Some remarks to the derivation of the “generalized Lippmann equation”

In the present communication, an attempt is made to demonstrate (once again) some of the problems with the derivation of the “generalized Lippmann equation” considered to be valid by many researchers for solid electrodes and to address the problems in the framework of the Gibbs model of the interface by using only the basic principles of thermodynamics. By surveying the relevant literature, it has been shown that during the derivation of the equation, it was completely ignored that the Gibbs-Duhem equation (i.e., the electrocapillary equation) is a mathematical consequence which follows directly from the homogeneous degree one property of the corresponding thermodynamic potential function; consequently, the resulting expression cannot be correct. Some alternative approaches have also been considered. The adequacy of the open system and the partly closed system approach has been critically discussed, together with the possibility of introducing new thermodynamic potential functions.

     

“Demonstration” vs. “designation” of measurement competence: the need to link accreditation to metrology

Formal acceptance of the results of chemical laboratories is increasingly organized through a) accreditation of measuring laboratories nationally and b) mutual recognition of accreditation internationally (through formal Multilateral Recognition Agreements, MRAs). However, real comparability of results of measurements is realized by using common (internationally agreed) measurement scales which make these results traceable to this scale, i.e. “traceable” to the same (internationally agreed) value of the unit of that scale. In addition, the criterion against which the evaluation is done, should be “external” to the measurement laboratories which are being evaluated. This is realized in IRMM’s International Measurement Evaluation Programme (IMEP) where evaluation is performed against values which are anchored using “metrology”, the science of measurement with its own rules, which offers a sound foundation for measurement in all scientific disciplines. It is argued in this paper that the demonstration of measurement capability against values on such scales provides a result-oriented rather than a procedure-oriented evaluation. Thus, competence can be “demonstrated” rather than just “designated” and this can be shown to both customers and regulators. It inspires more confidence.     

“Comment” on the Reply to the Paper “On the Elber–Karplus Reaction Path-Following Method and Related Procedures”

The flaws in the Reply [1] to our paper [2] have been pointed out. Elber and Karplus (EK) have not disproved our irrefutable global statement that the energy average cannot be minimized which rebuts the theoretical background of EK-type calculations. Another statement of ours has shown that even a curve for which the average energy is locally minimal for all directional perturbations in the sense of classical variational calculus cannot be identical with the reaction path (RP) defined as a steepest descent path (SDP). EK found an error in the early preprint of our theoretical paper [3] and because of this error they qualified our correct variational statement as false for all the SDPs consisting of a straight line each. Mixing global and variational arguments, EK refuted our criticism in a logically incorrect manner. In this Comment we prove that both of our earlier statements invariably remain in force and the criticism included in those has been as well-established and solid as was before.     

“In silico” study of the binding of two novel antagonists to the nociceptin receptor

Antagonists of the nociceptin receptor (NOP) are raising interest for their possible clinical use as antidepressant drugs. Recently, the structure of NOP in complex with some piperidine-based antagonists has been revealed by X-ray crystallography. In this study, a multi-flexible docking (MF-docking) procedure, i.e. docking to multiple receptor conformations extracted by preliminary molecular dynamics trajectories, together with hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have been carried out to provide the binding mode of two novel NOP antagonists, one of them selective (BTRX-246040, formerly named LY-2940094) and one non selective (AT-076), i.e. able to inactivate NOP as well as the classical µ- k- and δ-opioid receptors (MOP KOP and DOP). According to our results, the pivotal role of residue D130^3,32 (upper indexes are Ballesteros–Weinstein notations) is analogous to that enlighten by the already known X-ray structures of opioid receptors: binding of the molecules are predicted to require a slight readjustment of the hydrophobic pocket (residues Y131^3,33, M134^3,36, I219^5,43, Q280^6,52 and V283^6,55) in the orthosteric site of NOP, accommodating either the pyridine–pyrazole (BTRX-246040) or the isoquinoline (AT-076) moiety of the ligand, in turn allowing the protonated piperidine nitrogen to maximize interaction (salt-bridge) with residue D130^3,32 of the NOP, and the aromatic head to be sandwiched in optimal π-stacking between Y131^3,33 and M134^3,36. The QM/MM optimization after the MF-docking procedure has provided the more likely conformations for the binding to the NOP receptor of BTRX-246040 and AT-076, based on different pharmacophores and exhibiting different selectivity profiles. While the high selectivity for NOP of BTRX-246040 can be explained by interactions with NOP specific residues, the lack of selectivity of AT-076 could be associated to its ability to penetrate into the deep hydrophobic pocket of NOP, while retaining a conformation very similar to the one assumed by the antagonist JDTic into the K-opioid receptor. The proposed binding geometries fit better the binding pocket environment providing clues for experimental studies aimed to design selective or multifunctional opioid drugs.     

Erratum to: “Effect of the Conditions of Anodizing on the Morphology of Nanotitania”

Russian Journal of Physical Chemistry A - The list of authors and their affiliations should read: N. V. Roota, b, D. Yu. Kultina, L. M. Kustova, b, I. K. Kudryavtseva, and O. K. Lebedevaa,*...     

Application of the “Tg-Δ rule” to the local structural study of ferrate glasses

A linear relationship exists between the glass transition temperature (T _g) and the quadrupole splitting (Δ) of Fe(III). The linear relationship, termed ‘T _g-Δ rule’, has been verified in 60CaO·(40-x)Al₂O₃·xFe₂O₃, 60CaO·10BaO·(30-x) Al₂O₃·xFe₂O₃, 60CaO·(40-x)Ga₂O₃·xFe₂O₃, and 50CaO·(50-x)Ga₂O₃·xFe₂O₃ glasses. In these glasses, both theT _g and Δ decrease linearly with an increasing content of Fe₂O₃ (≈40 mol%). The slope of the straight line, obtained from the plot of theT _g vs. Δ, was calculated to be 670≈700, °C/(mm·s⁻¹), revealing that the Fe(III) constitutes the skeleton of aluminoferrate and galloferrate glasses.     

“Approximation”-Novel Methodology to Identify the Active Components from Compounds Library

Combinatorial chemistry has been regarded as one of the most efficient method in medicinal chemistry. Identification of active compounds from compounds library is one of the main steps of combinatorial chemistry. Many approaches have been developed for this purpose, such as deconvolution^[1] positional scanning^[2], SURF^[3],orthogonal library^[4], indexed library^[5], core molecule library^[6] etc. Actually, all the methods are based on the rule of determining the structure of "Active Components" or "Active Compounds"(AC) from "Active Compounds Library"(ACL) by identifying "Active Building Blocks"(ABB). In this way, more efficient method named "Approximation" was developed by reducing the ABB by half in every steps, which was depicted as below by taking "8ҿ8" library as a example.     

Preface to the Special Issue of“Chemical Research in Chinese Universitiess”

ＴｈｅＣｈｉｎｅｓｅＳｏｃｉｅｔｙｏｆＣｈｅｍｉｃａｌＳｃｉｅｎｃｅａｎｄＴｅｃｈｎｏｌｏｇｙｉｎｔｈｅＵＫ(ＣＳＣＳＴ ＵＫ)ｉｓａＣｈｉ ｎｅｓｅｓｅｌｆ ｏｒｇａｎｉｚｅｄｎｏｎ ｐｒｏｆｉｔａｂｌｅｃｈｅｍｉｃａｌｏｒｇａｎｉｚａｔｉｏｎ ,ｗｈｉｃｈｗａｓｅｓｔａｂｌｉｓｈｅｄｉｎＡｐｒｉｌ 1 994 .Ｍｏｒｅｔｈａｎ 4 0 0ＣｈｉｎｅｓｅＣｈｅｍｉｓｔｓａｎｄＣｈｅｍｉｃａｌＥｎｇｉｎｅｅｒｓｃｕｒｒｅｎｔｌｙｗｏｒｋｉｎｇｉｎｔｈｅＵＫａｒｅｍｅｍ ｂｅｒｓｏｆｔｈｅＣＳＣＳＴ ＵＫ .Ｉｔｓａｉｍ…     

From the “Brazuca” ball to octahedral fullerenes: their construction and classification

A simple cut-and-patch method is presented for the construction and classification for fullerenes belonging to the octahedral point groups, O or \(O_h\). In order to satisfy the symmetry requirement of the octahedral group, suitable numbers of four- and eight-member rings, in addition to the hexagons and pentagons, have to be introduced. An index consisting of four integers is introduced to specify an octahedral fullerenes. However, to specify an octahedral fullerene uniquely, we also found certain symmetry rules for these indices. Based on the transformation properties under the symmetry operations that an octahedral fullerene belongs to, we can identify four structural types of octahedral fullerenes.     

A “Low-Molecular” Approach to the Identification of Microorganisms by MALDI Mass Spectrometry

A new approach to the identification of microorganisms is presented. It includes the transformation of their MALDI mass spectra aimed at reducing mass scale by one order of magnitude and the use of standard software for building mass spectral libraries of low-molecular compounds and library searches. A library of 728 transformed (“rescaled”) mass spectra of 182 strains for some Streptococcus species was built. With this library, the rate of true microorganism identification was estimated by cross-comparison between library mass spectra (internal validation of the approach). The true identification rate was 84% for three Streptococcus species, which corresponds to the average trueness of species identification by MALDI as found in the literature. The proposed approach to identification can be considered as a method of choice for solving identification problems under consideration.     

In reply to “A query on the Mg2p of MgO”

Research on Chemical Intermediates -     

Correction to the paper “the condition of mechanical equilibrium on the surface of a nonuniform thin film” [1]

The correction is introduced to the definition of the disjoining pressure of wedge-shaped film formulated in the authors’ previous publication. In refined definition, the nondiagonal pattern of pressure tensor even in cylindrical coordinates is taken into account and the disjoining pressure is introduced by analogy with the case of the transition zone of wetting meniscus. The alternative procedure of the definition of the disjoining pressure through the diagonal pressure tensor in the middle of the wedge is also considered.     

How much does the SI,namely the proposed “New SI”, conform to principles of the Metre Treaty?

The International System of Units (SI) was first adopted in 1960, as the more recent implementation of the Metre Treaty signed in 1875. Basic features of the original SI are that (a) seven units are chosen as “base units”, all the others being “derived units”, and (b) the definitions of the base units should not create interdependence. This way, the SI conforms to the basic principle of the Metre Treaty that each signatory country can realise its choice of primary national standards of the very definitions of the units without needing to resort to calibrations obtained from another country, and without obligation to have them realised for all the units. A mismatch already occurs to some extent with respect to the above features in the present definitions of SI base units. This contribution, strictly based on metrological considerations, illustrates how the present proposal concerning new definitions for the base units, called “New SI”, would extend the mismatch. In this frame, also the meaning is discussed of the concepts of hierarchy and traceability in metrology. By outlining some of the consequences, a discussion is stimulated related to the status of base unit, to the meaning of calibration at the level of the standards of the unit definitions, and to the interdependence of countries’ standards.     

Reply to the Comment on “Realization of Lewis Basic Sodium Anion in the NaBH3− Cluster”

We reply to the comment by S. Pan and G. Frenking who challenged our interpretation of the Na⁻:→BH₃ dative bond in the recently synthesized NaBH₃⁻ cluster. Our conclusion remains the same as that in our original paper ( https://doi.org/10.1002/anie.201907089 and https://doi.org/10.1002/ange.201907089 ). This conclusion is additionally supported by the energetic pathways and NBO charges calculated at UCCSD and CASMP2(4,4) levels of theory. We also discussed the suitability of the Laplacian of electron density (QTAIM) and Adaptive Natural Density Partitioning (AdNDP) method for bond type assignment. It seems that AdNDP yields more sensible results. This discussion reveals that the complex realm of bonding is full of semantic inconsistencies, and we invite experimentalists and theoreticians to elaborate this topic and find solutions incorporating different views on the dative bond.     

“EXTSANGLE” — An extension of the efficiency conversion program “SOLANG” to sources with a diameter larger than that of the Ge-detector

The computer program SOLANG, originally developed by MOENS et al. for the efficiency conversion via effective solid angles (), is extended in this work to cylindrical sources with a diameter larger than that of the Ge-detector. New program, named EXTSANGLE, is experimentally checked in our three laboratories. For the most unfavourable case from the standpoint of the accuracy of (bulky source counted at the top of detector), discrepancies were below 7% in the whole range of gamma-energies considered (88–1115 keV), with an average of 3–4%. EXTSANGLE is extensive and flexible with respect to the data input, storage and output, thus contributing to the automation of a gamma-spectrometry laboratory dealing, for instance, with the k₀-NAA and/or environmental radioactivity monitoring.     

Why does the silica-binding protein “Si-tag” bind strongly to silica surfaces? Implications of conformational adaptation of the intrinsically disordered polypeptide to solid surfaces

We recently reported that the bacterial 50S ribosomal protein L2 binds strongly to silica surfaces even in the presence of high salt concentrations, detergents, and denaturants such as 8 M urea. We designated L2 as Si-tag, a fusion tag for immobilizing functional proteins on silica materials. Here we discuss the remarkable properties of the Si-tag polypeptide in order to understand the mechanism underlying this binding. Experimental and theoretical studies have shown that the 60-aa N-terminal region and the 71-aa C-terminal region, both of which are rich in positively charged residues, lack a well-defined three-dimensional structure under physiological conditions. This lack of a stable tertiary structure suggests that Si-tag belongs to a family of intrinsically disordered (ID) proteins that exist as dynamic ensembles of rapidly fluctuating structures in aqueous solution. Because of its inherent flexibility, Si-tag could form a large intermolecular interface and optimize its structure for surface interactions by conformational adaptation at the binding interface. Such conformational adaptation occurring concomitantly with binding is common to many ID proteins and is called "coupled folding and binding". Through this conformational adaptation, Si-tag could optimize the interactions between its positively charged side chains and ionized surface silanol groups and between its apolar side chains and hydrophobic surface siloxane sites. The cumulative contribution of these contacts would significantly strengthen the binding of Si-tag, resulting in strong, virtually irreversible binding. Our study suggests that flexible ID proteins have tremendous potential for connecting biomolecules to inorganic materials.     

“Lotus” Domain Formation by the Hydrolysis Reaction of Phospholipase D to Phospholipid Monolayer

Hydrolysis rection of L-α-dipalmitoylphosphatidylcholine(L-DPPC)monolayer with phospholipase D (PLD) has been investigated by Brewster angle microscopy (BAM) combined with the film balance.It has been found that the L-DPPC domains were changed into the “lotus“ structure by PLD.It suggests that the hydrolysis reaction is incomplete and the products together with the nonreacted materials undergo a molecular rearrangement at the interface.