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A database of thermally activated delayed fluorescent (TADF) molecules was automatically generated from the scientific literature. It consists of 25,482 data records with an overall precision of 82%. Among these, 5,349 records have chemical names in the form of SMILES strings which are represented with 91% accuracy; these are grouped in a subsidiary database. Each data record contains one of the following four properties: maximum emission wavelength (λEM), photoluminescence quantum yield (PLQY), singlet-triplet energy splitting (ΔEST), and delayed lifetime (τD). The databases were created through text mining using ChemDataExtractor, a chemistry-aware natural-language-processing toolkit, which has been adapted for TADF research. The text-mined corpus consisted of 2,733 papers from the Royal Society of Chemistry and Elsevier. To the best of our knowledge, these databases are the first databases that have been auto-generated for TADF molecules from existing publications. The databases have been publicly released for experimental and computational applications in the TADF research field. [ABSTRACT FROM AUTHOR]

A drug molecule is a substance that changes an organism's mental or physical state. Every approved drug has an indication, which refers to the therapeutic use of that drug for treating a particular medical condition. While the Large Language Model (LLM), a generative Artificial Intelligence (AI) technique, has recently demonstrated effectiveness in translating between molecules and their textual descriptions, there remains a gap in research regarding their application in facilitating the translation between drug molecules and indications (which describes the disease, condition or symptoms for which the drug is used), or vice versa. Addressing this challenge could greatly benefit the drug discovery process. The capability of generating a drug from a given indication would allow for the discovery of drugs targeting specific diseases or targets and ultimately provide patients with better treatments. In this paper, we first propose a new task, the translation between drug molecules and corresponding indications, and then test existing LLMs on this new task. Specifically, we consider nine variations of the T5 LLM and evaluate them on two public datasets obtained from ChEMBL and DrugBank. Our experiments show the early results of using LLMs for this task and provide a perspective on the state-of-the-art. We also emphasize the current limitations and discuss future work that has the potential to improve the performance on this task. The creation of molecules from indications, or vice versa, will allow for more efficient targeting of diseases and significantly reduce the cost of drug discovery, with the potential to revolutionize the field of drug discovery in the era of generative AI. [ABSTRACT FROM AUTHOR]

The paper presents the incorporation of in silico missenses and studies the effect of missenses to understand its effect on the ligand–protein interactions, of COVID-19 protein. In silico protein–ligand interaction, studies are being used to understand and investigate the drug-likeness of various molecules. 19 novel COVID-19 proteins are designed by inducing in silico missenses by mutating N691 amino acid residue in 7bv2 protein, the only residue forming H-bond with the ligand molecule in the parent protein. The work illustrates the effects of in silico-induced mutation on various interactions such as H-Bond, VDW, π-alkyl interactions, and changes in the number and type of surrounding amino acid residues. The results have suggested a common pattern of behaviour on mutation with T, V, W, and Y. Further, it is observed that the number and type of amino acid residues increase on mutation, suggesting the effect of mutation on the ligand–protein binding. [ABSTRACT FROM AUTHOR]

The molecular movement in single particle tracking (SPT) experiments shows a crucial role of diffusion in many biological processes such as signaling, cellular organization, transport mechanisms, and more. The SPT analysis detects not only classical Brownian motion but diffusion with other features. These include directed diffusion and confined motion. The behavior remains a challenging problem for several reasons. Due to the action of many physical processes, random trajectories of cellular molecules are segmented in different diffusive modes. Often their study requires sophisticated algorithms for the analysis of statistical properties. In this paper we consider the segment analysis for trajectories of G proteins and coupled-receptors in living cells. Their movement is often transient and switches among free diffusion, confined diffusion, directed diffusion, and immobility. Moreover, the confined segments can have both Gaussian and non-Gaussian statistics. The types of alternation of diffusive modes along the trajectories of G proteins and coupled-receptors are analyzed. [ABSTRACT FROM AUTHOR]

Analysis of the performance degradation for W-band lossy ceramic-loaded gyrotron traveling wave tubes (gyro-TWTs) caused by ionization of the released gas molecules is presented in this paper. The gas is released from the lossy ceramics during high average or continuous wave operation and ionized by colliding with the high-energy gyrating electrons. A potential well will be formed by the diffusion and accumulation of the ionization particles after the collision and then degrade the gyro-TWT performance. This process has been simulated based on a simplified model by introducing an equivalent ionization source combining ions and electrons. With a vacuum of 5.1 × 10 - 5 Pa, the theoretically calculated initial energy and equivalent ionization current are 0.01 eV and 0.5 A, respectively. It leads to a deterioration in the output power stability of the gyro-TWT. The performance degradation including spectrum and field pattern caused by gas ionization is also given and analyzed. One of the primary causes is the quality (pitch factor and velocity spread) degradation of the electron beam. According to the simulation and hot test experiments, the vacuum should be maintained below 2.1 × 10 - 6 Pa for stabilizing the amplified operation. [ABSTRACT FROM AUTHOR]

This paper is a cross fertilization of ideas about the importance of molecular aspects of breast cancer metastasis by basic scientists, a pathologist, and clinical oncologists at the Henry Ford Health symposium. We address four major topics: (i) the complex roles of lymphatic endothelial cells and the molecules that stimulate them to enhance lymph node and systemic metastasis and influence the anti-tumor immunity that might inhibit metastasis; (ii) the interaction of molecules and cells when breast cancer spreads to bone, and how bone metastases may themselves spread to internal viscera; (iii) how molecular expression and morphologic subtypes of breast cancer assist clinicians in determining which patients to treat with more or less aggressive therapies; (iv) how the outcomes of patients with oligometastases in breast cancer are different from those with multiple metastases and how that could justify the aggressive treatment of these patients with the hope of cure. [ABSTRACT FROM AUTHOR]

The paper offers a systematic reconstruction of the relations that, in Husserl's work, bind together our shared social world ("the spiritual world") with shared intentionality. It is claimed that, by sharing experiences, persons create social reasons and that these reasons impose a normative structure on the social world. Because there are two ways in which persons can share experiences (depending on whether these experiences rest on mutual communication or on group's identity), social normativity comes in two kinds. It is either directed (it has an addressee) or it is collective or absolute (it applies to all group members). Social normativity should be distinguished from axiological normativity: The first is grounded in shared intentionality, the second in values. [ABSTRACT FROM AUTHOR]

Highlights: Critical solvation structure changes the hydrogen bond network through "catchers". Catcher further arrests the active molecules to promote Zn2+ deposition. The Zn||Zn symmetric battery can stably cycle for 2250 h. Zn||V6O13 full battery achieved a capacity retention rate of 99.2% after 10,000 cycles. Aqueous Zn-ion batteries (AZIBs) have attracted increasing attention in next-generation energy storage systems due to their high safety and economic. Unfortunately, the side reactions, dendrites and hydrogen evolution effects at the zinc anode interface in aqueous electrolytes seriously hinder the application of aqueous zinc-ion batteries. Here, we report a critical solvation strategy to achieve reversible zinc electrochemistry by introducing a small polar molecule acetonitrile to form a "catcher" to arrest active molecules (bound water molecules). The stable solvation structure of [Zn(H2O)6]2+ is capable of maintaining and completely inhibiting free water molecules. When [Zn(H2O)6]2+ is partially desolvated in the Helmholtz outer layer, the separated active molecules will be arrested by the "catcher" formed by the strong hydrogen bond N–H bond, ensuring the stable desolvation of Zn2+. The Zn||Zn symmetric battery can stably cycle for 2250 h at 1 mAh cm−2, Zn||V6O13 full battery achieved a capacity retention rate of 99.2% after 10,000 cycles at 10 A g−1. This paper proposes a novel critical solvation strategy that paves the route for the construction of high-performance AZIBs. [ABSTRACT FROM AUTHOR]

The investigation of the relation between chemistry and quantum mechanics includes examining how the two theories each describe an isolated molecule. This paper focuses on one particular characteristic of chemistry's and quantum mechanics' descriptions of an isolated molecule; namely on the assumptions made by each description that an isolated molecule is stable and has structure. The paper argues that these assumptions are an idealisation. First, this is because stability and structure are partially determined by factors that concern the context in which a molecule is considered (i.e. thermodynamic conditions, time-range of experiment, environment, etc.). Secondly, the stability and structure of a molecule can only be empirically identified with reference to those factors. This paper examines these assumptions in the context of the philosophical literature on idealisations. This examination is a novel contribution that raises interesting questions about the relation between the two theories, the nature of stability and structure, and the function of these assumptions in the two theories. [ABSTRACT FROM AUTHOR]

This paper focuses the study of nonlinear absorption (NLA) features of anthraquinone dye namely, acid blue 129 with different polar solvents including ethanol, methanol, acetone, 1-proponal and DMSO. The acid blue 129 dye in polar solvents is characterized by UV–Visible absorption and fluorescence study. The NLA measurements of acid blue 129 dye is examined via open aperture (OA) Z-scan method employing at 650 nm wavelength. The OA Z-scan curve of the experimental dye exhibits both saturable absorption (SA) and reveres saturable absorption (RSA) signature, which results from negative and positive NLA coefficient (β). The order of ground and excited state absorption cross-section is measured to be 10˗22 m2 and 10˗18 m2, respectively and proved the existence of RSA in acid blue 129 dye. The order of NLA coefficient and imaginary component of the third-order nonlinear susceptibility of acid blue 129 dye in polar solvents is calculated to be 10˗3 cm/W and 10˗5 esu, respectively. The multi-parameter scale viz., Kamlet-Abboud-Taft is used to measure the influence of solvent parameters on solute molecule. The results from the experiments suggest that the acid blue 129 is a suitable candidate for nonlinear optical (NLO) applications. [ABSTRACT FROM AUTHOR]

This work is based on the productive idea of Mulliken about the alignment of electronegativities of atoms in the process of bond formation to their geometric mean value. The paper considers in detail the case of a binary molecule and obtains formulas for the dependence of the current values of the electronegativities of the two atoms forming the molecule on time, and finds a mathematical connection between the current and initial values of electronegativities. Also, in the work the theorem on the relation between the rates of alignment of electronegativities of atoms entering into chemical bonding is formulated and proved, and a special case of this theorem is considered. [ABSTRACT FROM AUTHOR]

Using the example of C59Fe, the paper describes a scheme for calculating the motion of a magneto-susceptible molecular object in an alternating magnetic field. Two modes of angular displacements of the molecular structure under consideration are determined by calculation. The possibility of forming the spin of the molecule is shown. [ABSTRACT FROM AUTHOR]

The movement of water molecules at the atomic scale within the calcium silicate hydrate (C–S–H) gel pores serves a dual role: it creates an environment for harmful chemical reactions within the pores and functions as a carrier for the transport of detrimental ions, thereby affects the mechanical properties and durability of cementitious materials. However, direct experimental observation poses substantial challenges. This study offers new insights into how temperature (253 K, 273 K, 293 K, and 313 K) affects the capillary transport of water molecules in epoxy-modified C–S–H. The findings demonstrate that the pore size undergoes continuous changes during immersion due to epoxy clustering or detachment, resulting in three scenarios: narrowing of epoxy/C–S–H channels (253 K, 273 K), channel blockage (293 K), and complete detachment (313 K). Moreover, the interactions between water molecules and epoxy lead to epoxy detachment or cluster formation on the C–S–H surface. As the temperature increases, the interaction between C–S–H and cross-linked epoxy resin weakens. The coordination between C–S–H and epoxy resin decreases, while the coordination with water increases. This paper provides valuable insights into the transport behavior of liquids within the epoxy-modified C–S–H pores of cement-based materials. It contributes to a better understanding of how liquids move and interact within the modified pore structure, which is beneficial for enhancing the performance and properties of cement-based materials. [ABSTRACT FROM AUTHOR]

With the premise that N-soliton solutions are acquired, this paper will focus on the nonlinear superposition between one lump and other types of localised waves of the (2+1)-dimensional generalized Caudrey-Dodd-Gibbon-Kotera-Sawada(gCDGKS) equation. By introducing a novel constraint, combining the long wave limit method and mode resonance method, it is guaranteed that there is no interaction between one lump (local waves that remain wave form invariant in space) and line solitons (analytic solutions in exponential form in both space and time), breather waves and resonant Y-type solitons ever or that one lump is always situated on at least one of line solitons, breather waves (shape is similar to the rise and fall of the breath) and resonant Y-type solitons (similar to the letter Y in spatial structure). In addition, by defining novel velocity resonance constraints, it is ensured that lump and line waves, lump and breather waves, breather and line wave have exactly the same velocity magnitude and direction, which means that they form new molecularly bound states. Remarkably, we find that one line and one breather wave can be transformed into two breather waves. In general, lump wave interact with other types of localised waves in three stages: before, during and after the interaction, but the results obtained in this paper break this perception and provide some references for the explanation of certain nonlinear phenomena occurring in fields such as shallow water waves, solitons and fluid mechanics. [ABSTRACT FROM AUTHOR]

The paper studies the sensor properties of poly[(9,9-dioctylfluorenyl-2,7-diyl) polymer with terminal dimethylphenyl (ADS129) groups to detect the nitro compound vapor in a laser oscillation mode after the formation of the nitro compound molecular complex. Different solvents are used to obtain ADS129 films. [ABSTRACT FROM AUTHOR]

Proton-type ionic liquids have been proved to be promising for the pretreatment of lignocellulosic biomass, because they can provide high yield cellulase hydrolysis and high lignin removal rate. In this work, three proton-type ionic liquids, ethyl methanesulfonamide (EAM), ethyl amine nitrate (EAN) and ethyl amine acetate (EAN[OAc]), were successfully synthesized to pretreat corn straw, and five sugar platform organic solvents were selected as co-solvents for biomass pretreatment. The experimental results showed that under the optimal pretreatment conditions (10 wt% EAM, 130 °C, 2 h, 7 wt% straw loading in PDO solvent), the delignification rate of corn straw could reach 96 wt%, the sugar yield of cellulose-rich substrate could reach 95 wt% in 96 h, the regeneration rate of lignin dissolved in the solvent was 86 wt%, and the remainder of the solvent was small molecular compound, the hemicellulose dissolved in the solvent is degraded to monomolecular sugars (xylose and arabinose). The XRD, SEM characterization data and spectrograms of cellulosic substrate also fully proved that the lignin was successfully dissolved and separated from corn straw by pretreatment of composite system, and in the remaining straw the content and crystallinity of cellulose was improved. In this paper, density functional theory (DFT) is used to explore the pretreatment principle. From the optimized structure, it can be seen that the interaction energy between the ionic liquid cosolvent system and lignin is higher than that in the pure ionic liquid system. The simulation results, experimental analysis and characterization can effectively explain the essence of the system for efficient straw pretreatment, and the system can provide new ideas for the development of biomass pretreatment. [ABSTRACT FROM AUTHOR]

Generating novel valid molecules is often a difficult task, because the vast chemical space relies on the intuition of experienced chemists. In recent years, deep learning models have helped accelerate this process. These advanced models can also help identify suitable molecules for disease treatment. In this paper, we propose Taiga, a transformer-based architecture for the generation of molecules with desired properties. Using a two-stage approach, we first treat the problem as a language modeling task of predicting the next token, using SMILES strings. Then, we use reinforcement learning to optimize molecular properties such as QED. This approach allows our model to learn the underlying rules of chemistry and more easily optimize for molecules with desired properties. Our evaluation of Taiga, which was performed with multiple datasets and tasks, shows that Taiga is comparable to, or even outperforms, state-of-the-art baselines for molecule optimization, with improvements in the QED ranging from 2 to over 20 percent. The improvement was demonstrated both on datasets containing lead molecules and random molecules. We also show that with its two stages, Taiga is capable of generating molecules with higher biological property scores than the same model without reinforcement learning. [ABSTRACT FROM AUTHOR]

Although various conjugates of single-walled carbon nanotubes (SWNTs) and biomolecules, such as nanobiosensors and nanobiodevices, have been reported, the conjugation of papain and SWNTs have not been reported because of the formation of unexpected aggregates. In this study, atomic force microscopy (AFM) in liquid was used to investigate the interactions between papain and DNA-wrapped SWNTs (DNA–SWNTs) at two different pH values (pH 3.0 and 10.5). The direct AFM observation of the mixture of papain and DNA–SWNTs confirmed the aggregation of papain molecules with DNA–SWNTs in the buffer solutions. The numerous and non-uniform adsorption of papain molecules onto DNA–SWNTs was more pronounced at pH 3.0 than that at pH 10.5. Furthermore, thick conjugates appeared when papain and DNA–SWNTs were simultaneously mixed. The near-infrared photoluminescence spectra of the SWNTs drastically changed when the papain molecules were injected into the DNA–SWNT suspension at pH 3.0. Thus, the regulation of electrostatic interactions is a key aspect in preparing optimal conjugates of papain and DNA–SWNTs. Furthermore, although previous papers reported AFM images of dried samples, this study demonstrates the potential of AFM in liquid in evaluating individual bioconjugates of SWNTs. [ABSTRACT FROM AUTHOR]

Soliton molecules were first discovered in optical systems and they have recently received reinvigorating scientific interests in physics and beyond. In this paper, we mainly study a typical model of nonlocal fifth-order KdV system. First, the model is obtained by using parity, time reversal invariance and Lax pairs. Secondly, we obtain soliton solutions by means of the bilinear method. Finally, based on the N-soliton solution, soliton molecules can be obtained via the velocity resonance mechanism. Especially, some soliton molecules have been observed successfully in the laboratory. [ABSTRACT FROM AUTHOR]

Soliton dynamics often exhibit a rich diversity and complexity, emerging from myriad combinations of nonlinearities and dispersions within nonlinear dynamical systems. This endeavor contributes to the novel exploration of intricate soliton interactions. In this paper, we investigate a multi-component Maccari system which can be used to depict optical pulse motions in multi-mode optical fibers. By employing the bilinear method, we obtain the system's analytical second-order solutions involving abundant parameters. Under taking suitable parameter settings, we observe some novel soliton interaction dynamics: soliton resonances from local to global ranges, transitions from soliton molecules to breathers, semi-elastic soliton collisions and soliton bifurcations (namely solitons' fission and fusion). Especially, all solitons in resonances, molecules and bifurcations hold stable propagation states. The findings also reveal new energy transition mechanism during soliton interactions by semi-elastic collisions and soliton bifurcations. [ABSTRACT FROM AUTHOR]

Employing the formalism of the joint density functional theory (JDFT) in the grand canonical ensemble, this paper studies the electronic structure and relative reactivity of an hydroxyl radical adsorbed on the surface of three different metal oxides that share the rutile-type structure and the (110) crystal plane; these materials are electrodes used in electrochemical advanced oxidation processes which consist in the generation of hydroxyl radicals, highly reactive species, that are able to oxidize organic compounds to CO 2 , making these anodes efficient for wastewater treatment. By analyzing the changes in the average number of electrons as a function of the applied chemical potential at fixed external potential, we studied two reactivity indices from conceptual density functional theory: global and local softness, to help us understand the differences between these materials, additionally we propose a new scheme to approximate the redox properties of clean surfaces or surfaces in contact with different adsorbed molecules so that these values can be arranged in a relative potential scale which would allow direct comparison with experimental results. [ABSTRACT FROM AUTHOR]

The paper presents a technique for broadband two-dimensional infrared spectroscopy with signal detection in visible range by nonlinear chirped-pulse upconversion. This approach helps to avoid direct measurement of the mid-infrared signal that requires cryogenic technology, and instead uses low-cost high-sensitivity multichannel silicon linear arrays. This leads to a reduction by two orders of magnitude of the measurement time of a single two-dimensional spectrum, which makes it possible to observe the fast dynamics of complex molecular compounds. The use of a quasi-phase-cycling achieved by sub-cycle delay modulation suppresses scattering background by almost two orders of magnitude and increases the measurement speed twice compared to optical chopping. Numerical simulation using the density matrix formalism and analysis of its evolution based on the solution of the Bloch–Redfield equation effectively reproduces the features of the two-dimensional infrared spectrum of inorganic octacarbonyl dicobalt compound. [ABSTRACT FROM AUTHOR]

In this paper the experimental and molecular dynamics studies have been performed for the adsorption processes of n-butanol and butyl acetate on the SiO2 surface. The experimental measurements of the adsorption/desorption processes of n-butanol and butyl acetate on the SiO2 surface include data from thermokinetic spectrometry. Additionally, the computer molecular dynamics (MD) simulations involved the analysis of temperature, energy, and structural characteristics of the adsorption processes of n-butanol and butyl acetate on the SiO2 surface. Based on the MD simulations of the triple system—surface (SiO2)—carrier gas (Ar)—target molecule (n-butanol, butyl acetate), radial distribution function (RDF) profiles were constructed and analyzed at three temperatures of the system: T = 300, 500, and 700 K. A comparative analysis of the results reveals that the addition of an acetate group enhances the affinity of the butyl acetate molecule towards the SiO2 surface. Consequently, the adsorption process of butyl acetate occurs more completely at higher temperatures compared to n-butanol. In addition, changes in size influence the arrangement of atoms within the butyl acetate molecule relative to the surface atoms of SiO2, leading to the observed "displacement" effect of an identical chain for both molecules (n-butanol and butyl acetate) of the carbon "skeleton" atoms (C1(Q=−3)–C2(Q=−2)–C3(Q=−2)–C4(Q=−1)–O1(Q=−2)). The experimental data on the desorption processes of n-butanol and butyl acetate from the SiO2 surface in the triple system "n-butanol/SiO2/argon" ("butyl acetate/SiO2/argon") yield an Arrhenius activation energy value of 78.83 kJ/mol (87.58 kJ/mol) and a pre-exponential multiplier value of 4.41 × 107 s−1 (1.81 × 1010 s−1). [ABSTRACT FROM AUTHOR]

The paper presents the Morse potential-based calculation of Franck–Condon factors which have not been investigated from the point of view of allowed transitions associated with the first negative and second positive systems. For nonallowed transitions, it is shown that the Morse potential provides an exact calculation of factors, depending on vibrational constants. During the vibrational number increase, the deviation is observed between calculated Franck–Condon factors and those determined by the more accurate Rydberg–Klein–Rees potential. [ABSTRACT FROM AUTHOR]

In this paper, we will study two various nonlinear models: the Atangana–Baleanu fractional system of equations for the ion sound and Langmuir waves (ISALWs) and Hirota Ramani equation to obtain variety of solitary wave solutions. We will obtain bright, dark, periodic wave and solitory wave for ISALWs equation. We will also retreived bell type, kink type, singular, Jacbion elliptic function, Weierstrass-elliptic function, hyperbolic functions, periodic functions and other solitary wave solutions for Hirota Ramani equation using Sub ODE technique under some constraint conditions. At the end we will present our solutions with the help of graphs in distinct dimensions. [ABSTRACT FROM AUTHOR]

The software for the IUPAC Chemical Identifier, InChI, is extraordinarily reliable. It has been tested on large databases around the world, and has proved itself to be an essential tool in the handling and integration of large chemical databases. InChI version 1.05 was released in January 2017 and version 1.06 in December 2020. In this paper, we report on the current state of the InChI Software, the details of the improvements in the v1.06 release, and the results of a test of the InChI run on PubChem, a database of more than a hundred million molecules. The upgrade introduces significant new features, including support for pseudo-element atoms and an improved description of polymers. We expect that few, if any, applications using the standard InChI will need to change as a result of the changes in version 1.06. Numerical instability was discovered for 0.002% of this database, and a small number of other molecules were discovered for which the algorithm did not run smoothly. On the basis of PubChem data, we can demonstrate that InChI version 1.05 was 99.996% accurate, and InChI version 1.06 represents a step closer to perfection. Finally, we look forward to future releases and extensions for the InChI Chemical identifier. [ABSTRACT FROM AUTHOR]

Halomonas spp. are the well-studied platform organisms or chassis for next-generation industrial biotechnology (NGIB) due to their contamination-resistant nature combined with their fast growth property. Several Halomonas spp. have been studied regarding their genomic information and molecular engineering approaches. Halomonas spp., especially Halomonas bluephagenesis, have been engineered to produce various biopolyesters such as polyhydroxyalkanoates (PHA), proteins including surfactants and enzymes, small molecular compounds including amino acids and derivates, as well as organic acids. This paper reviews all the progress reported in the last 10 years regarding this robust microbial cell factory. Key points: • Halomonas spp. are robust chassis for low-cost production of chemicals • Genomic information of some Halomonas spp. has been revealed • Molecular tools and approaches for Halomonas spp. have been developed • Halomonas spp. are becoming more and more important for biotechnology [ABSTRACT FROM AUTHOR]

Extraction of chemical formulas from images was not in the top priority of Computer Vision tasks for a while. The complexity both on the input and prediction sides has made this task challenging for the conventional Artificial Intelligence and Machine Learning problems. A binary input image which might seem trivial for convolutional analysis was not easy to classify, since the provided sample was not representative of the given molecule: to describe the same formula, a variety of graphical representations which do not resemble each other can be used. Considering the variety of molecules, the problem shifted from classification to that of formula generation, which makes Natural Language Processing (NLP) a good candidate for an effective solution. This paper describes the evolution of approaches from rule-based structure analyses to complex statistical models, and compares the efficiency of models and methodologies used in the recent years. Although the latest achievements deliver ideal results on particular datasets, the authors mention possible problems for various scenarios and provide suggestions for further development. [ABSTRACT FROM AUTHOR]

During the synthesis of h-BN nano-material, there unavoidably exist some N vacancies that will largely affect its physicochemical properties. Therefore, it is full of necessity to repair these defects before further investigations and applications. In this paper, we propose the use of NO molecules to heal the N vacancy in a h-BN monolayer through the NO disproportionation based on DFT calculation. Our calculations indicate that the repairing processes are energetically favorable and the repaired h-BN monolayer, from both geometric and electronic manners, has good similarity with the perfect counterpart. This theoretical work exhibits a promising approach to heal the N vacancy in h-BN monolayer, and we assume it is also feasible for repairing the N defects in other 2D nano-materials. [ABSTRACT FROM AUTHOR]

In common with many other countries, the Iranian science curriculum does not introduce primary children to atoms and molecules but instead leaves the teaching of these concepts until high school. This paper challenges this practice and describes the changes in elementary Iranian children's understanding of atoms and molecules following a 10-h teaching intervention about basic atomic-molecular theory, derived from recently published Australian research. The participants involved in this study are a group of 25 Iranian children aged 9 to 12 years old, who participated in a vacation summer school where they were taught about the structure of atoms and molecules. Thematic and content analysis of children's written responses and drawings before and after the intervention reveal significant changes in their conceptual thinking. The results also show the extent to which the children can generate microscopic representations of the states of matter from their understanding of atoms and molecules. [ABSTRACT FROM AUTHOR]

We study both the classical and quantum rotational dynamics of an asymmetric top molecule, controlled through three orthogonal electric fields that interact with its dipole moment. The main difficulties in studying the controllability of these infinite-dimensional quantum systems are the presence of severe spectral degeneracies in the drift Hamiltonian and the nonsolvability of the stationary free Schrödinger equation, which lead us to apply a perturbative Lie algebraic approach. In this paper we show that, while the classical equations given by the Hamiltonian system on SO (3) × R 3 are controllable for all values of the rotational constants and all dipole configurations, the Schödinger equation for the quantum evolution on L 2 (SO (3) , C) is approximately controllable for almost all values of the rotational constants if and only if the dipole is not parallel to any of the principal axes of inertia of the asymmetric rigid body. [ABSTRACT FROM AUTHOR]

Selecting diverse molecules from unexplored areas of chemical space is one of the most important tasks for discovering novel molecules and reactions. This paper proposes a new approach for selecting a subset of diverse molecules from a given molecular list by using two existing techniques studied in machine learning and mathematical optimization: graph neural networks (GNNs) for learning vector representation of molecules and a diverse-selection framework called submodular function maximization. Our method, called SubMo-GNN, first trains a GNN with property prediction tasks, and then the trained GNN transforms molecular graphs into molecular vectors, which capture both properties and structures of molecules. Finally, to obtain a subset of diverse molecules, we define a submodular function, which quantifies the diversity of molecular vectors, and find a subset of molecular vectors with a large submodular function value. This can be done efficiently by using the greedy algorithm, and the diversity of selected molecules measured by the submodular function value is mathematically guaranteed to be at least 63% of that of an optimal selection. We also introduce a new evaluation criterion to measure the diversity of selected molecules based on molecular properties. Computational experiments confirm that our SubMo-GNN successfully selects diverse molecules from the QM9 dataset regarding the property-based criterion, while performing comparably to existing methods regarding standard structure-based criteria. We also demonstrate that SubMo-GNN with a GNN trained on the QM9 dataset can select diverse molecules even from other MoleculeNet datasets whose domains are different from the QM9 dataset. The proposed method enables researchers to obtain diverse sets of molecules for discovering new molecules and novel chemical reactions, and the proposed diversity criterion is useful for discussing the diversity of molecular libraries from a new property-based perspective. [ABSTRACT FROM AUTHOR]

Surface-enhanced Raman spectroscopy (SERS)-based biosensors have recently been extensively developed because of their high sensitivity and nondestructive nature. Conventional SERS substrates are unsuitable for detecting biomolecules directly from human skin. As a result, considerable effort is being devoted on developing a gel-based SERS sensor capable of segregating and detecting biomolecules because of differences in molecular transport phenomena within the gel. However, no comprehensive studies on the transport processes of molecules in gels have been published for gel-type SERS sensors. This paper reports the differences in the transport phenomena of different molecules based on the time change of SERS spectrum intensity. The Au nanorod array substrate was coated with HEC gel to prepare a sample cell to study diffusion. The SERS spectra of aqueous solutions of 9 types of molecules were measured using the prepared sample cells. The rate at which each molecule diffuses into the gel differs depending on the molecule. The time variation of the characteristic SERS peak of each molecule was investigated on the basis of a one-dimensional diffusion model, and the diffusion coefficient D was calculated for each molecule. The diffusion coefficient was compared with the molecular weight and size, and it was discovered that the larger the molecular weight and size, the slower the diffusion, which is consistent with molecular motion theory and the inhibitory effect of the gel substance. [ABSTRACT FROM AUTHOR]

First principles were used to investigate electronic properties of Au-doped graphene, Ag-doped graphene, and Cu-doped graphene and the effect of adsorption behavior of hydrogen sulfide (H2S) molecule on their electronic properties. Doped graphene exhibits interesting electronic properties. The gap value of Ag-doped graphene is 0.29 eV, whereas Au-doped graphene is 0.48 eV which is the largest one in three doped systems, a clear difference of structure and electronic properties among three doped systems absorbing H2S molecule. The doped atom and the H2S molecule are on the same side of the graphene for Au-doped graphene and Cu-doped graphene, which belong to a kind of bonding orbital hybridization of electron cloud showed from charge difference density plots. However, Ag-doped graphene adsorbed with H2S molecule exhibits a kind of antibonding orbital hybridization. With the analysis in this paper, it is beneficial to research H2S gas sensors. [ABSTRACT FROM AUTHOR]

Quantum-dot is the result of elastic relaxation which has a straight relationship with the optical and electronic aspects of the quantum-dot-based devices. In nanotechnologies, Quantum-dot Cellular Automata (QCA) is a perfect transistor-less computation method where it tries to create general computation at the nanoscale with better switching frequency and enhanced scale integration to overcome the scaling shortfalls of CMOS technology. In this technology, binary information is represented based on the distribution of electron configuration in chemical molecules. Also, the comparator is the essential component in digital circuits, which takes two binary numbers as input and implements their resemblance. In this paper, a 1-bit comparator architecture in an optimized and efficient manner is suggested to bring a new phase of comparator circuit based on QCA, and then a novel 2-bit comparator structure is offered. The simulation and functionality of proposed comparators have been examined by the QCAdesigner tool, and comparison with formerly designs shows a high degree of compactness and consistent performance of proposed designs. Proposed 1-bit and 2-bit QCA comparators exhibit a delay of 0.75 and 2.75 clock cycle, occupy an active area of 0.04 and 0.19 μm2, and use 31 and 125 QCA cells, respectively. [ABSTRACT FROM AUTHOR]

The purpose of this paper is to provide a clear and simple introduction to the application of isotopically labelled molecules in the characterization of various surfaces by vibrational spectroscopies. Although the possible applications are multifarious, we have tried to systematize the most important of them in several groups. Initially we provide a brief theoretical background on the effect of isotopic substitution on the vibrational spectra and then consider the practical application of the technique for establishing the structure and composition of surface species, determination of the origin of particular atoms in these species and obtaining details on the interaction between adsorbed molecules. The second part of the paper describes three purpose-designed surface studies exemplifying the use of isotopically labelled molecules in order to: (i) determine of the maximal number of CO molecules than can be simultaneously bound to one Na cation from the NaY zeolite; (ii) measure the dynamic and static shift of CO molecules adsorbed on Ru/ZrO; (iii) prove the H dissociation on Ru/ZrO. [ABSTRACT FROM AUTHOR]

An Erratum to this paper has been published: https://doi.org/10.1134/S0012500823970013 [ABSTRACT FROM AUTHOR]

Computer simulation of the Raman lidar equation for measurement of the hydrogen molecules at the concentration level of 1013 cm–3 and higher in atmosphere at the ranging distances up to 100 m in the synchronous photon counting mode and selection of such a lidar optimal parameters have been fulfilled. It is shown that for hydrogen molecules concentration of N(z) = 1013 cm–3 measurement at the distances from 5 to 100 m the measurement time t is in the range from 3.83 s to 26.5 min, for measurement of concentration N(z) = 1015 cm–3—from 38 ms to 15.9 s and for the concentration measurement of N(z) = 1017cm–3—already from 0.4 ms to 160 ms, respectively. [ABSTRACT FROM AUTHOR]

As a type of water reducer, polycarboxylate superplasticizers (PCEs) has been widely used in the concrete industry. The concentration and molecule weight of PCEs have a profound impact on the performance of fresh concrete. Based on 1H low-field nuclear magnetic resonance (NMR) spectroscopy, this paper developed a novel method for the determination of the concentration and characterization of the molecule weight of PCEs. Five types of PCEs with various ether to acid ratios (3:1 to 5:1) and functional groups were synthetized in laboratory conditions, and their molecular structures were characterized by size exclusion chromatography. PCE solutions with concentrations from 0 to 40% were measured using the Carr–Purcell–Meiboom–Gill sequence by 1H low-field NMR. The results showed that the T2 value of the main peak has a linear relation with the PCE concentration. The signal intensity of peaks whose T2 values are smaller than 10 ms of the PCE solutions with a concentration of 20% is linearly correlated to the molecule weight of PCEs. [ABSTRACT FROM AUTHOR]

The determination of an absolute configuration is a challenge in the structure elucidation of chiral natural products. With advancements in computational chemistry of chiroptical spectroscopy, the time-dependent density functional theory (TDDFT) calculation has emerged as a very promising tool. This paper attempts to illustrate the applicability of computational approaches in comparison with experimental data to understand the conformation, interaction, and stabilization of the loliolide's isomers. The quantum chemical calculations were used from optimized geometries of the (6R,7aS)-, (6S,7aR)-, (6R,7aR)-, and (6S,7aS)-6-hydroxy-4,4,7a-trimethyl-6,7-dihydro-5H-1-benzofuran-2-one. The spectroscopic values were obtained for 13C NMR isotropic shielding by GIAO method in mPW1PW91/cc-pVTZ level, in TDDFT at the ωB97X-D/cc-pVTZ level to the circular dichroism, and in theoretical analyses of non-covalent interaction to study the isomer's stability. The TDDFT calculation of circular dichroism can be used to quantify the individual isomers and the nature of excitation in the molecule. The (6R,7aS) and (6R,7aR) isomers present a higher stability due to electronegativity associated at the hydroxyl group. [ABSTRACT FROM AUTHOR]

It is frequently mentioned that QSARs have not generally lived up to expectations, especially in cases where high predictability is expected yet failed to deliver satisfactory results. Even though outliers can provide an increased opportunity in drug discovery research, outliers in SAR and QSAR can contort predictions and affect the accuracy if proper attention is not given. The percentages of outliers in QSARs have not changed appreciably over the last decade. In our previous studies, we suggested two possible sources of outliers in SAR and QSAR. In this paper, we suggest an additional possible source of outliers in QSAR. We presented several literature examples that show one or more water molecules that play a critical role in protein–ligand binding interactions as observed in their crystal structures. These examples illustrate that failing to account for the effects of water molecules in protein–ligand interactions could mislead interpretation and possibly yield outliers in SAR and QSAR. Examples include cases where QSAR, considering the role of water molecules in protein–ligand crystal structures, provided deeper insight into the understanding and interpretation of the developed QSAR. [ABSTRACT FROM AUTHOR]

We continue the study of the variable exponent Morreyfied Triebel–Lizorkin spaces introduced in a previous paper. Here we give characterizations by means of atoms and molecules. We also show that in some cases the number of zero moments needed for molecules, in order that an infinite linear combination of them (with coefficients in a natural sequence space) converges in the space of tempered distributions, is much smaller than what is usually required. We also establish a Sobolev type theorem for related sequence spaces, which might have independent interest. [ABSTRACT FROM AUTHOR]

Ion beam therapy is one of the most progressive methods in cancer treatment. Studies of the water radiolysis process show that the most long-living species that occur in the medium of a biological cell under the action of ionizing irradiation are hydrogen peroxide ( H 2 O 2 ) molecules. But the role of H 2 O 2 molecules in the DNA deactivation of cancer cells in ion beam therapy has not been determined yet. In the present paper, the competitive interaction of hydrogen peroxide and water molecules with atomic groups of non-specific DNA recognition sites (phosphate groups PO 4 ) is investigated. The interaction energies and optimized spatial configurations of the considered molecular complexes are calculated with the help of molecular mechanics method and quantum chemistry approach. The results show that the H 2 O 2 molecule can form a complex with the PO 4 group (with and without a sodium counterion) that is more energetically stable than the same complex with the water molecule. Formation of such complexes can block genetic information transfer processes in cancer cells and can be an important factor during ion beam therapy treatment. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

The present paper displays new supramolecular structural forms of ammonia molecules. The computation reveals that two novel threading structures of C2F2·(NH3)6 and C2F2·(NH3)12 can be assembled between difluoroethyne and ammonia molecules, in which cyclohexamer (NH3)6 and dicyclohexamer (NH3)12 are constructed by robust N–H···N hydrogen bonds and stabilized all by π–ring–hole···N bonds as supporting spokes of annular structures. More interestingly, annular structures of NH3 still maintain stability as C2F2 is removed. Additionally, the electronic properties and nature of the related noncovalent bonds are explored, which illuminate the important role of π–ring–hole bond for the stabilization of annular structures of NH3. This study could provide valuable insights into chemistry of ammonia, new energy and astronomy aspects by single or multiple noncovalent interactions. Graphical abstract [ABSTRACT FROM AUTHOR]

This paper investigates the potential use of carbon nanocones as selective filtration devices. Using a continuum approach and the Lennard-Jones potential, we determine the energy of truncated carbon nanocones interacting with ions (Na + and Cl - ) and water molecules. The Verlet algorithm is adopted to determine the dynamics of the ions and the water molecules as a result of the interaction with the nanocones. The acceptance energy is derived to determine the minimum and critical radii of the truncated nanocones that block the ions and allow only water molecules to pass through. Our results show that the channel with apex angle of 19. 2 ∘ and opening radius in the range 3.368–3.528 Å gives highest suction energy. [ABSTRACT FROM AUTHOR]

In this paper, the property of the muscle titin protein to form in vitro specific amyloid-like aggregates is discussed. The main difference from the known amyloid aggregates is the formation of a quaternary structure that resembles cross-β, with no changes in the secondary structure. Based on the results obtained earlier, as well as the results of this study, we make assumptions about changes in the structure of titin that occur during the formation of amyloid-like aggregates. In particular, our X-ray diffraction data on the titin aggregates suggest that β-strands in the aggregates of this protein are not located perpendicular to the fibril axis, as described for other amyloid proteins, but in parallel. The distance between the β-sheets in the aggregates may vary, and the β-sheets themselves are not strictly oriented along one of the axes, which can lead to the appearance of a diffuse ring reflection of ~8–12 Å. In this regard, the titin aggregates should not be called amyloid, but amyloid-like, with a quaternary structure that resembles cross-β. It cannot be excluded that the formation of this quaternary structure can also occur due to the partial unfolding of titin domains, followed by the interaction of open β-strands between neighboring domains and/or domains of neighboring molecules. [ABSTRACT FROM AUTHOR]

In this paper we introduce variable exponent local Hardy spaces h L p (·) (R n) associated with a non-negative self-adjoint operator L. We assume that, for every t > 0 , the operator e - t L has an integral representation whose kernel satisfies a Gaussian upper bound. We define h L p (·) (R n) by using an area square integral involving the semigroup { e - t L } t > 0 . A molecular characterization of h L p (·) (R n) is established. As an application of the molecular characterization, we prove that h L p (·) (R n) coincides with the (global) Hardy space H L p (·) (R n) provided that 0 does not belong to the spectrum of L. Also, we show that h L p (·) (R n) = H L + I p (·) (R n) . [ABSTRACT FROM AUTHOR]

Although Hückel molecular orbital theory (HMO) has been generally outdated as a computational method for the energetics of organic molecules, there is still much we can learn from it. This paper explores two compounds, 1,4-divinylbenzene and 2-phenylbutadiene, which, according to Hückel theory, are isospectral, i.e., they have the same eigenvalues and orbital energy levels. However, by using a small, well-defined perturbation, we show it is mathematically possible to distinguish between these two compounds. We suggest that this is a general procedure for distinguishing isospectral pairs of molecules as opposed to the two species being identical. [ABSTRACT FROM AUTHOR]

The paper describes the preparation of a new salt spiropyran of indoline series containing vinyl-3H-indolium fragment in the 8' position of the 2H-chromene moiety and a chlorine atom in the benzene ring of the indoline fragment. The structure of the reaction product was studied by IR, 1H, and 13C NMR spectroscopy. The data of X-ray diffraction study indicate that the reaction leads to the partial exchange of the indoline hetarene fragment to provide previously described salt spiropyran containing no chlorine atom in the indoline portion of the molecule. [ABSTRACT FROM AUTHOR]