Hydrogen Bond Detection

In this Article we extend the idea of detecting a hydrogen bond solely on one single quantum chemically determined descriptor. We present an improvement of the method introduced by Reiher et al. (Theor. Chim. Acta 2001, 106, 379), who mapped the strength of the hydrogen bond onto an easily accessible quantity, namely, the two-center shared-electron number σHA. First, we show that the linear dependence between the interaction energy from the supermolecular approach and σHA is valid for a test set of about 120 hydrogen-bonded complexes. Furthermore, we demonstrate that a classification according to acceptor atoms of the hydrogen-bonded complexes can give more accurate results. We thus recommend to detect hydrogen bonds with a specific acceptor atom according to our subset linear regression analysis. Case studies on alcohols and isolated base pairs and trimers from RNA and DNA show the utility of the detection criterion. The shared-electron number method yields that the strength of the N1···N3 hydrogen bond is in the range of 30 kJ/mol. Furthermore the A−U pair is indeed stronger bound than the A−T complex if environmental effects are incorporated in the calculations

Understanding the Template Preorganization Step of an Artificial Arginine Receptor^§

A biomimetic complex which mimics the arginine−phosphonate diester interaction of the arginine fork is investigated with respect to structure and energetics of stable configurations. Within this work, we provide knowledge on local minima of the isolated system obtained from first-principles calculations. Non-negligible solvation effects are studied in a microsolvation approach. The interactions which govern the structural patterns of molecular recognition in this tweezer−guest complex can be significantly modulated by the action of hydrogen bond accepting and donating solvent molecules, such as dimethyl sulfoxide or water, which were present in experimental investigations on this system. Different tweezer−guest structures are evaluated with respect to their temperature-dependent thermodynamical properties as products of the first association reaction step of the bisphosphonate tweezer template and the guanidinium moiety

Complex Structural and Dynamical Interplay of Cyano-Based Ionic Liquids

We carried out ab initio molecular dynamics simulations for the three cyano-based ionic liquids, 1-ethyl-3-methylimidazolium tetracyanoborate ([C2C1Im]­[B­(CN)4]), 1-ethyl-3-methyl-imidazolium dicyanamide ([C2C1Im]­[N­(CN)2]), and 1-ethyl-3-methylimidazolium thiocyanate ([C2C1Im]­[SCN]). We found that the [SCN]-based ionic liquid is much more prone to π–π stacking interactions as opposed to the other two ionic liquids, contrary to the fact that all liquids bear the same cation. Hydrogen bonding is strong in the dicyanamide- and the thiocyanate-based ionic liquids and it is almost absent in the tetracyanoborate liquid. The anion prefers to stay on-top of the imidazolium ring with the highest priority for the [N­(CN)2]− anion followed by the [B­(CN)4]− anion. We find that experimental viscosity trends cannot be correlated to the hydrogen bond dynamics which is fastest for [B­(CN)4]− followed by [SCN]− and [N­(CN)2]−. For the dynamics of the cation on-top of itself, we find the order of [B­(CN)4]− followed by [N­(CN)2]− and finally by [SCN]−. Interestingly, this trend correlates well with the viscosity, suggesting a relation between the cation–cation dynamics and the viscosity at least for these cyano-based ionic liquids. These findings, especially the apparent correlation between cation–cation dynamics and the viscosity, might be useful for the suggestion of better ionic liquids in electrolyte applications

TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories

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

TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories

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

Classical Magnetic Dipole Moments for the Simulation of Vibrational Circular Dichroism by ab Initio Molecular Dynamics

We present a new approach for calculating vibrational circular dichroism spectra by ab initio molecular dynamics. In the context of molecular dynamics, these spectra are given by the Fourier transform of the cross-correlation function of magnetic dipole moment and electric dipole moment. We obtain the magnetic dipole moment from the electric current density according to the classical definition. The electric current density is computed by solving a partial differential equation derived from the continuity equation and the condition that eddy currents should be absent. In combination with a radical Voronoi tessellation, this yields an individual magnetic dipole moment for each molecule in a bulk phase simulation. Using the chiral alcohol 2-butanol as an example, we show that experimental spectra are reproduced very well. Our approach requires knowing only the electron density in each simulation step, and it is not restricted to any particular electronic structure method

CO₂ Absorption in the Protic Ionic Liquid Ethylammonium Nitrate

We present a first principles molecular dynamics study of carbon dioxide solvation by protic ionic liquids using ethylammonium nitrate as an example solvent. Microheterogeneity of the alkyl chains and the extended hydrogen bond network could be observed. Thus, the entire structure of the investigated protic ionic liquid mixed with CO2 closely resembles the one of the pure liquid. Our data indicates that CO2 most likely creates an energy loss due to entering the liquid via the too-small voids. But this is fully compensated by specific attractive interactions of CO2 with the cation and anions of ethylammonium nitrate. This result might serve as an explanation for the question of why the volume of the ionic liquid is not increasing through CO2 uptake. The CO2 cluster formation, which shows a structure similar to supercritical CO2, is guided by the dominance of the nonpolar groups in the CO2 solvation shell

CONANNovel Tool to Create and Analyze Liquids in Confined Space

Modeling of complex liquids at solid surfaces and in confinement is gaining attention due to an increase in computer power and advancement of simulation techniques. Therefore, tools to set up structures and for analysis are needed. In this paper, we present CONANa Python code designed to facilitate the study of liquids interacting with solid structures, such as walls or pores. Among other things, the program provides the option to generate a variety of different structures, including carbon walls and nanotubes and their boron nitride analogs, as well as the ability to analyze various structural properties of confined and interfacial liquids. In the case of the ionic liquid 1-butyl-3-methylimidazolium acetate in carbon nanotubes of different sizes, we demonstrate the abilities of our tool. The average density within the confinement highly depends on the carbon nanotube size, and it is generally lower than the density of the bulk liquid. The arrangement of the individual species within the tube also depends on size, with radial layers forming within the tubular confinement. The density is largely increased in the respective layers, while it is drastically reduced between the layers