Design of experimental routes and data processing for the determination of the depth-distribution of energy in real solids

No adequate thermodynamic definition of non-equilibrated solids is available at present. In this paper a method is suggested for the energetic characterization of solids by estimation of the distribution of the differential molar internal energies — as they appear during the breakdown of sample e.g. by chemical reaction, i.e. the ‘depth distribution of differential energies’ (DDE) of samples. Thermodynamic considerations are presented for approximating this quantity — and experimental possibilities proposed to attain the needed input information by thermoanalytical methods. Application of the suggested procedure is supposed to contribute to the better understanding of structure — energy — reactivity relations in real solids.     

Entropy production as a universal functional of reaction rate: chemical networks close to steady states

Entropy production rate (EPR) is the fundamental theoretical quantity in non-equilibrium thermodynamics whereas reaction rate is the primary experimental quantity for a chemical system out-of-equilibrium. In this work, we explore a connection between the above two quantities for general reaction networks. Both cyclic and linear networks of arbitrary dimension are studied, along with a mixed variety. The systems can attain a non-equilibrium steady state (NESS) under chemiostatic condition, which becomes the state of true thermodynamic equilibrium when detailed balance holds. We show that there exists a universal functional relationship of the EPR with reaction rate close to steady states for all the networks considered. Near a NESS, the former varies linearly with the reaction rate. On the other hand, around a true equilibrium, it varies quadratically with the latter. Numerical experiments justify our analytical findings quite transparently.     

Concept system on ‘quantity’: formation and terminology

The third edition of the International Vocabulary of Metrology occasions continued useful discussion. A Commentator, in four recent papers, presents viewpoints on the generic division of ‘property’, ‘quantity’, and ‘ordinal quantity’, as well as a perceived problem of inheritance. Alternative terms for ‘kind-of-quantity’, ‘kind-of-quantity with chosen sort of component’, and ‘dedicated kind-of-quantity’ are suggested to be formed by prefacing “quantity” with the respective adjectival modifiers “generic”, “subgeneric”, and “specific”. Furthermore, a neoterm for ‘quantity expressed by a measurement unit’ and a redefinition of ‘property’ are offered. The Commentator’s proposals and arguments are discussed with emphasis on ways of constructing concept systems to ensure proper inheritance. Some formal and semantic problems of the proposed alternative terms and definitions are advanced. Terminological concepts are defined in an Appendix.     

Kinetic and thermodynamic considerations of the bracketing method: Entropy-driven proton-transfer reactions in a Fourier transform mass spectrometer

Several reports of experimentally derived proton affinity values and gas-phase basicity values for amino acids and peptides have recently appeared in the literature. Here, we show that the thermodynamic quantity that is measured by the Fourier transform mass spectrometry proton transfer bracketing of amino acids and peptides is gas-phase basicity and not proton affinity. Both experimental and theoretical evidence supports this conclusion. The difference between the values determined by proton transfer bracketing measurements for lysine versus leucine is consistent with a difference in gas-phase basicity rather than proton affinity. The rate of proton transfer from protonated lysine to a series of reference compounds have been measured. Entropy-driven, endothermic proton transfer is found to occur at the collision rate. Recent ab initio and semi-empirical calculations of the proton affinity of lysine are found to agree with the value that is derived from bracketing studies when one assumes that gas-phase basicity is measured. While entropy-driven reactions have been observed previously in high-pressure mass spectrometers, this is the first evidence for such reactions at low pressure in a Fourier transform mass spectrometer.     

Kinetics and mechanism of cyclodextrin inclusion complexation incorporating bidirectional inclusion and formation of orientational isomers

The kinetics of cyclodextrin (CD) inclusion complexation has been usually analyzed in terms of a one-step reaction or a consecutive two-step reaction involving intracomplex structural transformation as a second step. These schemes presume the inclusion of guest molecules through only one side of the CD cavity and the formation of unidirectional CD complexes. However, there has been increasing experimental evidence for the inclusion of guests through both sides of the CD cavity and the formation of orientational isomers for noncentrosymmetric guest molecules. This article presents a novel parallel reaction scheme for CD inclusion complexation, incorporating bidirectional inclusion and the formation of orientational isomers into the scheme. It is shown that the parallel reaction scheme gives the same concentration versus reaction time relationship as the consecutive two-step reaction scheme. The experimental methods for determining the microscopic directional rate constants are presented. The kinetic parameters of the two-step reaction scheme are expressed as functions of the directional rate constants. The ratios of orientational isomers of alpha-CD-based [2]-pseudorotaxanes and the microscopic directional rate constants of the threading and dethreading reactions are estimated from the reported thermodynamic and kinetics data obtained by using either the one-step or two-step reaction scheme. It is shown that the thermodynamic preference of an isomer over the other is mainly due to the slow dethreading rate of the isomer.     

反应速率和反应进度的辩证关系——以甲基丙烯酸甲酯自由基聚合为例

化学反应速率与化学反应进度是非常相似的概念和知识点,同时又密切相关.在宏观层面或者说表象层面上看,都描述了过程变化的程度,但二者确具有完全不同的性质,一个是动力学量、一个是热力学量;一个是微观性质、一个是宏观性质.通过甲基丙烯酸甲酯自由基聚合过程的分析,深入讨论和揭示反应速率与反应进度的内涵、意义,明确二者的辩证本质关...     

Quasi-binary picture of thermotropic liquid crystals and its application to cubic mesophases

A quasi-binary (QB) picture of thermotropic liquid crystals is proposed on the basis of thermodynamic observations. The experimental conformational entropy of long alkyl chains attached to a (semi)rigid core of mesogenic molecules indicates that the chain is highly disordered in liquid crystalline states. These disordered chains serve as ‘intramolecular solvent’ or ‘self-solvent’ judging from a close resemblance between phase diagrams of neat (against chain length) and binary (against composition) systems. The application of the QB picture to the classic examples of thermotropic cubic mesophases (in ANBC series) shows that the essential structural motif is triply periodic minimal surface.     

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

The influence of a xenobiotic compound on an organism is usually summarized by the expression biological activity. If a controlled, therapeutically relevant, and regulatory action is observed the compound has potential as a drug, otherwise its toxicity on the biological system is of interest. However, what do we understand by the biological activity? In principle, the overall effect on an organism has to be considered. However, because of the complexity of the interrelated processes involved, as a simplification primarily the "main action" on the organism is taken into consideration. On the molecular level, biological activity corresponds to the binding of a (low-molecular weight) compound to a macromolecular receptor, usually a protein. Enzymatic reactions or signal-transduction cascades are thereby influenced with respect to their function for the organism. We regard this binding as a process under equilibrium conditions; thus, binding can be described as an association or dissociation process. Accordingly, biological activity is expressed as the affinity of both partners for each other, as a thermodynamic equilibrium quantity. How well do we understand these terms and how well are they theoretically predictable today? The holy grail of rational drug design is the prediction of the biological activity of a compound. The processes involving ligand binding are extremely complicated, both ligand and protein are flexible molecules, and the energy inventory between the bound and unbound states must be considered in aqueous solution. How sophisticated and reliable are our experimental approaches to obtaining the necessary insight? The present review summarizes our current understanding of the binding affinity of a small-molecule ligand to a protein. Both theoretical and empirical approaches for predicting binding affinity, starting from the three-dimensional structure of a protein-ligand complex, will be described and compared. Experimental methods, primarily microcalorimetry, will be discussed. As a perspective, our own knowledge-based approach towards affinity prediction and experimental data on factorizing binding contributions to protein-ligand binding will be presented.     

A discussion about the significance of Absorbance and sample optical thickness in conventional absorption spectrometry and wavelength-modulated laser absorption spectrometry

One of the most frequently used concepts in atomic absorption spectrometry (AAS) is that of Absorbance, an easily measurable quantity that is linear with the concentration of the analyte over a large range of concentrations whenever Beer's law is valid. Laser-based modulation techniques, however, in particular wavelength modulated diode laser absorption spectrometry (WMAS), do not measure exactly the same physical quantities as conventional AAS techniques do, since they do not rely upon separate measurements of the intensities in the presence and in the absence of the sample, but rather (a certain fraction of) the difference between the signals ‘on’ and ‘off’ resonance. Hence, Absorbance is not as natural for the modulated laser-based absorption techniques as it is for the conventional AAS techniques. The entity called sample optical thickness (SOT) appears to be a natural entity as well as a natural unit (denoted SOT units) for the quantification of signals in WMAS. The present paper discusses the concept of measurable quantities and their units in WMAS in some detail and compares them (theoretical and practical considerations) with those of conventional AAS. In particular, it makes a distinction between the ‘observed’ sample optical thickness and the ‘true’ sample optical thickness and shows how these two entities are related to the Absorbance entity. Finally, this work also introduces a dimensionless sensitivity of the WMAS technique, and shows this quantity to be equal to the nth Fourier coefficient of the wavelength modulated, peak-normalized line shape function.     

Thermodynamic examination of pH measurements

The electrometric determination of pH is essentially an evaluation of the thermodynamic quantity -loga(H(3)O)(+) from a measurement of an electrical potential difference between two electrodes. It is accordingly necessary to examine the electrometric method in light of thermodynamic concepts in order to disclose the meaning of experimental pH values and their limitations. In this paper it is shown by thermodynamic considerations that the evaluation of -loga(H(3)O)(+) is actually a special case of the evaluation of the thermodynamic quantity The operational definition of pH prescribes a general method to evaluate this quantity, but not -loga(H(3)O(+)) as commonly believed.     

FAST AND SLOW PHASES OF LUMINESCENCE IN CHLORELLA

Abstract— The decay of luminescence of Chlorella in repetitive steady-state flashing light displays two categories of phase, broadly characterized as ‘fast’ and ‘slow’. They are strongly contrasted in amplitude and lifetime; the transition from fast to slow occurs a few milliseconds after the flash.

• 1 The slow phases observed in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) are clearly of the deactivation type. i.e. the luminescence intensity is quantitatively correlated with the rate of relaxation of the System II reaction center to its photoactive state. The significance of the deactivation type is a reverse flow of the light-produced ⊕ and ? charges through the luminescence-producing recombination path. This mechanism is probably not limited to the DCMU-poisoned systems. The light regime (flash duration, flashing period, induction effects) modifies specifically the amplitude of the slow phases; this effect is strikingly not dependent on the presence of DCMU. Although the light-driven pH gradient is the likely explanation, it is argued that its action bears more directly on the exciton and/or emission yield of luminescence rather than on the rate of recombination itself.
• 2 Most of the fast-phase components are ascribed under normal conditions to stabilization steps involving the donor side of the System II reaction centers. However, when the reaction center turnover is much reduced (DCMU) or completely abolished (DCMU + NH₂OH, after preillumination), a fast luminescence phase is still visible. This phase is barely affected by the light regime (notably the flash duration). It must be attributed to an anomalous residual photochemical turnover of the reaction centers. Another type of fast photochemical turnover has been characterized with NH₂OH-pretreated cells. A two-quantum functioning of some sort seems required to account for the anomalous photochemical turnover. The importance of the luminescence loss during the fast phases and its possible connection with the ‘misses’ of the O₂-evolving system are discussed.

     

The glass paradigm for colloidal glasses,gels, and other arrested states driven by attractive interactions

For some time, there has existed the idea that dense colloidal systems with repulsive interactions can be interpreted using certain approaches to glass theory. Recent advances in understanding the role of short-ranged attractive interactions in driving another type of ‘glass-transition’ have considerably extended the range of potential applications for such systems. Within this framework, particle gels are now regarded as ‘attractive’ glasses, and for some concentration regimes the details of the density correlation as we approach gellation for a broad range of experimental systems seem to be well described by glass-transition ideas and laws. Initial suggestions that this might be so came from theory, but the close collaboration between theory, simulation, and experimental science has been mutually stimulating. New advances in the theory are now to be expected, and novel systems where the ideas might be applicable are emerging. The exploration of these ideas is still at the beginning, but there is a reasonable expectation that the glass paradigm will be more generally useful in many areas of soft matter and colloid science, perhaps gathering apparently disparate phenomena of particle gellation, polymer gellation, aggregation, and other aspects of ‘solidification’ into a common interpretive scheme.     

Glycan Side Reaction May Compromise ETD-Based Glycopeptide Identification

Tris(hydroxymethyl)aminomethane (Tris) is one of the most frequently used buffer ingredients. Among other things, it is recommended and is usually used for lectin-based affinity enrichment of glycopeptides. Here we report that sialic acid, a common ‘capping’ unit in both N- and O-linked glycans may react with this chemical, and this side reaction may compromise glycopeptide identification when ETD spectra are the only MS/MS data used in the database search. We show that the modification may alter N- as well as O-linked glycans, the Tris-derivative is still prone to fragmentation both in ‘beam-type’ CID (HCD) and ETD experiments, at the same time—since the acidic carboxyl group was ‘neutralized’—it will display a different retention time than its unmodified counterpart. We also suggest solutions that—when incorporated into existing search engines—may significantly improve the reliability of glycopeptide assignments.

What is a ‘gel’?

Some of the existing definitions of the term ‘gel’ are discussed and shortcomings are identified. A purely phenomenological definition is proposed: a gel is a soft, solid or solid-like material consisting of two or more components one of which is a liquid, present in substantial quantity. ‘Solid-like gels’ are further defined in terms of the dynamic mechanical properties.     

Description of the system HCl/H2O with a ‘local composition’ equation for the activity coefficient and a suitable dissociation model

The establishment of a dissociation model makes the application of a ‘local composition’ equation to electrolyte solutions possible. The model states, that only water is in the immediate neighbourhood of ions. This is considered by establishing an equilibrium reaction for the formation of complexes, which consist of water and ions. Only similar species are in the solution if the ion and its ‘water cloud’ are conceived as one component in the mixture.     

Equilibrium surface properties of lipid mixtures of retinal,phosphatidylcholine and fatty acid derivatives at the air/water interface

The miscibilities of phosphatidylcholine, retinal and saturated fatty acid derivatives in surface phases at the air/water interface are investigated on the basis of the thermodynamic two-dimensional phase rule. The latter is applied to the ‘collapse’ pressure and the equilibrium surface pressure characteristics of binary lipid monolayers or spread amphiphilic mixtures, respectively. The equilibrium surface pressures (ESPs), at which insoluble lipid monolayers are in equilibrium with three-dimensional lipid phases, are determined by spreading of single-component or binary solutions of lipids in organic solvent up to supersaturation at the air/water interface. The kinetics of establishment of steady surface pressure values at supersaturation is followed depending on the nature of the lipid samples. ESPs and ‘collapse’ pressures of mixtures of dilaur-oylphosphatidylcholine (DLPC), all-trans retinal (t-R) and lauric acid (LA) are studied at various lipid molar ratios. The compositional phase diagrams of the ESPs and ‘collapse’ pressures, obtained at a constant temperature, indicate that the interfacial miscibilities of both DLPC and t-R and DLPC and LA are non-ideal. Owing to its ‘bulky’ molecular structure and the tendency towards self-aggregation, dominated by intermolecular π-π interactions, the t-R component could be accommodated in the hydrophobic portion of the phospholipid membrane at mole fractions less than 0.5. The accommodation of the other neutral, rod-like fatty acid component in the DLPC matrix is probably favoured by the formation of intermolecular hydrogen bonding. Phase separation between DLPC and LA is evident from the thermodynamic results at high LA mole fractions (> 0.75) in the surface mixtures.     

Thermodynamic properties and equilibrium constant of chemical reaction in nanosystem: An theoretical and experimental study

The theoretical relations of thermodynamic properties, the equilibrium constant and reactant size in nanosystem are described. The effects of size on thermodynamic properties and the equilibrium constant were studied using nanosize zinc oxide and sodium bisulfate solution as a reaction system. The experimental results indicated that the molar Gibbs free energy, the molar enthalpy and the molar entropy of the reaction decrease, but the equilibrium constant increases with decreasing reactant size. Linear trends were observed between the reciprocal of size for nano-reactant and thermodynamic variable, which are consistent with the theoretical relations.     

硅乙烯异构化反应的理论研究——从头算水平上的热力学、动力学分析

据报道,含硅碳双键的化合物已能制备,但它在通常条件下不稳定,易于发生加成、异构化反应,研究最多的两个异构化反应是:     

Symmetry-broken reactant motion upon phase-related symmetrically modulated excitations: application to highly selective molecular sorting

This paper introduces a separation protocol relying on affinity chromatography that exhibits unprecedented selectivities. We submit the mixture contained in the separative medium to the simultaneous action of two symmetrically modulated excitations. The first is a uniform periodic field (e.g., electric field) with zero mean value, whereas the second is the periodic modulation of a thermodynamic parameter such as the temperature. Under appropriate tuning of the modulations with the dynamics of the discriminating chemical reaction, we predict a symmetry breaking of molecular motion: the mixture components that are addressed by their rate constants exhibit an oriented motion for a particular phase relation between the modulations of the field and the thermodynamic parameter. The resulting velocity of the mixture components depends on the rate constants and on a conjugated thermodynamic value such as the standard enthalpy of the discrimination process in the case of a temperature modulation. In particular, it may be possible to separate mixture components with identical rate constants. We use the present approach to design a protocol to sort nucleic acids by their sequence.