Molecular Dynamics simulation of organic materials: Structure, potentials and the MiCMoS computer platform

The science of organic crystals and materials has seen in a few decades a spectacular improvement from months to minutes for an X-ray structure determination and from single-point lattice energy...

Thermophysical and Transport Properties of the BaCl2-CsCl High Temperature Ionic Liquid Mixtures

High temperature ionic liquids (HTILs) densities and transport properties for mixtures BaCl2‑CsCl, x(BaCl2) = 0-1, have been studied as a function of composition and temperature. In terms of Arrhenius theory, the temperature correlation of all measured properties was made and discussed. Thermodynamic properties (isothermal compressibility, molecular volume, lattice energy, heat capacity, molar Gibbs energy, enthalpy and entropy) were derived for all the studied HTILs from experimental data. The viscosity isotherms show negative deviations from linearity, while conductivity isotherms have positive deviations which may be related to the formation of highly negative changed ion associated species. The evolution of the excess quantities: viscosity deviation (Δη), excess molar viscosity (ΔEη), excess molar conductivity (ΔEκ), show a very good parallelism. The linear behavior between conductivity and viscosity was determined using the fractional Walden rule and the average slope was found far from unity.

Molecular Recognition and Shape Studies of 3- and 4-Substituted Diarylamide Quasiracemates

Families of quasiracemic materials constructed from 3- and 4-substituted chiral diarylamide molecular frameworks were prepared, where the imposed functional group differences systematically varied from H to CF3–9 unique components for each isomeric framework. Cocrystallization from the melt via hot stage thermomicroscopy using all possible racemic and quasiracemic combinations probed the structural boundaries of quasiracemate formation. The crystal structures and lattice energies (differential scanning calorimetry and lattice energy calculations) for many of these systems showed that quasienantiomeric components organize with near inversion symmetry and lattice energetics closely resembling those found in the racemic counterparts. This study also compared the shape space of pairs of quasienantiomers using an in silico alignment-based method to approximate the differences in molecular shape and provide a diagnostic tool for quasiracemate prediction. Comparing these results to our recent report on related 2-substituted diarylamide quasiracemates shows that functional group position can have a marked effect on quasiracemic behavior and provide critical insight to a more complete shape space, essential for defining molecular recognition processes.

Cooperative electrolyte-PEG interactions drive the signal amplification in a solid-state nanopore

Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single molecule resolution. However, the analysis of several analytes like short nucleic acids or proteins with nanopores represents a sensitivity challenge, because their translocation lead to small signals difficult to distinguish from the noise. Here, we report a simple method to enhance the signal to noise ratio in nanopore experiments by a simple modification of the solution used in nanopore sensing. The addition of poly-ethylene glycol (PEG) and the careful selection of the supporting electrolyte leads to large signal enhancement. We observed that the translocation dynamics are in good agreement with an established method that uses the lattice energy of an electrolyte to approximate the affinity of an ion to PEG. We identified CsBr as the optimal supporting electrolyte to complement PEG to enable the analysis of dsDNA at 500 kHz bandwidth, and the detection of dsDNA as short as 75 bp.

Chemical Bonding 1: Basic Concepts

Chemical Bonding I: Basic Concepts examines general ideas of chemical bonding between atoms and ions and how this bonding affects the chemical properties of the elements. An overview of Lewis symbols, Lewis structures and the octet rule is presented including the role of valence electrons in ionic and covalent bonding. The energy changes that accompany ionic bond formation are also discussed with emphasis on lattice energy. The chapter covers guidelines and general procedures for writing Lewis structures or electron dot formulas for molecular compounds and polyatomic ions. The concepts and applications of resonance, formal charge and exceptions to the octet rules are presented, along with coverage of the relationship between bond polarity and electronegativity.

Pixel calculations using Orca or GAUSSIAN for electron density automated within the Oscail package

Many discussions of the intermolecular interactions in crystal structures concentrate almost exclusively on an analysis of hydrogen bonding. A simple analysis of atom–atom distances is all that is required to detect and analyse hydrogen bonding. However, for typical small-molecule organic crystal structures, hydrogen-bonding interactions are often responsible for less than 50% of the crystal lattice energy. It is more difficult to analyse intermolecular interactions based on van der Waals interactions. The Pixel program can calculate and partition intermolecular energies into Coulombic, polarization, dispersion and repulsion energies, and help put crystal structure discussions onto a rational basis. This Windows PC implementation of Pixel within the Oscail package requires minimal setup and can automatically use GAUSSIAN or Orca for the calculation of electron density.

Modified Born-Lande Equation to calculate Lattice Energy in a theoretical approach

Defects in ionic solid are very much common, which is increased with the rise in temperature. It causes the change in the value of many physical properties and varieties of physical parameters and the Lattice Energy is one such parameter to control the physical properties of the crystals. Considering the loss of ions from lattice points as random, the examination of each of the defects individually is going to be unpredictable, thus leading to almost nonattainment of the correct crystal structure with the theoretical calculations applying for available models. Here, in this present work, we have used some statistical methods and probabilistic approximation to introduce a novel idea of calculating the Madelung constant, and then Lattice Energy analytically. To make the understanding more lucid, we have taken one of the very common crystals, very popular in the crystallographic community, NaCl crystal having 6:6 co-ordination number, for which a significant number of Schottky defects are observed. During this study, we are bound to assume the random distribution of defects as Poisson distribution due to the fact that the number of defects is very less with respect to the total numbers of lattice points present in the crystal to calculate the Madelung Constant.

Structures of a Phosphoryl Derivative of 4-Allyl-2,4-dihydro-3H-1,2,4-triazole-3-thione: An Illustrative Example of Conformational Polymorphism

Two polymorphic forms of a conformationally flexible molecule, 5-[(Diphenylphosphoryl)methyl]-4-(prop-2-en-1-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione, were obtained by crystallization and characterized by X-ray diffraction analysis and differential scanning calorimetry. The relative stability of polymorphic forms was estimated with DFT calculations of crystal structures and isolated molecules. It turns out, that in the first more dense polymorph with higher cohesion energy and crystal lattice energy, the molecule adopts an energetically unfavorable conformation, and forms dimers with lower H-bond strength, as compared to the second polymorph. On the other hand, in the second polymorph, the molecule adopts almost the lowest-energy conformation and forms infinite chains via strong H-bonds. The first form that seems to be more thermodynamically stable at room temperature transforms into the second form via two endothermic phase transitions; the apparent irreversibility of the transition is due to high energy difference between the molecular conformations in crystals.