Submolecular Units Research Articles

Configuration entropy and potential energy landscape in thermodynamics and dynamics of supercooled liquids

In thermodynamics of supercooled liquids, sub-molecular units, referred to as “beads,” are used. It has been reported that all thermodynamic functions as well as the parameters in the empirical distribution functions of the potential energy landscape approach appear to be explicit functions of the number of beads in molecules. This finding opens the possibility of measuring the number of beads from each of these functions and estimating the configuration and vibration components in their formation. An enthalpy factor has been introduced and found that within the temperature domain of the invariable enthalpy factor, the molecules partition to a constant number of beads. A correlation has been observed between temperature dependence of the potential barriers, restricting cooperative rearrangement of beads and heat capacity of liquids. Relations connecting the landscape approach with the number of beads in the molecules have been estimated. The molecular equation for configuration entropy obtained can provide guidance for the development of new materials with a desirable configuration entropy. A method for predicting thermodynamic and statistical quantities of supercooled liquids from kinetics is also suggested.

Thermodynamic Functions and Molecular Structure of Glass-forming Liquid

In cooperative molecular dynamics, the molecules of the glass-forming liquids are partitioned to sub-molecular units named “beads”. The beads have been empirically defined. Recently, a method for measuring the beads has been suggested. In this method the difference between entropy of the liquid and the crystal, known as excess entropy, has been used. Here, it is found that all other thermodynamic quantities are functions of the number of beads in the molecules, and their number can be measured from each of them. A subject of special interest is to measure the number of beads from the difference in the heat capacity between the liquid and the crystal, and the liquid and the glass as the configuration and the vibrational components in the number of the beads, can be separated. In Adam–Gibbs, post Adam–Gibbs theories as well as the potential energy landscape paradigm the thermodynamic nature of the dynamical phenomena is being studied. From the obtained equations, transition in the opposite direction became possible, namely the thermodynamic functions can be estimated from the dynamic experiments, if the number of the beads in the molecules are known. The theory is examined from the experimental results of 3-bromopentane.

Electronic and molecular structures of organic dye/TiO2 interfaces for solar cell applications: a core level photoelectron spectroscopy study

The electronic and molecular properties of three organic dye molecules with the general structure donor-linker-anchor have been investigated using core level photoelectron spectroscopy (PES). The molecules contain a diphenylaniline donor unit, a thiophene linker unit, and cyanoacrylic acid or rhodanine-3-acetic acid anchor units. They have been investigated both in the form of a multilayer and adsorbed onto nanoporous TiO(2) and the experimental results were also compared with DFT calculations. The changes at the dye-sensitized TiO(2) surface due to the modification of either the donor unit or the anchor unit was investigated and the results showed important differences in coverage as well as in electronic and molecular surface properties. By measuring the core level binding energies, the sub-molecular properties were characterized and the result showed that the adsorption to the TiO(2) influences the energy levels of the sub-molecular units differently.

Molecular theory of dendritic liquid crystals: self-organisation and phase transitions

We present tractable molecular theory descriptions of liquid crystalline dendrimers based on clearly defined approximations and in terms of the dominant interactions underlying the self-organisation of these large and complex supermolecular entities. We formulate the configurational partition function for dendrimers, taking explicit account of their conformations and segmental interactions. Two approximate schemes are presented: the first is based on the effective interactions of the dendrimers as a whole while the second scheme is based on the interactions among the mesogenic units contained in the dendrimers. Results of lattice calculations for phase transitions in the context of the first scheme are presented and they show that the minimal inclusion of shape anisotropy and of sub-molecular partitioning into chemically distinct parts is sufficient to reproduce the variety of phases and phase sequences observed experimentally and provides insights into the conformational aspect of these transitions. In the second scheme, the description of the dendromesogenic system reduces to that of an ensemble of mesogenic dimers. This scheme can be readily extended to the description liquid crystalline oligomers and polymers consisting of mesogenic units connected by flexible spacers in various architectures. It thus provides a unified approach for treating mesomorphic phase transitions of supermolecular and macromolecular systems that can be built by connecting the same submolecular units in topologically different ways.

Swift heavy ion induced modification of C60 thin films

Modification of thin film samples of C60 on Si and quartz substrates, induced by irradiation of 110 MeV Ni ions at various fluences, was studied. The pristine and irradiated samples were investigated using Raman spectroscopy, electrical conductivity, and optical absorption spectroscopy. The Raman data and band gap measurements indicate that swift ions at low fluences result in aggregate formations involving multiple molecular units such as dimers or polymers. High fluence irradiation results in submolecular formations and amorphous semiconducting carbon, indicating overall damage (fragmentation) of the fullerene molecules. These submolecular units in the amorphous carbon network have been identified as nanocrystalline graphite.

Irradiation of swift heavy ions on thin films of C 60—a comparative study

Thin films of C 60 were irradiated with swift heavy ions of Au (100 MeV) , Ni (110 MeV) and O (70 MeV) to study the irradiation effects. Films of C 60 with thickness ∼230 nm were deposited on quartz and float glass substrates. The samples irradiated by different fluences of ions were studied using optical absorption spectroscopy, in situ conductivity measurements and Raman spectroscopy. Obtained data indicate that swift ions at low fluences result in multiple molecular units like dimer or polymer. High fluence irradiation result in sub-molecular formations in amorphous semiconducting carbon network, indicating overall damage of the fullerene molecules. These sub-molecular units have been identified as nanocrystalline graphite. Observations with optical absorption spectroscopy of decrease in bandgap with increase in fluence, and with in situ resistivity measurements, are in conformity with understanding of structural changes from Raman spectroscopy. A comparison of changes produced by irradiation of these ions which have different electronic energy loss ( S e) values, is presented.

The effect of mechanical interlocking on crystal packing: predictions and testing.

The first statistical analyses of the X-ray crystal structures of mechanically interlocked molecular architectures, the first molecular mechanics-based solid-state calculations on such structures and atomic force microscopy (AFM) experiments are used in combination to predict and test which types of benzylic amide macrocycle-containing rotaxanes possess mobile components in the crystalline phase and thus could form the basis of solid-state devices that function through mechanical motion at the molecular level. The statistical studies and calculations show that crystals formed by rotaxanes possess similarities and unanticipated differences with respect to the crystal packing of noninterlocked molecules. Trends in the rotaxane series correlate quantities related to crystal packing, molecular size, stoichiometry, and H-bonding. In accordance with the findings of Gavezzotti et al. for conventional molecular architectures, a principal component analysis (PCA) showed that three vectors related to the size, packing parameters, and stoichiometry are sufficient to describe the crystal properties of benzylic amide macrocycle-containing rotaxanes. When hydrogen bond-related quantities are included in a second PCA, they combine with the size and the stoichiometry vectors but not with packing-related parameters, indicating that the intramolecular "saturation" of the H-bonds (between the interlocked components) takes precedence over crystal assembly (i.e., intermolecular packing) in these systems. However, cluster analyses also suggest a major role for the energy of interaction between the macrocycle and its crystal environment. The identification of such a "privileged" interaction is of fundamental importance to the development of rotaxanes with in-crystal mobility of one or more of their interlocked components, a prerequisite for the exploitation of molecular level mechanical motion in the solid state. The set of trends found, together with the calculated energies, was used to propose guidelines for which benzylic amide macrocycle-containing rotaxanes are best suited to become building blocks for systems with mobile submolecular units in the crystalline phase. An experimental test of the predictive power of such guidelines was carried out using AFM on a rotaxane and its thread, identified by the study as a promising candidate for solid-state mobility. Intuitively, the rotaxane should be less mobile in the solid state since it has multiple sets of both hydrogen bond donors and acceptors that can form strong inter- and intramolecular H-bonds. Conversely, the thread has no hydrogen bond donors and cannot form such bonds. The AFM experiments, however, confirm the statistical analysis prediction that the rotaxane is considerably more mobile in the solid than the thread.

Shape Parameters and Uniaxial Deformability of Mesogenic Dimers with Flexible Spacers

We introduce a set of statistical shape parameters that quantify the concept of the “average shape” of flexible molecules in isotropic and in nematic media. These shape parameters are obtained as conformational averages of geometrical tensors constructed from the relative positions and orientations of the sub-molecular units. The deformability of the average molecular shape is quantified in terms of the variation of the respective shape parameters under the action of an ordering field. The quantification of shape and deformability is applied to the description of dimers consisting of two rod-like mesogenic units connected by an alkyl spacer.

A nucleosome model for the simulation of DNA strand break experiments.

Using a set of Monte Carlo simulation models, track structures of 125I Auger electrons generated in liquid water are superimposed on a nucleosome DNA model able to precisely localize energy deposition events on sub-molecular units of the DNA strands. After scoring direct hits taking place during the physical phase (at about 10(-15) s) the radiation chemistry of the whole system is simulated between 10(-12) and 10(-8) s, taking into account all reactions between water radio-chemical species, radicals, sub-molecular units of DNA (Ribose, Adenine, Thymine, Guanine, and Cytosine), and scavengers like Tris or Formate ions. The model's possibility to distinguish between direct and indirect hits has been utilized to introduce different assumptions for strand break induction by both hit modes. The number of SSB and DSB as well as their local distribution will be given and compared with experimental and theoretical results from the literature.

Molecular Ordering in Nematics: The Modular Formulation of the Potential of Mean Torque

Abstract The general framework for the description of orientational ordering of (flexible) molecules in the nematic phase in terms of ordering properties of submolecular units in a modular fashion is presented. Various choices of the elementary submolecular units (segments) leading to different representations of the potential of mean torque are discussed. Transformations among such representations are studied in order to clarify the physical significance of intersegmental correlation terms. It is shown that for n-alkane solutes and chains pendant to nematogenic cores in neat materials, the uncorrelated bond representation (each C‒C bond segment individually interacts with the nematic mean field) used in most of the previous studies of this type gives a poor description of chain ordering. The introduction of orientational correlations among bond segments (particularly nearest neighbor correlations) improves the quality of fits of the order parameter profiles and explains the difficiency of previous models...

Reaginic Antibody against Insulin: Demonstration of Antigenic Distinction between Native and Extracted Insulin

Abstract Reaginic antibody against insulin mediated a generalized systemic reaction. The antibody was demonstrated to be against the insulin molecule and not against contaminating non-insulin proteins. The reaginic antibody was consistent with localization in a γE type of immunoglobulin. Reactivity was directed against insulins of several species including human insulin. The antibody reacted with various submolecular units of insulin but not against isolated A- and B-chains. The presence of reactivity against human synthetic insulin and insulin prepared from recombination of polypeptide subunits demonstrated the related antigenicity of these molecules. The reaginic antibody reacted only against extracted insulin including autologous insulin and not against endogenous circulating insulin.

Viscosité superficielle et structure moléculaire des couches de protéines

For all the protein monolayers studied we are led to consider different domains inside which the mechanical properties of the film are different. Below a certain surface pressure p n the viscosity is newtonian and the films of protein behave like those of fatty substances. On the other hand, protein films form a gel by compression in the neighbourhood of a surface pressure p g well defined for each protein. Between the surface pressures p n and p g the viscosity of protein films is no longer newtonian. The knowledge of the dimensions and form of molecules allows us to calculate the viscosity coefficient of monolayers. If this calculation corresponding to one molecule is made, extremely high values are found, impossible to compare with the experimental values. We must therefore suppose that the unit of flow is much smaller than one molecule. The theory of Eyring and Moore relates the surface viscosity to the free energy of activation of viscous flow. This energy of activation is a very rapidly increasing function of the diameter of the elementary particles. For all the proteins studied the viscosity coefficient at the point of appearance of the non-newtonian viscosity is of the same order of magnitude; hence the submolecular units have dimension practically independent from the nature of the protein. The direct calculation of the energy of activation arising from the energy of interaction between the elementary functional groups allows us to determine the diameter of the units of flow. We find for the area of these elementary particles about 90 A° 2. We discuss the meaning of this result.