Fast Marching Method for Calculating Reactive Trajectories for Chemical Reactions

We present a method for computing classical Newtonian trajectories that minimize the path length or transit time from reactant to product. Our approach is based on a generalization of the fast-marching method, which allows us to construct the solution of the Hamilton-Jacobi equation for the action that optimizes the desired quantity. The resulting “reactive paths” can be interpreted as reaction coordinates but, unlike more conventional choices, they contain dynamical information about the chemical system of interest.     

Ultrafast fluorescence resonance energy transfer in a bile salt aggregate: Excitation wavelength dependence

Fluorescence resonance energy transfer (FRET) from Coumarin 153 (C153) to Rhodamine 6G (R6G) in a secondary aggregate of a bile salt (sodium deoxycholate, NaDC) is studied by femtosecond up-conversion. The emission spectrum of C153 in NaDC is analysed in terms of two spectra-one with emission maximum at 480 nm which corresponds to a non-polar and hydrophobic site and another with maximum at ∼530 nm which arises from a polar hydrophilic site. The time constants of FRET were obtained from the rise time of the emission of the acceptor (R6G). In the NaDC aggregate, FRET occurs in multiple time scales — 4 ps and 3700 ps. The 4 ps component is assigned to FRET from a donor (D) to an acceptor (A) held at a close distance (R _DA ∼ 17 ?) inside the bile salt aggregate. The 3700 ps component corresponds to a donor-acceptor distance ∼48 ?. The long (3700 ps) component may involve diffusion of the donor. With increase in the excitation wavelength (λ _ex) from 375 to 435 nm, the relative contribution of the ultrafast component of FRET (∼4 ps) increases from 3 to 40% with a concomitant decrease in the contribution of the ultraslow component (∼3700 ps) from 97 to 60%. The λ _ex dependence is attributed to the presence of donors at different locations. At a long λ _ex (435 nm) donors in the highly polar peripheral region are excited. A short λ _ex (375 nm) ‘selects’ donor at a hydrophobic location.     

Catalysis by ionic liquid: a simple, green and efficient procedure for the Michael addition of thiols and thiophosphate to conjugated alkenes in ionic liquid, [pmIm]Br

A room temperature ionic liquid, 1-pentyl-3-methylimidazolium bromide, [pmIm]Br efficiently catalyzes Michael addition of thiols and diethyl dithiophosphate to a variety of conjugated alkenes such as α,β-unsaturated carbonyl compounds, carboxylic esters, nitriles and chalcones without requiring any other organic solvent and catalyst. The ionic liquid can be recycled for subsequent reactions without any appreciable loss of efficiency.     

Simplified synthesis, H, C, N, Sn NMR spectra and X-ray structures of diorganotin(IV) complexes containing the 4-phenyl-2,4-butanedionebenzoylhydrazone(2−) ligand

Two diorganotin(IV) complexes of the general formula R₂Sn[Ph(O)CCH-C(Me)N-NC(O)Ph] (R=Ph, 1; R=Me, 2) have been synthesised from the corresponding diorganotin(IV) dichloride and the ligand 4-phenyl-2,4-butanedionebenzoylhydrazone(2−) (H₂L), derived from benzoyl acetone and benzoyl hydrazide in methanol at room temperature in presence of triethylamine. The syntheses were performed under very mild conditions, at room temperature and without exclusion of air or moisture from the reaction vessel. Previously, rigorous conditions have been considered necessary for these species. The two compounds have been characterised by elemental analysis, IR and ¹H, ¹³C, ¹⁵N, ¹¹⁹Sn NMR spectra, and their structures have been confirmed single crystal X-ray structure analysis. The central tin atom of both complexes adopts a distorted trigonal bipyramidal coordination with two ligand oxygen atoms in axial positions, the nitrogen atom of the ligand and two organic groups on tin occupying equatorial sites. 2 has crystallised with two crystallographically independent molecules in the asymmetric unit. The δ(¹¹⁹Sn) values for the complexes 1 and 2 are −151.5 and −146.8 ppm, respectively, thus indicating penta-coordinated tin centres.     

Concise Enantioselective Synthesis of Naturally Active (S)-3-Hydroxypiperidine

A short and efficient enantioselective synthesis of natural product (S)-3-hydroxypiperidine has been achieved starting from commercially available raw materials employing two catalytic routes: (i) cocatalyzed hydrolytic kinetic resolution (HKR) of racemic methyl-3-(oxiran-2-yl)propanoate; (ii) proline-catalyzed α-aminooxylation followed by Horner–Wardsworth–Emmons olefination in high enantiomeric purity (97% ee) and high overall yield (38%).     

Study of electron transfer in ferrocene-labeled collagen-like peptides

This study describes the electron transfer (ET) phenomenon through a series of (Pro-Hyp-Gly) repeat units containing collagen mimics. The peptides contain redox-active ferrocene (Fc) and thiol-functionalized cystein (Cys) at the N- and C-terminals, respectively. Peptide films were prepared on gold surfaces and characterized by X-ray photoelectron spectroscopy (XPS), ellipsometry, and Fourier transform-reflection absorption infrared spectroscopy (FT-RAIRS). Electrochemical investigations of the films showed a linear but weakly distance-dependent ET. The importance of H-bonding was realized, and the possibility of a conformationally gated ET mechanism has been discussed.     

Sulfur K-edge XAS and DFT calculations on [Fe4S4]2+ clusters: effects of H-bonding and structural distortion on covalency and spin topology

Sulfur K-edge X-ray absorption spectroscopy of a hydrogen-bonded elongated [Fe4S4]2+ cube is reported. The data show that this synthetic cube is less covalent than a normal compressed cube with no hydrogen bonding. DFT calculations reveal that the observed difference in electronic structure has significant contributions from both the cluster distortion and from hydrogen bonding. The elongated and compressed Fe4S4 structures are found to have different spin topologies (i.e., orientation of the delocalized Fe2S2 subclusters which are antiferromagnetically coupled to each other). It is suggested that the H-bonding interaction with the counterion does not contribute to the cluster elongation. A magneto-structural correlation is developed for the Fe4S4 cube that is used to identify the redox-active Fe2S2 subclusters in active sites of HiPIP and ferredoxin proteins involving these clusters.     

Non-Hermitian systems of Euclidean Lie algebraic type with real energy spectra

We study several classes of non-Hermitian Hamiltonian systems, which can be expressed in terms of bilinear combinations of Euclidean–Lie algebraic generators. The classes are distinguished by different versions of antilinear (PT)-symmetries exhibiting various types of qualitative behaviour. On the basis of explicitly computed non-perturbative Dyson maps we construct metric operators, isospectral Hermitian counterparts for which we solve the corresponding time-independent Schrödinger equation for specific choices of the coupling constants. In these cases general analytical expressions for the solutions are obtained in the form of Mathieu functions, which we analyze numerically to obtain the corresponding energy spectra. We identify regions in the parameter space for which the corresponding spectra are entirely real and also domains where the PT symmetry is spontaneously broken and sometimes also regained at exceptional points. In some cases it is shown explicitly how the threshold region from real to complex spectra is characterized by the breakdown of the Dyson maps or the metric operator. We establish the explicit relationship to models currently under investigation in the context of beam dynamics in optical lattices.     

Investigation of short‐range structural order in Zr69.5Cu12Ni11Al7.5 and Zr41.5Ti41.5Ni17 glasses,using X‐ray absorption spectroscopy and ab initio molecular dynamics simulations

Short‐range order has been investigated in Zr_69.5Cu₁₂Ni₁₁Al_7.5 and Zr_41.5Ti_41.5Ni₁₇ metallic glasses using X‐ray absorption spectroscopy and ab initio molecular dynamics simulations. While both of these alloys are good glass formers, there is a difference in their glass‐forming abilities (Zr_41.5Ti_41.5Ni₁₇ > Zr_69.5Cu₁₂Ni₁₁Al_7.5). This difference is explained by inciting the relative importance of strong chemical order, icosahedral content, cluster symmetry and configuration diversity.     

High resolution 1H NMR of a lipid cubic phase using a solution NMR probe

The cubic mesophase formed by monoacylglycerols and water is an important medium for the in meso crystallogenesis of membrane proteins. To investigate molecular level lipid and additive interactions within the cubic phase, a method was developed for improving the resolution of (1)H NMR spectra when using a conventional solution state NMR probe. Using this approach we obtained well-resolved J-coupling multiplets in the one-dimensional NMR spectrum of the cubic-Ia3d phase prepared with hydrated monoolein. A high resolution t-ROESY two-dimensional (1)H NMR spectrum of the cubic-Ia3d phase is also reported. Using this new methodology, we have investigated the interaction of two additive molecules, L-tryptophan and ruthenium-tris(2,2-bipyridyl) dichloride (rubipy), with the cubic mesophase. Based on the measured chemical shift differences when changing from an aqueous solution to the cubic phase, we conclude that L-tryptophan experiences specific interactions with the bilayer interface, whereas rubipy remains in the aqueous channels and does not associate with the lipid bilayer.