stacked lumiflavin complexes of benzene, phenol, and indole, mimicking phenyl alanine, tryptophan, and tyrosine side chains, respectively, of an enzyme. The stacked complex of naphthalene and flavin showed little change in flavin's redox potential indicating insignificant effect on the thermodynamics of the hydride transfer reaction. In contrast, the hydride transfer reaction with the hydride donor N-methyl nicotinamide tells a different story, as the transition state was found to be strongly impacted by the stacking interactions. A comparison of performance between the density functional theory (DFT) and the computationally less expensive dispersion-corrected self-consistent density functional tight-binding (SCC-DFTB-D) theory revealed that the latter produces consistent energetics for this hydride transfer reaction and additional DFT-computed perturbative corrections could significantly improve these results.
Four-electron correlated integrals evaluation
The evaluation of some four-electron correlated integrals with a Slater basis arising in linear and nonlinear r12 theories
Contributor: King, F. W.
Where it's published: Journal of Physics B: Atomic, Molecular and Optical Physics, 2016, 49, 105001
Abstract: This study considers the analytic evaluation of correlated integrals involving explicit inter-electron separation distances using a basis of standard Slater-type functions. These basis functions are employed in Hylleraas-CI calculations, Hylleraas calculations on atomic four-electron systems, and in non-Born–Oppenheimer calculations on small molecular systems. A Fourier transform approach allows a principal auxiliary integral to be evaluated analytically, permitting a number of four-electron integrals to be reduced to various one-dimensional Cauchy–Frullani integrals, which can be evaluated in closed form. The stability of some of the formulas with respect to numerical evaluation, particularly for the high-order derivative cases, is discussed in detail. Numerical values for a selection of test integrals are provided.
A density functional theory study
Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study
Contributors: Reinhardt, C. R.*, Jaglinski, T. C.*, Kastenschmidt, A. M.*, Song, E. H.*, Krause, A. J.*, Gollmar, J. M.*, Meise, K. J.*, Stenerson, Z. S.*, Weibel, T. J.*, Dison, A.*, Finnegan, M. R.*, Griesi, D. S.*, Gross, A. K.*, Heltne, M. D.*, Hughes, T. G.*, Hunt, C. D.*, Jansen, K. A.*, Xiong, A. H.*, Hati, S., and Bhattacharyya, S.
Where it's published: Springer Link
Abstract: The kinetics and equilibrium of the hydride transfer reaction between lumiflavin and a number of substituted quinones was studied using density functional theory. The impact of electron withdrawing/donating substituents on the redox potentials of quinones was studied. In addition, the role of these substituents on the kinetics of the hydride transfer reaction with lumiflavin was investigated in detail under the transition state (TS) theory assumption. The hydride transfer reactions were found to be more favorable for an electron-withdrawing substituent. The activation barrier exhibited a quadratic relationship with the driving force of these reactions as derived under the formalism of modified Marcus theory. The present study found a significant extent of electron delocalization in the TS that is stabilized by enhanced electrostatic, polarization, and exchange interactions. Analysis of geometry, bond-orders, and energetics revealed a predominant parallel (Leffler-Hammond) effect on the TS. Closer scrutiny reveals that electron-withdrawing substituents, although located on the acceptor ring, reduce the N–H bond order of the donor fragment in the precursor complex. Carried out in the gas-phase, this is the first ever report of a theoretical study of flavin's hydride transfer reactions with quinones, providing an unfiltered view of the electronic effect on the nuclear reorganization of donor–acceptor complexes.