Project description:Procedures for the purification and subsequent crystallization of the slightly soluble four-coordinate metallporphines, the simplest possible porphyrin derivatives, are described. Crystals of the porphine derivatives of cobalt(II), copper(II), platinum(II), and two polymorphs of zinc(II) were obtained. Analysis of the crystal and molecular structures shows that all except the platinum(II) derivative form an unusual trimeric species in the solid state. The isomorphous cobalt(II), copper(II), and one zinc(II) polymorph pack in the unit cell to form dimers as well as the trimers. Interplanar spacings between porphine rings are similar in both the dimers and trimers and range between 3.24 and 3.37 Å. Porphine rings are strongly overlapped with lateral shifts between ring centers in both the dimers and trimers with values between 1.52 and 1.70 Å or in Category S as originally defined by Scheidt and Lee. Periodic trends in the M-Np bond distances parallel those observed previously for tetraphenyl- and octaethylporphyrin derivatives.
Project description:Local Shannon entropy lies at the heart of modern thermodynamics, with much discussion of trajectory-dependent entropy production. When taken at both boundaries of a process in phase space, it reproduces the second law of thermodynamics over a finite time interval for small scale systems. However, given that entropy is an ensemble property, it has never been clear how one can assign such a quantity locally. Given such a fundamental omission in our knowledge, we construct a new ensemble composed of trajectories reaching an individual microstate, and show that locally defined entropy, information, and free energy are properties of the ensemble, or trajectory-independent true thermodynamic potentials. We find that the Boltzmann-Gibbs distribution and Landauer's principle can be generalized naturally as properties of the ensemble, and that trajectory-free state functions of the ensemble govern the exact mechanism of non-equilibrium relaxation.
Project description:Anatase TiO2 is a promising anode material for sodium-ion batteries (SIBs). However, its sodium storage mechanisms in terms of crystal structure transformation during sodiation/de-sodiation processes are far from clear. Here, by analyzing the redox thermodynamics and kinetics under near-equilibrium states, we observe, for the first time, that upon Na-ion uptake, the anatase TiO2 undergoes a phase transition and then an irreversible crystal structure disintegration. Additionally, unlike previous theoretical studies which investigate only the two end points of the sodiation process (i.e., TiO2 and NaTiO2), we study the progressive crystal structure changes of anatase TiO2 upon step-by-step Na-ion uptake (Na x TiO2, x = 0.0625, 0.125, 0.25, 0.5, 0.75, and 1) for the first time. It is found that the anatase TiO2 goes through a thermodynamically unstable intermediate phase (Na0.25TiO2) before reaching crystalline NaTiO2, confirming the inevitable crystal structure disintegration during sodiation. These combined experimental and theoretical studies provide new insights into the sodium storage mechanisms of TiO2 and are expected to provide useful information for further improving the performance of TiO2-based anodes for SIB applications.
Project description:We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys. 2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide.
Project description:Many doubly charged heteronuclear dimers are metastable or even thermodynamically stable with respect to charge separation. Homonuclear dicationic dimers, however, are more difficult to form. He22+ was the first noble gas dimer predicted to be metastable and, decades later, observed. Ne22+ is the only other dicationic noble gas dimer that has been detected so far. Here, we present a novel approach to form fragile dicationic species, by post-ionization of singly charged ions that are embedded in helium nanodroplets (HNDs). Bare ions are then extracted by colliding the HNDs with helium gas. We detect homonuclear doubly charged dimers and trimers of krypton and xenon, but not argon. Our multi-reference ab initio calculations confirm the stability of Kr22+, Kr32+, Xe22+, Xe32+, and Ar22+, but put the stability of Ar32+ towards dissociation to Ar+ + Ar2+ into question.
Project description:This work examines, first, the non-equilibrium character of the glassy state of polymer systems and its significance in the development of novel materials for important technological applications. Subsequently, it summarizes the essentials of the generalized lattice fluid approach for the description of this highly complex non-equilibrium behavior with an approximate and simple, yet analytically powerful formalism. The working equations are derived in a straightforward and consistent manner by clearly defining the universal and specific variables needed to describe the discussed properties. The role of the non-random distribution of molecular species and free volume in the glassy system is also examined, as is the role of strong specific interactions, such as hydrogen-bonding networks. This work also reports examples of applications in a variety of representative systems, including glass densification, retrograde vitrification, increase in glass-transition temperature in hydrogen-bonded polymer mixtures, and hysteresis phenomena in sorption-desorption from glassy polymer matrices.
Project description:The template-directed formation of phosphodiester bonds between two nucleic acid components is a pivotal process in biology. To induce such a reaction in the absence of enzymes is a challenge. This challenge has been met for the extension of a primer with mononucleotides, but the ligation of short oligonucleotides (dimers or trimers) has proven difficult. Here we report a method for ligating dimers and trimers of ribonucleotides using in situ activation in aqueous buffer. All 16 different dimers and two trimers were tested. Binding studies by NMR showed low millimolar dissociation constants for complexes between representative dimers and hairpins mimicking primer-template duplexes, confirming that a weak template effect is not the cause of the poor ligating properties of these short oligomers. Rather, cyclization was found to compete with ligation, with up to 90% of dimer being converted to the cyclic form during the course of an assay. This side reaction is strongly sequence dependent and more pronounced for dimers than for trimers. Under optimized reaction conditions, high yields were observed with strongly pairing purines at the 3'-terminus. These results show that short oligomers of ribonucleotides are competent reactants in enzyme-free copying.
Project description:Flavonoids are a large family of compounds associated with a broad range of biologically useful properties. In recent years, synthetic compounds that contain two flavonoid units linked together have attracted attention in drug discovery and development projects. Numerous flavonoid dimer systems, incorporating a range of monomers attached via different linkers, have been reported to exhibit interesting bioactivities. From a medicinal chemistry perspective, the 1,2,3-triazole ring system has been identified as a particularly attractive linker moiety in dimeric derivatives (owing to several favourable attributes including proven biological relevance and metabolic stability) and triazole-bridged flavonoid dimers possessing anticancer and antimalarial activities have recently been reported. However, there are relatively few examples of libraries of triazole-bridged flavonoid dimers and the diversity of flavonoid subunits present within these is typically limited. Thus, this compound type arguably remains underexplored within drug discovery. Herein, we report a modular strategy for the synthesis of novel and biologically interesting triazole-bridged flavonoid heterodimers and also very rare heterotrimers from readily available starting materials. Application of this strategy has enabled step-efficient and systematic access to a library of structurally diverse compounds of this sort, with a variety of monomer units belonging to six different structural subclasses of flavonoid successfully incorporated.
Project description:Temperature-programmed desorption (TPD) experiments in surface science are usually analyzed using the Polanyi-Wigner equation and/or transition-state theory. These methods are far from straightforward, and the determination of the pre-exponential factor is often problematic. We present a different method based on equilibrium thermodynamics, which builds on an approach previously used for TPD by Kreuzer et al. (Surf. Sci. 1988). Equations for the desorption rate are presented for three different types of surface-adsorbate interactions: (i) a 2D ideal hard-sphere gas with a negligible diffusion barrier, (ii) an ideal lattice gas, that is, fixed adsorption sites without interaction between the adsorbates, and (iii) a lattice gas with a distribution of (site-dependent) adsorption energies. We show that the coverage dependence of the sticking coefficient for adsorption at the desorption temperature determines whether the desorption process can be described by first- or second-order kinetics. The sticking coefficient at the desorption temperature must also be known for a quantitative determination of the adsorption energy, but it has a rather weak influence (like the pre-exponential factor in a traditional TPD analysis). Quantitative analysis is also influenced by the vibrational contributions to the energy and entropy. For the case of a single adsorption energy, we provide equations to directly convert peak temperatures into adsorption energies. These equations also provide an approximation of the desorption energy in cases that cannot be described by a fixed pre-exponential factor. For the case of a distribution of adsorption energies, the desorption spectra cannot be considered a superposition of desorption spectra corresponding to the different energies. Nevertheless, we present a method to extract the distribution of adsorption energies from TPD spectra, and we rationalize the energy resolution of TPD experiments. The analytical results are complemented by a program for simulation and analysis of TPD data.
Project description:Bacterial chemoreceptors provide an important model for understanding signalling processes. In the serine receptor Tsr from E. coli, a binding event in the periplasmic domain of the receptor dimer causes a shift in a single transmembrane helix of roughly 0.15 nm towards the cytoplasm. This small change is propagated through the ≈ 22 nm length of the receptor, causing downstream inhibition of the kinase CheA. This requires interactions within a trimer of receptor dimers. Additionally, the signal is amplified across a 53,000 nm(2) array of chemoreceptor proteins, including ≈ 5,200 receptor trimers-of-dimers, at the cell pole. Despite a wealth of experimental data on the system, including high resolution structures of individual domains and extensive mutagenesis data, it remains uncertain how information is communicated across the receptor from the binding event to the downstream effectors. We present a molecular model of the entire Tsr dimer, and examine its behaviour using coarse-grained molecular dynamics and elastic network modelling. We observe a large bending in dimer models between the linker domain HAMP and coiled-coil domains, which is supported by experimental data. Models of the trimer of dimers, built from the dimer models, are more constrained and likely represent the signalling state. Simulations of the models in a 70 nm diameter vesicle with a biologically realistic lipid mixture reveal specific lipid interactions and oligomerisation of the trimer of dimers. The results indicate a mechanism whereby small motions of a single helix can be amplified through HAMP domain packing, to initiate large changes in the whole receptor structure.