HE(I) Photoelectron spectra of 1,2-ethanediol in the liquid and gas phases

Nine bands in the He(I) gas-phase photoelectron spectrum of 1,2-ethanediol are assigned by means of ab initio calculation and by comparison with the sp     

Markov interest rate models

A general procedure for creating Markovian interest rate models is presented. The models created by this procedure automatically fit within the HJM framework and fit the initial term structure exactly. Therefore they are arbitrage free. Because the models created by this procedure have only one state variable per factor, twoand even three-factor models can be computed efficiently, without resorting to Monte Carlo techniques. This computational efficiency makes calibration of the new models to market prices straightforward. Extended Hull- White, extended CIR, Black-Karasinski, Jamshidian's Brownian path independent models, and Flesaker and Hughston's rational log normal models are one-state variable models which fit naturally within this theoretical framework. The ‘separable’ n-factor models of Cheyette and Li, Ritchken, and Sankarasubramanian - which require n(n + 3)/2 state variables - are degenerate members of the new class of models with n(n + 3)/2 factors. The procedure is used to create a new class of one-factor models, the ‘β-η models.’ These models can match the implied volatility smiles of swaptions and caplets, and thus enable one to eliminate smile error. The β-η models are also exactly solvable in that their transition densities can be written explicitly. For these models accurate - but not exact - formulas are presented for caplet and swaption prices, and it is indicated how these closed form expressions can be used to efficiently calibrate the models to market prices.     

Single-Molecule Observation of Intermediates in Bioorthogonal 2-Cyanobenzothiazole Chemistry

We report a single-molecule mechanistic investigation into 2-cyanobenzothiazole (CBT) chemistry within a protein nanoreactor. When simple thiols reacted reversibly with CBT, the thioimidate monoadduct was approximately 80-fold longer-lived than the tetrahedral bisadduct, with important implications for the design of molecular walkers. Irreversible condensation between CBT derivatives and N-terminal cysteine residues has been established as a biocompatible reaction for site-selective biomolecular labeling and imaging. During the reaction between CBT and aminothiols, we resolved two transient intermediates, the thioimidate and the cyclic precursor of the thiazoline product, and determined the rate constants associated with the stepwise condensation, thereby providing critical information for a variety of applications, including the covalent inhibition of protein targets and dynamic combinatorial chemistry.     

Bioorthogonal Cycloadditions with Sub‐Millisecond Intermediates

Tetrazine‐ and sydnone‐based click reactions have emerged as important bioconjugation strategies with fast kinetics and N₂ or CO₂ as the only byproduct. Mechanistic studies of these reactions have focused on the initial rate‐determining cycloaddition steps. The subsequent N₂ or CO₂ release from the bicyclic intermediates has been approached mainly through computational studies, which have predicted lifetimes of femtoseconds. In the present study, bioorthogonal cycloadditions involving N₂ or CO₂ extrusion have been examined experimentally at the single‐molecule level by using a protein nanoreactor. At the resolution of this approach, the reactions appeared to occur in a single step, which places an upper limit on the lifetimes of the intermediates of about 80 μs, which is consistent with the computational work.     

Asymmetric droplet interface bilayers

In cell membranes, the lipid compositions of the inner and outer leaflets differ. Therefore, a robust model system that enables single-channel electrical recording with asymmetric bilayers would be very useful. We and others recently developed the droplet interface bilayer (DIB), which is formed by connecting lipid monolayer-encased aqueous droplets submerged in an oil-lipid mixture. Here, we incorporate lipid vesicles of different compositions into aqueous droplets and immerse them in an oil bath to form asymmetric DIBs (a-DIBs). Both alpha-helical and beta-barrel membrane proteins insert readily into a-DIBs, and their activity can be measured by single-channel electrical recording. We show that the gating behavior of outer membrane protein G (OmpG) from Escherichia coli differs depending on the side of insertion in an asymmetric DIB with a positively charged leaflet opposing a negatively charged leaflet. The a-DIB system provides a general platform for studying the effects of bilayer leaflet composition on the behavior of ion channels and pores.     

Parametrization of analytic interatomic potential functions using neural networks

A generalized method that permits the parameters of an arbitrary empirical potential to be efficiently and accurately fitted to a database is presented. The method permits the values of a subset of the potential parameters to be considered as general functions of the internal coordinates that define the instantaneous configuration of the system. The parameters in this subset are computed by a generalized neural network (NN) with one or more hidden layers and an input vector with at least 3n-6 elements, where n is the number of atoms in the system. The Levenberg-Marquardt algorithm is employed to efficiently affect the optimization of the weights and biases of the NN as well as all other potential parameters being treated as constants rather than as functions of the input coordinates. In order to effect this minimization, the usual Jacobian employed in NN operations is modified to include the Jacobian of the computed errors with respect to the parameters of the potential function. The total Jacobian employed in each epoch of minimization is the concatenation of two Jacobians, one containing derivatives of the errors with respect to the weights and biases of the network, and the other with respect to the constant parameters of the potential function. The method provides three principal advantages. First, it obviates the problem of selecting the form of the functional dependence of the parameters upon the system's coordinates by employing a NN. If this network contains a sufficient number of neurons, it will automatically find something close to the best functional form. This is the case since Hornik et al., [Neural Networks 2, 359 (1989)] have shown that two-layer NNs with sigmoid transfer functions in the first hidden layer and linear functions in the output layer are universal approximators for analytic functions. Second, the entire fitting procedure is automated so that excellent fits are obtained rapidly with little human effort. Third, the method provides a procedure to avoid local minima in the multidimensional parameter hyperspace. As an illustrative example, the general method has been applied to the specific case of fitting the ab initio energies of Si(5) clusters that are observed in a molecular dynamics (MD) simulation of the machining of a silicon workpiece. The energies of the Si(5) configurations obtained in the MD calculations are computed using the B3LYP procedure with a 6-31G(**) basis set. The final ab initio database, which comprises the density functional theory energies of 10 202 Si(5) clusters, is fitted to an empirical Tersoff potential containing nine adjustable parameters, two of which are allowed to be the functions of the Si(5) configuration. The fitting error averaged over all 10 202 points is 0.0148 eV (1.43 kJ mol(-1)). This result is comparable to the accuracy achieved by more general fitting methods that do not rely on an assumed functional form for the potential surface.