The Sequential Occupancy Problem through Group Throwing of Indistinguishable Balls

The occupancy problem is generalized to the case where instead of throwing one ball at a time, a fixed size group of indistinguishable balls are distributed sequentially into cells. Bose-Einstein statistics is used for analyzing the distribution of the waiting time until each cell is occupied by at least one ball. Each trial is classified according to its jump size, i.e. the number of newly occupied cells. We propose an approach to decompose the occupancy and filling processes in terms of the jumps sizes using a multi-dimensional representation. A set of recursive equations is built in order to obtain the joint generating probability function of a series of random variables, each of which denotes the number of trials for a given jump size that occurred during the filling process. As a special case, the joint probability function of these random variables is obtained.     

Structural elucidation of amino amide‐type local anesthetic drugs and their main metabolites in urine by LC‐MS after derivatization and its application for differentiation between positional isomers of prilocaine

The demand for clinical toxicology analytical methods for identifying drugs of abuse and medicinal drugs is steadily increasing. Structural elucidation of amino amide‐type local anesthetic drugs and their main metabolites by GC‐EI‐MS and LC‐ESI‐MS/MS is of great analytical challenge. These compounds exhibit only/mostly fragments/product ions representing the amine‐containing residue, while the aromatic amide moiety remains unidentified. This task becomes even more complicated when discrimination between positional isomers of such compounds is required. Here, we report the development of a derivatization procedure for the differentiation and structural elucidation of a mixture of local anesthetic drugs and their metabolites that possess tertiary and secondary amines in water and urine. A method based on two sequential “in‐vial” instantaneous derivatization processes at ambient temperature followed by LC‐ESI‐MS/MS analysis was developed. 2,2,2‐Trichloro‐1,1‐dimethylethyl chloroformate (TCDMECF) was utilized to selectively convert the secondary amines into their carbamate derivatives, followed by hydrogen peroxide addition to produce the corresponding tertiary amine oxides. The resulting derivatives exhibited rich fragmentation patterns, enabling improved structural elucidation of the original compounds. The developed method was successfully applied to the differentiation and structural elucidation of prilocaine and its four positional isomers, which all possess similar GC and LC retention times and four of them exhibit almost identical EI‐MS and ESI‐MS/MS spectra, enabling their structural elucidation in a single LC‐ESI‐MS/MS analysis. The developed technique is fast and simple and enables discrimination between isomers based on different diagnostic ions/fragmentation patterns.     

Cohomologically trivial internal categories in categories of groups with operations

We describe cohomologically trivial internal categories in the categoryC of groups with operations satisfying certain conditions ([15], [16]). As particular cases we obtain: ifC=Gr, H⁰(C, –)=0 iff C is a connected internal category; ifC=Ab,H ¹(C, –)=0 iff C is equivalent to the discrete internal category (Cokerd, Cokerd, 1, 1, 1, 1). We also discuss related questions concerning extensions, internal categories, their cohomology and equivalence in the categoryC.     

A truncated Newton minimizer adapted for CHARMM and biomolecular applications

We report the adaptation of the truncated Newton minimization package TNPACK for CHARMM and biomolecular energy minimization. TNPACK is based on the preconditioned linear conjugate–gradient technique for solving the Newton equations. The structure of the problem—sparsity of the Hessian—is exploited for preconditioning. Experience with the new version of TNPACK is presented on a series of molecular systems of biological and numerical interest: alanine dipeptide (N-methyl-alanyl-acetamide), a dimer of N-methyl-acetamide, deca-alanine, mellitin (26 residues), avian pancreatic polypeptide (36 residues), rubredoxin (52 residues), bovine pancreatic trypsin inhibitor (58 residues), a dimer of insulin (99 residues), and lysozyme (130 residues). Detailed comparisons among the minimization algorithms available in CHARMM, particularly those used for large-scale problems, are presented along with new mathematical developments in TNPACK. The new TNPACK version performs significantly better than ABNR, the most competitive minimizer in CHARMM, for all systems tested in terms of CPU time when curvature information (Hessian/vector product) is calculated by a finite-difference of gradients (the numeric option of TNPACK). The remaining derivative quantities are, however, evaluated analytically in TNPACK. The CPU gain is 50% or more (speedup factors of 1.5 to 2.5) for the largest molecular systems tested and even greater for smaller systems (CPU factors of 1 to 4 for small systems and 1 to 5 for medium systems). TNPACK uses curvature information to escape from undesired configurational regions and to ensure the identification of true local minima. It converges rapidly once a convex region is reached and achieves very low final gradient norms, such as of order 10^?8, with little additional work. Even greater overall CPU gains are expected for large-scale minimization problems by making the architectures of CHARMM and TNPACK more compatible with respect to the second-derivative calculations. © 1994 by John Wiley & Sons, Inc.     

An analysis of the structural and energetic properties of deoxyribose by potential energy methods

We discuss the three fundamental issues of a computational approach in structure prediction by potential energy minimization, and analyze them for the nucleic acid component deoxyribose. Predicting the conformation of deoxyribose is important not only because of the molecule's central conformational role in the nucleotide backbone, but also because energetic and geometric discrepancies from experimental data have exposed some underlying uncertainties in potential energy calculations. The three fundamental issues examined here are: (i) choice of coordinate system to represent the molecular conformation; (ii) construction of the potential energy function; and (iii) choice of the minimization technique. For our study, we use the following combination. First, the molecular conformation is represented in cartesian coordinate space with the full set of degrees of freedom. This provides an opportunity for comparison with the pseudorotation approximation. Second, the potential energy function is constructed so that all the interactions other than the nonbonded terms are represented by polynomials of the coordinate variables. Third, two powerful Newton methods that are globally and quadratically convergent are implemented: Gill and Murray's Modified Newton method and a Truncated Newton method, specifically developed for potential energy minimization. These strategies have produced the two experimentally-observed structures of deoxyribose with geometric data (bond angles and dihedral angles) in very good agreement with experiment. More generally, the application of these modeling and minimization techniques to potential energy investigations is promising. The use of cartesian variables and polynomial representation of bond length, bond angle and torsional potentials promotes efficient second-derivative computation and, hence, application of Newton methods. The truncated Newton, in particular, is ideally suited for potential energy minimization not only because the storage and computational requirements of Newton methods are made manageable, but also because it contains an important algorithmic adaptive feature: the minimization search is diverted from regions where the function is nonconvex and is directed quickly toward physically interesting regions.     

Protic ionic liquids: physicochemical properties and behavior as amphiphile self-assembly solvents

The physicochemical properties of 22 protic ionic liquids (PILs) and 6 protic molten salts, and the self-assembly behavior of 3 amphiphiles in the PILs, are reported. Structure-property relationships have been explored for the PILs, including the effect of increasing the substitution of ammonium cations and the presence of methoxy and hydroxyl moieties in the cation. Anion choices included the formate, pivalate, trifluoroacetate, nitrate, and hydrogen sulfate anions. This series of PILs had a diverse range of physicochemical properties, with ionic conductivities up to 51.10 mS/cm, viscosities down to 5.4 mPa.s, surface tensions between 38.3 and 82.1 mN/m, and densities between 0.990 and 1.558 g/cm3. PILs were designed with various levels of solvent cohesiveness, as quantified by the Gordon parameter. Fourteen PILs were found to promote the self-assembly of amphiphiles. High-throughput polarized optical microscopy was used to identify lamellar, hexagonal, and bicontinuous cubic amphiphile self-assembly phases. The presence and extent of amphiphile self-assembly have been discussed in terms of the Gordon parameter.     

Optimal control of molecular alignment in dissipative media

We explore the controllability of nonadiabatic alignment in dissipative media, and the information content of control experiments regarding the bath properties and the bath system interactions. Our approach is based on a solution of the quantum Liouville equation within the multilevel Bloch formalism, assuming Markovian dynamics. We find that the time and energy characteristics of the laser fields that produce desired alignment characteristics at a predetermined instant respond in distinct manners to decoherence and to population relaxation, and are sensitive to both time scales. In particular, the time-evolving spectral composition of the optimal pulse mirrors the time-evolving rotational composition of the wave packet, and points to different mechanisms of rotational excitation in isolated systems, in systems subject to a decoherering bath, and in ones subject to a population relaxing bath.     

Information content of high harmonics generated from aligned molecules

We derive an expression for the harmonic signal from nonadiabatically aligned molecules that accounts for both electronic and rotational motions. We identify a single approximation, which converts the expression into a physically transparent and computationally convenient form. Our analytical result gives explicitly the time dependence of the harmonic spectra, thus explaining the observations of a class of recent experiments. Moreover, it points to new opportunities for generating insights into the structure and dynamics of molecular systems through harmonic generation experiments from aligned molecules. This includes information regarding the rotational and electronic dynamics of isolated systems, as well as regarding the decoherence and relaxation in molecules subject to a dissipative environment.     

Nanostructure changes in protic ionic liquids (PILs) through adding solutes and mixing PILs

The effect of adding primary n-alcohols with aliphatic chains and hexane on the nanostructure of a series of 14 protic ionic liquids (PILs) was explored using small and wide angle X-ray scattering (SAXS and WAXS). PILs were investigated with primary, secondary and tertiary ammonium cations containing different alkyl chain lengths, with and without hydroxyl substitution of the alkyl chain. Formate or nitrate anions were paired with these cations. The PILs which had no identified intermediate range order between 5-16 ? had very low solubilities of the solutes. The other PILs, which had non-polar domains present, were mostly miscible with the primary alcohols of ethanol, propanol and butanol. When the alkyl chain length of the alcohols was similar to the PILs then the alcohols co-partitioned with the alkylammonium cation components of the PILs and caused either an increase or decrease in the size of the non-polar domains, depending on whether the alcohol chain length was longer or shorter than that of the cation in the PIL respectively. For ethylammonium nitrate (EAN) with propanol or butanol and propylammonium nitrate (PAN) with butanol, the difference between the alcohol chain length and the alkyl chain length was too great to lead to a modified nanostructure, and instead large aggregates were present. The solubility of hexane in the alkylammonium nitrate PILs had a very strong correlation to the alkyl chain length. The addition of hexane had very little effect on the non-polar domain sizes, which was attributed to it not being orientated in alignment with the alkylammonium cations in the non-polar domains. Lastly, seven binary PIL-PIL solution series were investigated using SAXS and WAXS to show how the nanostructure of these systems can be fine tuned to control the size and structure of the non-polar domains.     

Spectroscopy of molecular junctions

In this tutorial review we present in detail recent studies in which molecular junctions were simultaneously probed by conductance measurements and optical spectroscopy methods such as electroluminescence (EL) and Raman scattering. The advantages of combining these experimental approaches to improve our understanding of charge transport through molecular junctions are discussed and routes for future developments are suggested.