Vibronic coupling simulations for linear and nonlinear optical processes: simulation results

A vibronic coupling model based on time-dependent wavepacket approach is applied to simulate linear optical processes, such as one-photon absorbance and resonance Raman scattering, and nonlinear optical processes, such as two-photon absorbance and resonance hyper-Raman scattering, on a series of small molecules. Simulations employing both the long-range corrected approach in density functional theory and coupled cluster are compared and also examined based on available experimental data. Although many of the small molecules are prone to anharmonicity in their potential energy surfaces, the harmonic approach performs adequately. A detailed discussion of the non-Condon effects is illustrated by the molecules presented in this work. Linear and nonlinear Raman scattering simulations allow for the quantification of interference between the Franck-Condon and Herzberg-Teller terms for different molecules.     

Synthesis of dopamine and serotonin derivatives for immobilization on a solid support

The two important neurotransmitters dopamine and serotonin are synthesized with short PEG tethers and immobilized on a magnetic solid support. The tether is attached to the aromatic moiety of the neurotransmitters to conserve their original functional groups. This approach causes minimal alteration of the original structure with the aim of optimizing the immobilized neurotransmitters for aptamer selection by SELEX. For the dopamine derivative, the tether is attached to the aromatic core of a dopamine precursor by the Sonogashira reaction. For serotonin, a link to the indole core is introduced by a Claisen rearrangement from the allylated phenol moiety of serotonin. The tethers are azide-functionalized, which enables coupling to alkyne-modified magnetic beads. The coupling to the magnetic beads is quantified by UV spectroscopy using Fmoc-monitoring of the immobilized dopamine and serotonin derivatives.     

Perfluoroalkyl chains direct novel self-assembly of insulin

The self-assembly of biopharmaceutical peptides into multimeric, nanoscale objects, as well as their disassembly to monomers, is central for their mode of action. Here, we describe a bioorthogonal strategy, using a non-native recognition principle, for control of protein self-assembly based on intermolecular fluorous interactions and demonstrate it for the small protein insulin. Perfluorinated alkyl chains of varying length were attached to desB30 human insulin by acylation of the ε-amine of the side-chain of LysB29. The insulin analogues were formulated with Zn(II) and phenol to form hexamers. The self-segregation of fluorous groups directed the insulin hexamers to self-assemble. The structures of the systems were investigated by circular dichroism (CD) spectroscopy and synchrotron small-angle X-ray scattering. Also, the binding affinity to the insulin receptor was measured. Interestingly, varying the length of the perfluoroalkyl chain provided three different scenarios for self-assembly; the short chains hardly affected the native hexameric structure, the medium-length chains induced fractal-like structures with the insulin hexamer as the fundamental building block, while the longest chains lead to the formation of structures with local cylindrical geometry. This hierarchical self-assembly system, which combines Zn(II) mediated hexamer formation with fluorous interactions, is a promising tool to control the formation of high molecular weight complexes of insulin and potentially other proteins.     

Homo‐ and Heteronuclear meso,meso‐(E)‐Ethene‐1,2‐diyl‐Linked Diporphyrins: Preparation,X‐ray Crystal Structure,Electronic Absorption and Emission Spectra and Density Functional Theory Calculations

Homo‐ and heteronuclear meso,meso‐(E)‐ethene‐1,2‐diyl‐linked diporphyrins have been prepared by the Suzuki coupling of porphyrinylboronates and iodovinylporphyrins. Combinations comprising 5,10,15‐triphenylporphyrin (TriPP) on both ends of the ethene‐1,2‐diyl bridge M₂10 (M₂=H₂/Ni, Ni₂, Ni/Zn, H₄, H₂Zn, Zn₂) and 5,15‐bis(3,5‐di‐tert‐butylphenyl)porphyrinato‐nickel(II) on one end and H₂, Ni, and ZnTriPP on the other ( M₂11 ), enable the first studies of this class of compounds possessing intrinsic polarity. The compounds were characterized by electronic absorption and steady state emission spectra, ¹H NMR spectra, and for the Ni₂ bis(TriPP) complex Ni₂10 , single crystal X‐ray structure determination. The crystal structure shows ruffled distortions of the porphyrin rings, typical of Ni^II porphyrins, and the (E)‐C₂H₂ bridge makes a dihedral angle of 50° with the mean planes of the macrocycles. The result is a stepped parallel arrangement of the porphyrin rings. The dihedral angles in the solid state reflect the interplay of steric and electronic effects of the bridge on interporphyrin communication. The emission spectra in particular, suggest energy transfer across the bridge is fast in conformations in which the bridge is nearly coplanar with the rings. Comparisons of the fluorescence behaviour of H₄10 and H₂Ni10 show strong quenching of the free base fluorescence when the complex is excited at the lower energy component of the Soret band, a feature associated in the literature with more planar conformations. TDDFT calculations on the gas‐phase optimized geometry of Ni₂10 reproduce the features of the experimental electronic absorption spectrum within 0.1 eV.     

Watching Nanoparticles Form: An In Situ (Small‐/Wide‐Angle X‐ray Scattering/Total Scattering) Study of the Growth of Yttria‐Stabilised Zirconia in Supercritical Fluids

Understanding nanoparticle‐formation reactions requires multi‐technique in situ characterisation, since no single characterisation technique provides adequate information. Here, the first combined small‐angle X‐ray scattering (SAXS)/wide‐angle X‐ray scattering (WAXS)/total‐scattering study of nanoparticle formation is presented. We report on the formation and growth of yttria‐stabilised zirconia (YSZ) under the extreme conditions of supercritical methanol for particles with Y₂O₃ equivalent molar fractions of 0, 4, 8, 12 and 25 %. Simultaneous in situ SAXS and WAXS reveals a quick formation (seconds) of sub‐nanometre amorphous material forming larger agglomerates with subsequent slow crystallisation (minutes) into nanocrystallites. The amount of yttria dopant is shown to strongly affect the crystallite size and unit‐cell dimensions. At yttria‐doping levels larger than 8 %, which is known to be the stoichiometry with maximum ionic conductivity, the strain on the crystal lattice is significantly increased. Time‐resolved nanoparticle size distributions are calculated based on whole‐powder‐pattern modelling of the WAXS data, which reveals that concurrent with increasing average particle sizes, a broadening of the particle‐size distributions occur. In situ total scattering provides structural insight into the sub‐nanometre amorphous phase prior to crystallite growth, and the data reveal an atomic rearrangement from six‐coordinated zirconium atoms in the initial amorphous clusters to eight‐coordinated zirconia atoms in stable crystallites. Representative samples prepared ex situ and investigated by transmission electron microscopy confirm a transformation from an amorphous material to crystalline nanoparticles upon increased synthesis duration.     

Vibrational frequencies and structural determination of tetraazidogermane

The vibrational frequencies and corresponding normal mode assignments of tetraazidogermane are examined theoretically using the Gaussian98 set of quantum chemistry codes. All normal modes were successfully assigned to one of seven types of motion predicted by a group theoretical analysis (N-N-N asymmetric stretch, N-N-N symmetric stretch, Ge-N stretch, N-N-N bend, Ge-N-N bend, N-Ge-N bend, and N-Ge-N-N torsion) utilizing the S(4) symmetry of the molecule. The molecular orbitals of Ge(N(3))(4) are examined.     

Higher-order Brunnian structures and possible physical realizations

We consider few-body bound state systems and provide precise definitions of Borromean and Brunnian systems. The initial concepts are more than a hundred years old and originated in mathematical knot-theory as purely geometric considerations. About thirty years ago they were generalized and applied to the binding of systems in nature. It now appears that recent generalization to higher-order Brunnian structures may potentially be realized as laboratory-made or naturally occurring systems. With the binding energy as measure, we discuss possibilities of physical realization in nuclei, cold atoms, and condensedmatter systems. Appearance is not excluded. However, both the form and the strengths of the interactions must be rather special. The most promising subfields for present searches would be in cold atoms because of external control of effective interactions, or perhaps in condensed-matter systems with nonlocal interactions. In nuclei, it would only be by sheer luck due to a lack of tunability.     

Disjoint 3‐Cycles in Tournaments: A Proof of The Bermond–Thomassen Conjecture for Tournaments

We prove that every tournament with minimum out‐degree at least contains k disjoint 3‐cycles. This provides additional support for the conjecture by Bermond and Thomassen that every digraph D of minimum out‐degree contains k vertex disjoint cycles. We also prove that for every , when k is large enough, every tournament with minimum out‐degree at least contains k disjoint cycles. The linear factor 1.5 is best possible as shown by the regular tournaments.     

The Steiner Problem on Surfaces of Revolution

While the Steiner problem has been extensively studied in the Euclidean plane, it remains an open problem to solve the Steiner problem on arbitrary non-planar (piecewise smooth) surfaces. We suggest an algorithm for solving the n-point Steiner problem on surfaces of revolution which have a non-decreasing generating function by constructing an isometric framework on a plane endowed with a weighted distance metric, thus propelling a new analytical avenue for studying the Steiner problem on surfaces with non-constant curvature.     

Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6‐31G* level) is used to optimize the solution structure of the 304‐atom Trp‐cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the α‐helix, β‐turn and the extended form in solution are elucidated for polyalanine. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010