Barbara Kirchner

Bio: Barbara Kirchner is an academic researcher from University of Bonn. The author has contributed to research in topics: Ionic liquid & Hydrogen bond. The author has an hindex of 57, co-authored 239 publications receiving 11054 citations. Previous affiliations of Barbara Kirchner include Jawaharlal Nehru Centre for Advanced Scientific Research & Chemnitz University of Technology.

TRAVIS - a free analyzer and visualizer for Monte Carlo and molecular dynamics trajectories.

Abstract: We present TRAVIS (“TRajectory Analyzer and VISualizer”), a free program package for analyzing and visualizing Monte Carlo and molecular dynamics trajectories. The aim of TRAVIS is to collect as many analyses as possible in one program, creating a powerful tool and making it unnecessary to use many different programs for evaluating simulations. This should greatly rationalize and simplify the workflow of analyzing trajectories. TRAVIS is written in C++, open-source freeware and licensed under the terms of the GNU General Public License (GPLv3). It is easy to install (platform independent, no external libraries) and easy to use. In this article, we present some of the algorithms that are implemented in TRAVIS - many of them widely known for a long time, but some of them also to appear in literature for the first time. All shown analyses only require a standard MD trajectory as input data.

Characterising the Electronic Structure of Ionic Liquids: An Examination of the 1‐Butyl‐3‐Methylimidazolium Chloride Ion Pair

Abstract: In this paper we analyse the electronic properties of gas-phase 1-butyl-3-methylimidazolium Cl ion pairs, [C(4)C(1)im]Cl, in order to deepen our understanding of ionic liquids in general. Examination of charge densities, natural bond orbitals (NBO), and delocalised molecular orbitals computed at the B3LYP and MP2/6-31(++)G(d,p) levels have enabled us to explain a number of experimental phenomena: the relative acidity of different sites on the imidazolium ring, variations in hydrogen-bond donor and acceptor abilities, the apparent contradiction of the hydrogen-bond-donor parameters for different types of solute, the low probability of finding a Cl(-) anion at the rear of the imidazolium ring and the expansion of the imidazolium ring in the presence of a strong hydrogen-bond acceptor. The unreactive but coordinating environment and large electrochemical window have also been accounted for, as has the strong electron-donating character of the carbon atoms to the rear of the ring in associated imidazolylidenes. The electronic structure of the [C(4)C(1)im](+) cation is best described by a C(4)==C(5) double bond at the rear, and a delocalised three-centre 4 e(-) component across the front (N(1)-C(2)-N(3)) of the imidazolium ring; delocalisation between these regions is also significant. Hydrogen-bond formation is driven by Coulombic stabilisation, which compensates for an associated destabilisation of the electronic part of the system. Interactions are dominated by a large positive charge at C(2) and the build up of pi-electron density above and below the ring, particularly that associated with the double bond between C(4) and C(5). The NBO partial charges have been computed and compared with those used in a number of classical simulations.

Task-specific ionic liquid for solubilizing metal oxides

Abstract: Protonated betaine bis(trifluoromethylsulfonyl)imide is an ionic liquid with the ability to dissolve large quantities of metal oxides. This metal-solubilizing power is selective. Soluble are oxides of the trivalent rare earths, uranium(VI) oxide, zinc(II) oxide, cadmium(II) oxide, mercury(II) oxide, nickel(II) oxide, copper(II) oxide, palladium(II) oxide, lead(II) oxide, manganese(II) oxide, and silver(I) oxide. Insoluble or very poorly soluble are iron(III), manganese(IV), and cobalt oxides, as well as aluminum oxide and silicon dioxide. The metals can be stripped from the ionic liquid by treatment of the ionic liquid with an acidic aqueous solution. After transfer of the metal ions to the aqueous phase, the ionic liquid can be recycled for reuse. Betainium bis(trifluoromethylsulfonyl)imide forms one phase with water at high temperatures, whereas phase separation occurs below 55.5 degrees C (temperature switch behavior). The mixtures of the ionic liquid with water also show a pH-dependent phase behavior: two phases occur at low pH, whereas one phase is present under neutral or alkaline conditions. The structures, the energetics, and the charge distribution of the betaine cation and the bis(trifluoromethylsulfonyl)imide anion, as well as the cation-anion pairs, were studied by density functional theory calculations.

Computing vibrational spectra from ab initio molecular dynamics

Abstract: We review several methods for the calculation of vibrational spectra from ab initio molecular dynamics (AIMD) simulations and we present a new implementation in the trajectory analyzer TRAVIS. In particular, we show mass-weighted power spectra, infrared spectra, and Raman spectra with corresponding depolarization ratios, which are based on time-correlation functions of velocities, dipole moments, and polarizabilities, respectively. Using the four organic molecules methanol, acetone, nitromethane, and pinacol as test systems, we compare the spectra from AIMD simulations of the isolated molecules in gas phase to static calculations relying on the harmonic approximation and to experimental spectra recorded in a nonpolar solvent. The AIMD approach turns out to give superior results when anharmonicity effects are of particular importance. Using the example of methanol, we demonstrate the application to bulk phase systems, which are not directly accessible by static calculations, but for which the AIMD spectra also provide a very good approximation to experimental data. Finally, we investigate the influence of simulation time and temperature in the AIMD on the resulting spectra.

Pnicogen bonds: a new molecular linker?

Abstract: In the past decades a lot of progress has been achieved inthe design of miniaturized systems. For instance, the manu-facture of computer chips employing optical technologies,for example, phototemplating, is well established. However,optical procedures are limited to approximately 50 nm. Al-ternatively, nanostructures may be formed by means of selfassembly systems. Besides the arrangement of the molecularbuilding blocks by hydrogen bonds or inorganic metal–ligand bonds, unexpected strong chalcogen–chalcogen inter-actions or halogen bonds have captured interest as connec-tors.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Kirk-Othmer Encyclopedia of Chemical Technology数据库介绍及实例

Abstract: 介绍了Kirk—Othmer Encyclopedia of Chemical Technology（化工技术百科全书）（第五版）电子图书网络版数据库，并对该数据库使用方法和检索途径作出了说明，且结合实例简单地介绍了该数据库的检索方法。

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

Abstract: Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

The Halogen Bond

Abstract: The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.