Combinatorial invariants and covariants as tools for conical intersections

The combinatorial invariant and covariant are introduced as practical tools for analysis of conical intersections in molecules. The combinatorial invariant is a quantity depending on adiabatic electronic states taken at discrete nuclear configuration points. It is invariant to the phase choice (gauge) of these states. In the limit that the points trace a loop in nuclear configuration space, the value of the invariant approaches the corresponding Berry phase factor. The Berry phase indicates the presence of an odd or even number of conical intersections on surfaces bounded by these loops. Based on the combinatorial invariant, we develop a computationally simple and efficient method for locating conical intersections. The method is robust due to its use of gauge invariant nature. It does not rely on the landscape of intersecting potential energy surfaces nor does it require the computation of nonadiabatic couplings. We generalize the concept to open paths and combinatorial covariants for higher dimensions obtaining a technique for the construction of the gauge-covariant adiabatic-diabatic transformation matrix. This too does not make use of nonadiabatic couplings. The importance of using gauge-covariant expressions is underlined throughout. These techniques can be readily implemented by standard quantum chemistry codes.     

Molecular recognition and conductance in crown ethers

Crown ethers have the remarkable property of recognizing and binding specific metal cations in complex mixtures. We propose to combine molecular recognition with molecular electric conductance. The question we address is: can the event of binding a cation be sensed by a change in conductance? Specifically, we study a short molecular wire (MW) containing a crown-6 molecule connected via sulfur atoms to two gold atomic wires acting as metallic leads. Upon binding a cation, the density of states of the system is only slightly affected. This reflects the fact that the cation binding is largely electrostatic in nature and is accompanied by little electronic reorganization. Yet, the cationic binding does significantly lower conductance. We also identify strong interference affecting the conductance. A striking feature is the insensitivity of conductance to the type of ligand with the exception of the proton.     

Photoionization dynamics of glycine adsorbed on a silicon cluster: "on-the-fly" simulations

Dynamics of glycine chemisorbed on the surface of a silicon cluster is studied for a process that involves single-photon ionization, followed by recombination with the electron after a selected time delay. The process is studied by "on-the-fly" molecular dynamics simulations, using the semiempirical parametric method number 3 (PM3) potential energy surface. The system is taken to be in the ground state prior to photoionization, and time delays from 5 to 50 fs before the recombination are considered. The time evolution is computed over 10 ps. The main findings are (1) the positive charge after ionization is initially mostly distributed on the silicon cluster. (2) After ionization the major structural changes are on the silicon cluster. These include Si-Si bond breaking and formation and hydrogen transfer between different silicon atoms. (3) The transient ionization event gives rise to dynamical behavior that depends sensitively on the ion state lifetime. Subsequent to 45 fs evolution in the charged state, the glycine molecule starts to rotate on the silicon cluster. Implications of the results to various processes that are induced by transient transition to a charged state are discussed. These include inelastic tunneling in molecular devices, photochemistry on conducting surfaces, and electron-molecule scattering.     

Acylation of novobiocin by carboxylic acid anhydrides: preparation and characterization of semi-synthetic novenamines

The acylation of novobiocin by carboxylic acid anhydrides leading to preparation of three families of semi-synthetic acylated novenamine analogues is reported. ESI-MS was used to monitor the reaction progress and enabled the isolation of intermediate compounds that provided insights into the sequence of acylation steps during the reaction. The chemoselectivity of the reaction depends on the carboxylic acid anhydride. The potential of the acylated novenamine analogues as leads for the development of antibacterial agents is discussed.     

Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks

A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package.     

Efficient linear-response method circumventing the exchange-correlation kernel: theory for molecular conductance under finite bias

An iterative approach for calculating the frequency domain linear response of molecular systems within time-dependent density-functional theory is presented. The method completely avoids computing the exchange-correlation kernel which is typically the most expensive step for large systems. In particular, virtual orbitals are not needed. This approach may be useful for treating the response of large systems. We give an outline of the theory and a demonstration on a jellium model of an elliptic gold cluster. A detailed theory is appended discussing the computation of conductance and ac impedance of molecular junctions under bias.     

On the mapping of time-dependent densities onto potentials in quantum mechanics

The mapping of time-dependent densities on potentials in systems of identical quantum mechanical particles is examined. This mapping is of significance ever since Runge and Gross [Phys. Rev. Lett. 52, 997 (1984)] established its uniqueness, forming the theoretical basis for time-dependent density functional theory. Beyond uniqueness there are two important issues: existence, often called v-representability, and stability. We show that v-representability for localized densities in turn-on situations is not assured and we give a simple example of nonexistence. As for stability, we discuss an inversion procedure and by computing its Lyapunov exponents we demonstrate that the mapping is unstable with respect to fluctuations in the initial state. We argue that such instabilities will plague any inversion procedure.     

A spline for your saddle

Pinpointing extrema on a multidimensional hypersurface is an important generic problem with a broad scope of application in statistical mechanics, biophysics, chemical reaction dynamics, and quantum chemistry. Local minima of the hypersurface correspond to metastable structures and are usually the most important points to look for. They are relatively easy to find using standard minimizing algorithms. A considerably more difficult task is the location of saddle points. The saddle points most sought for are those which form the lowest barriers between given minima and are usually required for determining rates of rare events. We formulate a path functional minimum principle for the saddle point. We then develop a cubic spline method for applying this principle and locating the saddle point(s) separating two local minima on a potential hypersurface. A quasi-Newton algorithm is used for minimization. The algorithm does not involve second derivatives of the hypersurface and the number of potential gradients evaluated is usually less than 10% of the number of potential evaluations. We demonstrate the performance of the method on several standard examples and on a concerted exchange mechanism for self-diffusion in diamond. Finally, we show that the method may be used for solving large constrained minimization problems which are relevant for self-consistent field iterations in large systems.     

A nonlinear symmetry breaking effect in shear cracks

Shear cracks propagation is a basic dynamical process that mediates interfacial failure. We develop a general weakly nonlinear elastic theory of shear cracks and show that these experience tensile-mode crack tip deformation, including possibly opening displacements, in agreement with Stephenson's prediction. We quantify this nonlinear symmetry breaking effect, under two-dimensional deformation conditions, by an explicit inequality in terms of the first and second order elastic constants in the quasi-static regime and by semi-analytic calculations in the fully dynamic regime. Our general results are applied to various materials. Finally, we discuss related works in the literature and note the potential relevance of elastic nonlinearities for various problem, including frictional sliding.