Structure and bonding in [M6X8] units of nonmetallic transition metal cluster compounds

A simple quantum mechanical method, based on the Wolfsberg-Helmholtz approximation, has been applied to some nonmetallic4d and5d transition metal cluster compounds containing M₆X₈ units. Our aim was to calculate bonding energies ofM₆ clusters as a function of electronic configuration and symmetry. Energy sequences of clusters containing elements adjacent to each other in the periodic table are discussed, in particular, niobium and molybdenum as well as tungsten and rhenium. Compared with experimentally well-characterized compounds, the computional results show good qualitative agreement. So the occurrence ofM₆ clusters withO_h or lower symmetry can be explained by electronic effects.     

Quantitative effect of nonionic surfactant partitioning on the hydrophile-lipophile balance temperature

Phase behaviors of water/nonionic surfactants/isooctane systems are determined experimentally in temperature-global surfactant concentration diagrams. The surfactants are monodistributed polyoxyethylene glycol n-dodecyl ether. They are used as model mixtures of two, three, or five compounds or as constituents of a commercial surfactant. It is found that the phase diagrams of these systems are bent gradually toward the highest temperatures as the global surfactant concentration decreases. Each phase diagram is well-characterized by the curve of the HLB (hydrophile-lipophile balance) temperature versus the global surfactant concentration. For any fixed global surfactant concentration, this temperature is the middle temperature of the three-phase region; it can be calculated from an additive rule of the HLB temperatures of the surfactants weighted by their mole fractions at the water/oil interface. These mole fractions are determined through the pseudophase model using surfactant partitioning. Calculations require the knowledge of the critical micelle concentration, the partition coefficient between water and oil, and the HLB temperature of each surfactant of the mixture. This treatment can be used to correctly predict the variation of the HLB temperatures of the surfactant mixtures studied versus the global surfactant concentration. Furthermore, these calculations show that the observed curvature of the phase diagrams at the lowest global concentrations is due to the most favorable partitioning toward the oil of the lowest ethoxylated surfactant molecules.     

Experimental studies of the efficiency of electroflotation recovery of poorly soluble lanthanum compounds from aqueous solutions

Features of electroflotation recovery of poorly soluble lanthanum compounds from aqueous solutions containing sodium salts were experimentally determined and studied for the first time. The role was identified that anionic, cationic, and nonionic surfactants added to various supporting electrolytes (sulfate, chloride, carbonate, nitrate) play in the efficiency of electroflotation recovery of poorly soluble lanthanum compounds. The possibility of electroflotation recovery of lanthanum hydroxide with an efficiency of 95–99% was experimentally and theoretically substantiated.     

Molecular docking and competitive binding study discovered different binding modes of microsomal prostaglandin E synthase-1 inhibitors

Microsomal prostaglandin E synthase-1 (mPGES-1) is a newly recognized therapeutic target for the treatment of inflammation, pain, cancer, atherosclerosis, and stroke. Many mPGES-1 inhibitors have been discovered. However, as the structure of the binding site is not well-characterized, none of these inhibitors was designed based on the mPGES-1 structure, and their inhibition mechanism remains to be fully disclosed. Recently, we built a new structural model of mPGES-1 which was well supported by experimental data. Based on this model, molecular docking and competition experiments were used to investigate the binding modes of four representive mPGES-1 inhibitors. As the inhibitor binding sites predicted by docking overlapped with both the substrate and the cofactor binding sites, mPGES-1 inhibitors might act as dual-site inhibitors. This inhibitory mechanism was further verified by inhibitor-cofactor and inhibitor-substrate competition experiments. To investigate the potency-binding site relationships of mPGES-1 inhibitors, we also carried out molecular docking studies for another series of compounds. The docking results correlated well with the different inhibitory effects observed experimentally. Our data revealed that mPGES-1 inhibitors could bind to the substrate and the cofactor binding sites simultaneously, and this dual-site binding mode improved their potency. Future rational design and optimization of mPGES-1 inhibitors can be carried out based on this binding mechanism.     

Generalized Prediction of Enthalpies of Formation Using DLPNO-CCSD(T) Ab Initio Calculations for Molecules Containing the Elements H,C, N,O, F,S, Cl,Br

The prediction of thermochemical properties such as enthalpies of formation is of crucial importance, both in research and industrial applications, especially for systems involving not well-characterized molecules, such as biomass systems (bio-oils), or systems involving new compounds (new-generation refrigerants). It is highly desirable to obtain an efficient method by which these values can be predicted. Ab initio-based calculations can be very accurate for predicting gas phase thermochemical properties and are usually more versatile than group contribution methods. In this work, we propose a general extension of the work of Paulechka and Kazakov, using very accurate and efficient domain-based local pair natural orbital-coupled cluster theory ab initio calculations, to determine the enthalpies of formation of a broad variety of molecules. New sets of regressed atomic contributions are proposed for a larger group of elements: H, C, N, O, F, S, Cl, and Br. Excellent predictions are obtained for the most studied compounds (bio-oil compounds and refrigerants). © 2019 Wiley Periodicals, Inc.     

Predictive power of molecular dynamics receptor structures in virtual screening

Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and unbound configurations. Results from such VS predictions are discussed with respect to experimentally determined structures. In all cases, MD simulations provide snapshots that improve VS predictive power over known crystal structures, possibly due to sampling more relevant receptor conformations. Additionally, MD can move conformations previously not amenable to docking into the predictive range.     

Bio-Organometallic Derivatives of Antibacterial Drugs

Overuse and misuse of antibacterial drugs has resulted in bacteria resistance and in an increase in mortality rates due to bacterial infections. Therefore, there is an imperative necessity of new antibacterial drugs. Bio-organometallic derivatives of antibacterial agents offer an opportunity to discover new active antibacterial drugs. These compounds are well-characterized products and, in several examples, their antibacterial activities have been studied. Both inhibition of the antibacterial activity and strong increase in the antibiotic activity of the parent drug have been found. The synthesis of the main classes of bio-organometallic derivatives of these drugs, as well as examples of the use of structure–activity relation (SAR) studies to increase the activity and to understand the mode of action of bio-organometallic antimicrobial peptides (BOAMPs) and platensimicyn bio-organometallic mimics is presented in this article.     

Adiabatic ionization energies from charge transfer equilibrium constants; experimental determinations of entropy changes for charge transfer equilibria

Equilibrium constants have been measured as a function of temperature for the charge transfer equilibria in mixtures of NO with aromatic compounds, and mixtures of aromatic compounds. The experimentally determined entropy changes are in good agreement with entropy changes calculated from statistical mechanical considerations provided an intermolecular component is included. The enthalpy changes for the charge transfer reactions correspond to the differences in the adiabatic ionization potentials of the compounds.     

Solid-state NMR analysis of the orientation and dynamics of epigallocatechin gallate, a green tea polyphenol, incorporated into lipid bilayers

Catechins are the principle polyphenolic compounds in green tea; the four major compounds identified are epicatechin (EC), epigallocatechin (EGC), epicatechin gallate (ECg) and epigallocatechin gallate (EGCg). Tea catechins tend to attach externally to their targets, such as viral envelopes, cell membranes, or the surface of low-density lipoproteins. In order to further our understanding of the molecular mobility of these compounds in cells, we examined the interaction of tea catechins with lipid membranes using solid-state NMR techniques. Our previous work indicated that the EGCg molecule is incorporated into lipid bilayers in a unique orientation. However, the detailed configuration, orientation, and dynamics of EGCg in lipid bilayers have not been well-characterized. Here, we investigated the orientation and dynamics of EGCg incorporated into multi-lamellar vesicles (MLVs) and bicelles using solid-state NMR spectroscopy.     

Oxidation number: issues of its determination and range

The paper is aimed at the issues of oxidation state determination and limiting values. The possibility of existence of compounds containing an atom with the oxidation number beyond the current common values, i.e., below −IV and above +VIII are discussed. Three principal modes of preparation of compounds with the oxidation number exceeding VIII, electrochemical anodic oxidation, photoionization, and nuclear β-decay, are evaluated. Failure to prepare compounds containing an atom with the oxidation number below −IV is rationalized. The paper provides an opinion on uncertainties in oxidation state determination in three kinds of compounds: binary compounds, nitrosyl complexes, and compounds containing mutually bonded atoms of the same element. The questions are discussed from the viewpoint of correlation of “man-made” quantities and objective, experimentally obtainable data.     

logD7.4 modeling using Bayesian Regularized Neural Networks. Assessment and correction of the errors of prediction

Bayesian Regularized Neural Networks (BRNNs) employing Automatic Relevance Determination (ARD) are used to construct a predictive model for the distribution coefficient logD7.4 from an in-house data set of 5000 compounds with experimental endpoints. A method for assessing the accuracy of prediction is established based upon a query compound's distance to the training set. logD7.4 predictions are also dynamically corrected with an associated library of compounds of continuously updated, experimentally measured logD7.4 values. A comparison of local models and associated libraries comprising separate ionization class subsets of compounds to compounds of a homogeneous ionization class reveals in this case that local models and libraries have no advantage over global models and libraries.     

Prognostication of the composition of a solution for electrodeposition of Sn-Co alloy and determination of its color characteristics

Composition of complex compounds was prognosticated by using a unified model for choosing ligands in development of new solution compositions for electrodeposition of alloys. The possibility of electrodeposition of an Sn-Co alloy from a solution of gluconate complexes of tin and cobalt was experimentally confirmed.     

The structure of the dinitromethyl anion in aromatic and heterocyclic compounds

It is shown experimentally that in salts of dinitromethyl derivatives of aromatic and heterocyclic compounds the nitro groups are equivalent, and participate equally in anion formation. It is shown that both in the free state, and as an anion, the dinitromethyl group in aromatic and heterocyclic compounds has just the same spectral characteristics as in aliphatic compounds. These characteristics can be utilized for analytical purposes. The IR spectra do not reveal conjugation between the mono- or dinitromethyl group and the benzene ring. Judging by the UV spectra the benzene ring is not conjugated with the dinitromethyl anion. It is found that in the solid state 2-dinitromethylpyridine is an internal salt.     

Photochromism of organometallic compounds with structural rearrangement

This article introduces photochromic properties together with structures of organometallic compounds that undergo photo-induced structural rearrangement. The aim of this review is to survey the research on photochromism by using organometallics which possess by their own nature the properties responsible for the photochromism such as bonding and structural fluxionality, electronic state fluctuation, and photochemically active characteristic in both solution and the solid state. Therefore, the organometallics which include the well-characterized organic photochromic moieties, considered to be derivatives of such kinds of organic photochromic compounds, are excluded in this article. Mono-, di-, and poly-nuclear organometallic compounds are presented based on the reaction types such as linkage isomerization, haptotropic rearrangement, and reorganization of metal–ligand and/or metal–metal bonds. Very recently, the crystalline-state photochromism is becoming an attractive field of photochromic chemistry. As a demonstrative example, the photochromism of organometallic rhodium dinuclear complexes having a dithionite ligand (μ-O₂SSO₂), which shows 100% reversible interconversion in the crystalline-state and have been developed in the authors’ laboratory, will be discussed.     

Determination of cyclo C6 and C7 peroxides and hydroperoxides by gas chromatography

Summary A method for determining cyclo C₆-C₇-peroxides and hydroperoxides by high-resolution capillary GC has been developed. The compounds were synthesized in the liquid phase and identified in chromatograms of the reaction mixture of cyclohexyl hydroperoxide and cycloheptane using GC-MS. Peroxy compounds were determined using an FID. The effective carbon number (ECN) concept was used to calculate response factors of the peroxy compounds analysed. The experimentally determined response factor for cyclohexyl hydroperoxide was identical (within error limits) with that calculated.     

Spectral deep learning for prediction and prospective validation of functional groups

State-of-the-art identification of the functional groups present in an unknown chemical entity requires the expertise of a skilled spectroscopist to analyse and interpret Fourier transform infra-red (FTIR), mass spectroscopy (MS) and/or nuclear magnetic resonance (NMR) data. This process can be time-consuming and error-prone, especially for complex chemical entities that are poorly characterised in the literature, or inefficient to use with synthetic robots producing molecules at an accelerated rate. Herein, we introduce a fast, multi-label deep neural network for accurately identifying all the functional groups of unknown compounds using a combination of FTIR and MS spectra. We do not use any database, pre-established rules, procedures, or peak-matching methods. Our trained neural network reveals patterns typically used by human chemists to identify standard groups. Finally, we experimentally validated our neural network, trained on single compounds, to predict functional groups in compound mixtures. Our methodology showcases practical utility for future use in autonomous analytical detection.

A new multi-label deep neural network architecture is used to combine Infrared and mass spectra, trained on single compounds to predict functional groups, and experimentally validated on complex mixtures.