Ultraviolet absorption and vibrational spectra of 2-fluoro-5-bromopyridine

The ultraviolet absorption spectrum in the range 340-185 nm in the vapour and solution phase has been measured for 2-fluoro-5-bromopyridine. Three fairly intense band systems identified as the pi* <-- pi transitions II, III and IV have been observed. A detailed vibronic analysis of the vapor and solution spectra is presented. The first system of bands is resolved into about sixty-two distinct vibronic bands in the vapour-phase spectrum. The 0,0 band is located at 35944 cm(-1). Two well-developed progressions, in which the excited state frequencies nu'25 (283 cm(-1)) and nu'19 (550 cm(-1)) are excited by several quanta, have been observed. The corresponding excited state vibrational and anharmonicity constants are found to be omega'i = 292 cm(-1), x'ii = 4.5 cm(-1) (i = 25) and omega'i = 563.8 cm(-1), x'ii = 6.9 cm(-1) (i = 19). The other two band systems show no vibronic structure, the band maxima being located at 48346 and 52701 cm(-1), respectively. The oscillator strength of the band systems in different solutions and the excited state dipole moments associated with the first two transitions have been determined by the solvent-shift method. The infrared spectrum in the region 4000-130 cm(-1) and the laser Raman spectrum of the molecule in the liquid state have been measured and a complete vibrational assignment of the observed frequencies is given. A correlation of the ground and excited state fundamental frequencies observed in the UV absorption spectrum with the Raman or infrared frequencies is presented.     

Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.     

Macromol. Biosci. 1/2013

Front Cover: Highly aligned 3D silk scaffolds using directional freezing in a custom designed chamber was demonstrated. The method is versatile and holds potential to produce complex, multicomponent aligned structures for various tissue engineering and biomedical applications, needing immediate cell alignment to mimic native tissue hierarchy and function. Further details can be found in the article by B. B. Mandal, E. S. Gil, B. Panilaitis, and D. L. Kaplan* on page 48 .

     

Vibrational phase relaxation along the critical isochore of nitrogen: the role of local density fluctuations in the rate enhancement

Vibrational dephasing of the nitrogen molecule is known to show highly interesting anomalies near its gas-liquid critical point. Here we present theoretical and computational studies of the Raman linewidth of nitrogen along the critical isochore. The linewidth is found to have a lambda-shaped temperature dependence near the critical point. As observed in experimental studies, the calculated line shape becomes Gaussian as the critical temperature (T(c)) is approached. Both the present simulation and a mode coupling theory analysis show that the slow decay of the enhanced density fluctuations near the critical point, probed at the subpicosecond time scales by vibrational frequency modulation, along with an enhanced vibration-rotation coupling, are the main causes of the observed anomalies.     

Parallel bundle-based decomposition for large-scale structured mathematical programming problems

In this paper, we present parallel bundle-based decomposition algorithms to solve a class of structured large-scale convex optimization problems. An example in this class of problems is the block-angular linear programming problem. By dualizing, we transform the original problem to an unconstrained nonsmooth concave optimization problem which is in turn solved by using a modified bundle method. Further, this dual problem consists of a collection of smaller independent subproblems which give rise to the parallel algorithms. We discuss the implementation on the CRYSTAL multi-computer. Finally, we present computational experience with block-angular linear programming problems and observe that more than 70% efficiency can be obtained using up to eleven processors for one group of test problems, and more than 60% efficiency can be obtained for relatively smaller problems using up to five processors for another group of problems.     

Bundle-based decomposition for large-scale convex optimization: Error estimate and application to block-angular linear programs

Robinson has proposed the bundle-based decomposition algorithm to solve a class of structured large-scale convex optimization problems. In this method, the original problem is transformed (by dualization) to an unconstrained nonsmooth concave optimization problem which is in turn solved by using a modified bundle method. In this paper, we give a posteriori error estimates on the approximate primal optimal solution and on the duality gap. We describe implementation and present computational experience with a special case of this class of problems, namely, block-angular linear programming problems. We observe that the method is efficient in obtaining the approximate optimal solution and compares favorably with MINOS and an advanced implementation of the Dantzig—Wolfe decomposition method.     

Non-exponentiality in electron transfer kinetics: Static versus dynamic disorder models

Non-exponential electron transfer kinetics in complex systems are often analyzed in terms of a quenched, static disorder model. In this work we present an alternative analysis in terms of a simple dynamic disorder model where the solvent is characterized by highly non-exponential dynamics. We consider both low and high barrier reactions. For the former, the main result is a simple analytical expression for the survival probability of the reactant. In this case, electron transfer, in the long time, is controlled by the solvent polarization relaxation—in agreement with the analyses of Rips and Jortner and of Nadler and Marcus. The short time dynamics is also non-exponential, but for different reasons. The high barrier reactions, on the other hand, show an interesting dynamic dependence on the electronic coupling element,V _el.     

Dielectric friction and solvation dynamics: Novel results on relaxation in dipolar liquids

In this article we present a new, general but simple, microscopic expression for time-dependent solvation energy of an ion. This expression is surprisingly similar to the expression for the time-dependent dielectric friction on a moving ion. We show that both the Chandra-Bagchi and the Fried-Mukamel formulations of solvation dynamics can be easily derived from this expression. This expression leads to an almost perfect agreement of the theory with all the available computer simulation results. Second, we show here for the first time that the mobility of a light solute ion can significantly accelerate its own solvation, specially in the underdamped limit. The latter result is also in excellent agreement with the computer simulations.     

Handling of intrinsic divergence in the orthogonal gradient method of orbital optimization in an MC-SCF framework and geometry optimization in pathological cases: I (propynal in excited states)

It is demonstrated that a generalized version of the orthogonal gradient method of orbital optimization may sometimes encounter a specific divergence problem which may be termed intrinsic to the first order method. Instead of switching over to a more sophisticated second order method one can cure the divergence problem at the first order level itself by suitably tailoring the MC-SCF operator or the MC-SCF energy matrix. Results of complete geometry optimization of propynal in^l,3nπ* and³ππ* states (pathological cases) are reported to demonstrate the usefulness of the method at an INDO-MCSCF level of approximation. The results of structure calculations are further rationalized from generalized quantum chemical bond order indices.