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To all appearances, electron impact mass spectrometer (EI-MS) is considered a "chirally blind" instrument. Yet, numerous non-identical R (right) and S (left) configurations of prochiral alcohols' mass spectra alcohols have appeared in the literature with almost no justification. Such observations are often attributed to impurities, experimental circumstances, inaccurate measurements, etc. In an experimental attempt to explain this phenomenon, here we have avoided the above mentioned pitfalls by conducting control experiments using different pure enantiomers under the same circumstances. Hence, we report the mass spectra of R- and S-enantiomers of 2-octanol (1R, 1S) and 1-octyn-3-ol (2R, 2S) collected by running 20 independent experiments for each R- and S-enantiomer. Statistical analyses confirmed that the peak intensities were significant to an acceptable level of confidence. The 1R and 1S enantiomers were separated reasonably in the PC space, implying that the chirally blind EI-MS is able to discriminate between R and S prochiral alcohols. Theoretically, self-complexation through H-bonding for S (or R) appears to give a new chiral center at the H-bonded oxygen atom, producing a new dimeric pair of diastereomers SRS and SSS (or RRR and RSR) before ionization, and SRS.+ and SSS.+ (or RRR.+ and RSR.+) after ionization. The results of our calculations have explicitly shown that these hydrogen bonds formed. Interestingly, the latter four ionized diastereomers appear with different structural and thermodynamic parameters at the M06-2X/6-311++g (d,p) level of theory.

Patchy colloidal model with three and four equivalent patches, confined in the attractive random porous media, undergo re-entrant gas-liquid phase separation with the possibility for the liquid phase density to approach zero. This unusual behavior is caused by an interplay between strong fluid-fluid bonding interactions and weak fluid-matrix attractions. At high temperature the shape of the phase diagram is determined by the attractive interaction between the fluid particles; weak Yukawa attraction between fluid and obstacles only slightly enhances the fluid-fluid bonding. At low enough temperature the network of the fluid particles is formed and the shape of the phase diagram becomes defined by the Yukawa fluid-obstacle attraction. Due to this interaction a layer of mutually bonded particles around the obstacles is formed and the network becomes fluid particles in the network is defined by a spatial arrangement of the matrix particles. These features may open a new possibilities in making the equilibrium gels with the predefined nonuniform distribution of the particles., Comment: 5 pages, 4 figures

Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a "bespoke" fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibility. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations.

A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models. Ambiguity in molecular models often stems from the dissemination of molecular force fields in a format that is not directly usable or is ambiguously documented via a non-machine readable mechanism. Specifically, the lack of a general tool for performing automated atom-typing under the rules of a particular force field facilitates errors in model parameterization that may go unnoticed if other researchers are unable reproduce this process. Here, we present Foyer, a Python tool that enables users to define force field atom-typing rules in a format that is both machine- and human-readable thus eliminating ambiguity in atom-typing and additionally providing a framework for force field dissemination. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type. Herein we describe the underlying methodology of the Foyer package, highlighting its advantages over typical atom-typing approaches and demonstrate is application in several use-cases., Comment: 39 Page, 4 Figures, 8 Listings

A simple model of dimerizing hard spheres with highly nontrivial fluid-solid phase behaviour is proposed. The model is studied using the recently proposed resummed thermodynamic perturbation theory for central force (RTPT-CF) associating potentials. The phase diagram has the fluid branch of the fluid-solid coexistence curve located at a temperatures lower than those of the solid branch. This unusual behaviour is related to the strong dependence of the system excluded volume on the temperature, which for the model at hand decreases with increasing temperature. This effect can be also seen for a wide family of fluid models with an effective interaction that combines short range attraction and repulsion at a larger distance. We expect that for sufficiently high repulsive barrier, such systems may show similar phase behaviour.

It is well-known that room temperature ionic liquids (RTILs) often adopt a charge-separated layered structure, i.e., with alternating cation- and anion-rich layers, at electrified interfaces. However, the dynamic response of the layered structure to temporal variations in applied potential is not well understood. We used in situ, real-time X-ray reflectivity (XR) to study the potential-dependent electric double layer (EDL) structure of an imidazolium-based RTIL on charged epitaxial graphene during potential cycling as a function of temperature. The results suggest that the graphene-RTIL interfacial structure is bistable in which the EDL structure at any intermediate potential can be described by the combination of two extreme-potential structures whose proportions vary depending on the polarity and magnitude of the applied potential. This picture is supported by the EDL structures obtained by fully atomistic molecular dynamics (MD) simulations at various static potentials. The potential-driven transition between the two structures is characterized by an increasing width but with an approximately fixed hysteresis magnitude as a function of temperature. The results are consistent with the coexistence of distinct anion and cation adsorbed structures separated by an energy barrier (~0.15 eV).

We perform a large-scale statistical analysis (> 2000 independent simulations) of the elongation and rupture of gold nanowires, probing the validity and scope of the recently proposed ductile-to-brittle transition that occurs with increasing nanowire length [Wu et. al., Nano Lett., 12, 910-914 (2012)]. To facilitate a high-throughput simulation approach, we implement the second-moment approximation to the tight-binding (TB-SMA) potential within HOOMD-Blue, a molecular dynamics package which runs on massively parallel graphics processing units (GPUs). In a statistical sense, we find that the nanowires obey the ductile-to-brittle model quite well; however, we observe several unexpected features from the simulations that build on our understanding of the ductile-to-brittle transition. First, occasional failure behavior is observed that qualitatively differs from that predicted by the model prediction; this is attributed to stochastic thermal motion of the Au atoms and occurs at temperatures as low as 10 K. In addition, we also find that the ductile-to-brittle model, which was developed using classical dislocation theory, holds for nanowires as small as 3 nm in diameter. Finally, we demonstrate that the nanowire critical length is higher at 298 K relative to 10 K, a result that is not predicted by the ductile-to-brittle model. These results offer practical design strategies for adjusting nanowire failure and structure, and also demonstrate that GPU computing is an excellent tool for studies requiring a large number independent trajectories in order to fully characterize a system's behavior., Comment: To appear in Journal of Chemical Theory and Computation; 10 figures, 25 pages

We report state-of-the-art atomistic simulations combined with high-fidelity conductance calculations to probe structure-conductance relationships in Au-benzenedithiolate(BDT)-Au junctions under elongation. Our results demonstrate that large increases in conductance are associated with the formation of monatomic chains (MACs) of Au atoms directly connected to BDT. An analysis of the electronic structure of the simulated junctions reveals that enhancement in the s-like states in Au MACs causes the increases in conductance. Other structures also result in increased conductance but are too short-lived to be detected in experiment, while MACs remain stable for long simulation times. Examinations of thermally evolved junctions with and without MACs show negligible overlap between conductance histograms, indicating that the increase in conductance is related to this unique structural change and not thermal fluctuation. These results, which provide an excellent explanation for a recently observed anomalous experimental result [Bruot et al., Nature Nanotech., 2012, 7, 35-40], should aid in the development of mechanically responsive molecular electronic devices., Comment: To appear in Nanoscale; 5 pages, 4 figures

We report detailed atomistic simulations combined with high-fidelity conductance calculations to probe the structural origins of conductance fluctuations in thermally evolving Au-benzene-1,4-dithiolate-Au junctions. We compare the behavior of structurally ideal junctions (electrodes with flat surfaces) to structurally realistic, experimentally representative junctions resulting from break junction simulations. The enhanced mobility of metal atoms in structurally realistic junctions results in significant changes to the magnitude and origin of the conductance fluctuations. Fluctuations are larger by a factor of 2-3 in realistic junctions compared to ideal junctions. Moreover, in junctions with highly deformed electrodes, the conductance fluctuations arise primarily from changes in the Au geometry, in contrast to results for junctions with non-deformed electrodes, where the conductance fluctuations are dominated by changes in the molecule geometry. These results provide important guidance to experimentalists developing strategies to control molecular conductance for device applications, and also to theoreticians invoking simplified structural models of junctions to predict their behavior., Comment: 15 pages, 4 figures, to appear in Journal of Physical Chemistry Letters

Using an updated simulation tool, we examine molecular junctions comprised of benzene-1,4-dithiolate bonded between gold nanotips, focusing on the importance of environmental factors and inter-electrode distance on the formation and structure of bridged molecules. We investigate the complex relationship between monolayer density and tip separation, finding that the formation of multi-molecule junctions is favored at low monolayer density, while single-molecule junctions are favored at high density. We demonstrate that tip geometry and monolayer interactions, two factors that are often neglected in simulation, affect the bonding geometry and tilt angle of bridged molecules. We further show that the structures of bridged molecules at 298 and 77 K are similar., Comment: To appear in ACS Nano, 30 pages, 5 figures

We report comprehensive high-accuracy molecular dynamics simulations using the ReaxFF forcefield to explore the structural changes that occur as Au nanowires are elongated, establishing trends as a function of both temperature and nanowire diameter. Our simulations and subsequent quantitative structural analysis reveal that polytetrahedral structures (e.g., icosahedra) form within the "amorphous" neck regions, most prominently for systems with small diameter at high temperature. We demonstrate that the formation of polytetrahedra diminishes the conductance quantization as compared to systems without this structural motif. We demonstrate that use of the ReaxFF forcefield, fitted to high-accuracy first principles calculations of Au, combines the accuracy of quantum calculations with the speed of semi-empirical methods., Comment: 26 pages (double spaced), 5 figures

Using molecular dynamics simulations, we study the impact of physisorbing adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs) undergoing elongation. We used various adsorbate models in our simulations, with each model giving rise to a different surface coverage and mobility of the adsorbed phase. We find that the local structure and mobility of the adsorbed phase remains relatively uniform across all segments of an elongating AuNW, except for the thinning region of the wire where the high mobility of Au atoms disrupts the monolayer structure, giving rise to higher solvent mobility. We analyzed the AuNW trajectories by measuring the ductile elongation of the wires and detecting the presence of characteristic structural motifs that appeared during elongation. Our findings indicate that adsorbates facilitate the formation of high-energy structural motifs and lead to significantly higher ductile elongations. In particular, our simulations result in a large number of monatomic chains and helical structures possessing mechanical stability in excess of what we observe in vacuum. Conversely, we find that a molecular species that interacts weakly (i.e., does not adsorb) with AuNWs worsens the mechanical stability of monatomic chains., Comment: To appear in Journal of Physical Chemistry C