Orientation dependent molecular friction on organic layer compound crystals

High resolution friction force maps of the benzylammonium terminated crystalline surface of a layer compound are presented. The lateral force map acquired with an atomic force microscope, reveals a significant contrast between different molecular orientations yielding molecular rows which differ from their neighboring ones. The single crystals are formed by stacks of copper oxalate sheets sandwiched between stereoregular organic cations, resulting in highly organized surface structures. Single molecular defects are observed at small loads. The experimental results are compared with numerical calculations which indicate a transition from an unperturbed state at small loads to a distorted state at higher loads. (C) 2011 American Institute of Physics.

High-resolution imaging of 2D outer membrane protein F (OmpF) crystals by atomic force microscopy

In this chapter the methodological bases are provided to achieve subnanometer resolution on two-dimensional (2D) membrane protein crystals by atomic force microscopy (AFM). This is outlined in detail with the example of AFM studies of the outer membrane protein F (OmpF) from the bacterium Escherichia coli (E. coli). We describe in detail the high-resolution imaging of 2D OmpF crystals in aqueous solution and under near-physiological conditions. The topographs of OmpF, and stylus effects and artifacts encountered when imaging by AFM are discussed.

Determining gypsum growth temperatures using monophase fluid inclusions-Application to the giant gypsum crystals of Naica, Mexico

Determining the formation temperature of minerals using fluid inclusions is a crucial step in understanding rock-forming scenarios. Unfortunately, fluid inclusions in minerals formed at low temperature, such as gypsum, are commonly in a metastable monophase liquid state. To overcome this problem, ultra-short laser pulses can be used to induce vapor bubble nucleation, thus creating a stable two-phase fluid inclusion appropriate for subsequent measurements of the liquid-vapor homogenization temperature, T-h. In this study we evaluate the applicability of T-h data to accurately determine gypsum formation temperatures. We used fluid inclusions in synthetic gypsum crystals grown in the laboratory at different temperatures between 40 degrees C and 80 degrees C under atmospheric pressure conditions. We found an asymmetric distribution of the T-h values, which are systematically lower than the actual crystal growth temperatures, T-g; this is due to (1) the effect of surface tension on liquid-vapor homogenization, and (2) plastic deformation of the inclusion walls due to internal tensile stress occurring in the metastable state of the inclusions. Based on this understanding, we have determined growth temperatures of natural giant gypsum crystals from Naica (Mexico), yielding 47 +/- 1.5 degrees C for crystals grown in the Cave of Swords (120 m below surface) and 54.5 +/- 2 degrees C for giant crystals grown in the Cave of Crystals (290 m below surface). These results support the earlier hypothesis that the population and the size of the Naica crystals were controlled by temperature. In addition, this experimental method opens a door to determining the growth temperature of minerals forming in low-temperature environments.

Molecular and ionic sublimation of erbium tribromide

The molecular and ionic composition of vapor over erbium tribromide sublimed from the Knudsen effusion cell and the open surface of a single crystal was studied by high-temperature mass spectrometry. The partial pressures of ErBr3 and Er2Br6 molecules in saturated vapor and the ratio between their sublimation coefficients under free vaporization conditions were determined. The enthalpies and activation energies of sublimation of ErBr3 crystals in the form of monomers and dimers were calculated. The emission of and Er2 was recorded in studies of ionic sublimation in both modes. The enthalpies of formation of gas molecules and ions were determined.

A stochastic principle behind polar properties of condensed molecular matter

A statistical mechanics view leads to the conclusion that polar molecules allowed to populate a degree of freedom for orientational disorder in a condensed phase thermalize into a bi-polar state featuring zero net polarity. In cases of orientational disorder polar order of condensed molecular matter can only exist in corresponding sectors of opposite average polarities. Channel type inclusion compounds, single component molecular crystals, solid solutions, optically anomalous crystals, inorganic ionic crystals, biomimetic crystals and biological tissues investigated by scanning pyroelectric and phase sensitive second harmonic generation microscopy all showed domains of opposite polarities in their final grown state. For reported polar molecular crystal structures it is assumed that kinetic hindrance along one direction of the polar axis is preventing the formation of a bi-polar state, thus allowing for a kinetically controlled mono-domain state. In this review we summarize theoretical and experimental findings leading to far reaching conclusions on the polar state of solid molecular matter. “… no stationary state … of a system has an electrical dipole moment.” P. W. Anderson, Science, 1972, 177, 393.

Symmetry and the polar state of condensed molecular matter

Polar molecular crystals seem to contradict a quantum mechanical statement, according to which no stationary state of a system features a permanent electrical polarization. By stationary we understand here an ensemble for which thermal averaging applies. In the language of statistical mechanics we have thus to ask for the thermal expectation value of the polarization in molecular crystals. Nucleation aggregates and growing crystal surfaces can provide a single degree of freedom for polar molecules required to average the polarization. By means of group theoretical reasoning and Monte Carlo simulations we show that such systems thermalize into a bi-polar state featuring zero bulk polarity. A two domain, i.e. bipolar state is obtained because boundaries are setting up opposing effective electrical fields. Described phenomena can be understood as a process of partial ergodicity-restoring. Experimentally, a bi-polar state of molecular crystals was demonstrated using phase sensitive second harmonic generation and scanning pyroelectric microscopy

Calculation of crystal optical properties from molecular electron density

We have recently developed a method to obtain distributed atomic polarizabilities adopting a partitioning of the molecular electron density (for example, the Quantum Theory of Atoms in Molecules, [1]), calculated with or without an applied electric field. The procedure [2] allows to obtained atomic polarizability tensors, which are perfectly exportable, because quite representative of an atom in a given functional group. Among the many applications of this idea, the calculation of crystal susceptibility is easily available, either from a rough estimation (the polarizability of the isolated molecule is used) or from a more precise estimation (the polarizability of a molecule embedded in a cluster representing the first coordination sphere is used). Lorentz factor is applied to include the long range effect of packing, which is enhancing the molecular polarizability. Simple properties like linear refractive index or the gyration tensor can be calculated at relatively low costs and with good precision. This approach is particularly useful within the field of crystal engineering of organic/organometallic materials, because it would allow a relatively easy prediction of a property as a function of the packing, thus allowing "reverse crystal engineering". Examples of some amino acid crystals and salts of amino acids [3] will be illustrated, together with other crystallographic or non-crystallographic applications. For example, the induction and dispersion energies of intermolecular interactions could be calculated with superior precision (allowing anisotropic van der Waals interactions). This could allow revision of some commonly misunderstood intermolecular interactions, like the halogen bonding (see for example the recent remarks by Stone or Gilli [4]). Moreover, the chemical reactivity of coordination complexes could be reinvestigated, by coupling the conventional analysis of the electrostatic potential (useful only in the circumstances of hard nucleophilic/electrophilic interaction) with the distributed atomic polarizability. The enhanced reactivity of coordinated organic ligands would be better appreciated. [1] R. F. W. Bader, Atoms in Molecules: A Quantum Theory. Oxford Univ. Press, 1990. [2] A. Krawczuk-Pantula, D. Pérez, K. Stadnicka, P. Macchi, Trans. Amer. Cryst. Ass. 2011, 1-25 [3] A. S. Chimpri1, M. Gryl, L. H.R. Dos Santos1, A. Krawczuk, P. Macchi Crystal Growth & Design, in the press. [4] a) A. J. Stone, J. Am. Chem. Soc. 2013, 135, 7005−7009; b) V. Bertolasi, P. Gilli, G. Gilli Crystal Growth & Design, 2013, 12, 4758-4770.

Direct observation of liquid crystals using cryo-TEM: Specimen preparation and low-dose imaging

Liquid crystals (LCs) represent a challenging group of materials for direct transmission electron microscopy (TEM) studies due to the complications in specimen preparation and the severe radiation damage. In this paper, we summarize a series of specimen preparation methods, including thin film and cryo-sectioning approaches, as a comprehensive toolset enabling high-resolution direct cryo-TEM observation of a broad range of LCs. We also present comparative analysis using cryo-TEM and replica freeze-fracture TEM on both thermotropic and lyotropic LCs. In addition to the revisits of previous practices, some new concepts are introduced, e.g., suspended thermotropic LC thin films, combined high-pressure freezing and cryo-sectioning of lyotropic LCs, and the complementary applications of direct TEM and indirect replica TEM techniques. The significance of subnanometer resolution cryo-TEM observation is demonstrated in a few important issues in LC studies, including providing direct evidences for the existence of nanoscale smectic domains in nematic bent-core thermotropic LCs, comprehensive understanding of the twist-bend nematic phase, and probing the packing of columnar aggregates in lyotropic chromonic LCs. Direct TEM observation opens ways to a variety of TEM techniques, suggesting that TEM (replica, cryo, and in situ techniques), in general, may be a promising part of the solution to the lack of effective structural probe at the molecular scale in LC studies. Microsc. Res. Tech. 77:754-772, 2014. © 2014 Wiley Periodicals, Inc.