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Ytterbium monohydroxide is a promising molecule in the search for new physics. It is well known that levels of opposite parity, separated by energy split, the so-called l-doublets, define the experimental electric field strength required for molecule polarization. In addition, in our previous paper [Phys. Rev. A 105, L050801 (2022)], we have shown that the value of l-doubling directly influences the sensitivity of linear triatomic molecules toward the P , T -odd effects. In our work [J. Chem. Phys. 155, 164301 (2021)], we have calculated the value of l-doubling for YbOH molecules with the approximation of fixed O–H bond length. Taking the importance of this property into account, in the present study, we consider the additional degree of freedom corresponding to ligand (OH) deformation. [ABSTRACT FROM AUTHOR]

At the 2006 IEEE International Conference on Systems of Systems Engineering, Boardman and Sauser presented a set of characteristics based on an integrative review of the literature. These characteristics are the foundation of the Boardman–Sauser system of systems (SoS) theory. We accept this theory as the basis of collaborative SoS and desire a means to validate this assertion. While numerous simulations have been published, the target SoS is usually a specific implementation. These specialized simulations produce results applicable primarily to the system under study but not necessarily SoS in general. Simulating the mathematical model of the Boardman–Sauser SoS theory in the form of an agent-based model produces results that can be compared with chemical reactions. This paper contends that the formation of molecules from atoms is an analog of systems forming any collaborative SoS, which we call our molecule organization model. The result is a supported logical argument that validates the Boardman–Sauser SoS theory as definitive of a generic SoS with behavior applicable to collaborative SoS. This paper seeks to provide a unique contribution to the SoS body of knowledge by increasing our understanding of collaboration in an SoS, so we may better understand their health, maintenance, replication, and evolution. [ABSTRACT FROM PUBLISHER]

Background: Molecular biology is crucial for drug discovery, protein design, and human health. Due to the vastness of the drug-like chemical space, depending on biomedical experts to manually design molecules is exceedingly expensive. Utilizing generative methods with deep learning technology offers an effective approach to streamline the search space for molecular design and save costs. This paper introduces a novel E(3)-equivariant score-based diffusion framework for 3D molecular generation via SDEs, aiming to address the constraints of unified Gaussian diffusion methods. Within the proposed framework EMDS, the complete diffusion is decomposed into separate diffusion processes for distinct components of the molecular feature space, while the modeling processes also capture the complex dependency among these components. Moreover, angle and torsion angle information is integrated into the networks to enhance the modeling of atom coordinates and utilize spatial information more effectively. Results: Experiments on the widely utilized QM9 dataset demonstrate that our proposed framework significantly outperforms the state-of-the-art methods in all evaluation metrics for 3D molecular generation. Additionally, ablation experiments are conducted to highlight the contribution of key components in our framework, demonstrating the effectiveness of the proposed framework and the performance improvements of incorporating angle and torsion angle information for molecular generation. Finally, the comparative results of distribution show that our method is highly effective in generating molecules that closely resemble the actual scenario. Conclusion: Through the experiments and comparative results, our framework clearly outperforms previous 3D molecular generation methods, exhibiting significantly better capacity for modeling chemically realistic molecules. The excellent performance of EMDS in 3D molecular generation brings novel and encouraging opportunities for tackling challenging biomedical molecule and protein scenarios. [ABSTRACT FROM AUTHOR]

Oil-immersed power transformers generate characteristic gases after failure,Therefore, it is necessary to analyse and monitor the soluble gases in transformer oil samples. In this study, the DFT calculation method was used to study the adsorption properties of H2, CO, C2H2, and C2H4 gases in oil on both intrinsic MoTe2 and Rh-doped MoTe2 films. In order to analyse the adsorption characteristics, this paper first obtains the most stable Rh-doped MoTe2 monolayer model through the modelling and computational analysis of different doping sites, then, the adsorption of these gases on the material surface is studied by analysing adsorption energy, charge transfer, total state density, parting density, energy band structure, differential charge density map, molecular front orbital and desorption time, and finally concludes that Rh-MoTe2 monolayer film is the ideal material for hydrogen sensing elements, due to the extremely long desorption time of CO gas, indicating that CO gas is hard to desorption on the surface of adsorbent,which shows that this process has played a certain role in promoting CO removal. Highlights Study focused on gas adsorption using DFT: Rh-MoTe2 ideal for hydrogen sensing and effective for CO removal, intrinsic MoTe2 ineffective and required metal doping. Rh doping enhanced conductivity and gas adsorption capacity in MoTe2. Rh-MoTe2 was suitable for detecting H2, C2H2, and C2H4 gases. Desorption times vary with temperature, with CO removal particularly effective at higher temperatures. Findings suggest potential applications for Rh-MoTe2 in gas sensing and removal. [ABSTRACT FROM AUTHOR]

Quinones are valuable structural motifs found in numerous natural products and pharmaceuticals. In particular, p-benzoquinones are of great interest because of their ready availability and versatile reactivity. They can serve as good Michael acceptors and participate in many cycloaddition, nucleophilic addition and multicomponent reactions. However, the construction of polycyclic architectures with increased stereochemical features is another perspective of quinone chemistry. The present review summarizes the recent advances (2018–2023) in stereoselective annulation involving p-benzoquinones for the construction of fused, spiro and bridged/cage frameworks. In this regard, different types of annulations, such as [3+2], [3+3], [3+2+1], [4+2] and [2+2], are discussed for accessing diverse fused heterocycles in a stereoselective manner. Some novel annulation methods are reviewed for building spiro heterocycles and cage molecules. Most of the reactions described in this review are simple, providing quick formation of the desired products with high stereoselectivity. In this regard, typical reaction mechanisms are presented to understand how quinoidal scaffolds show variable reactivity towards reaction partners. [ABSTRACT FROM AUTHOR]

Recently, increasing attention of researchers in the field of membrane technology has been paid to the development of membranes based on biopolymers. One of the well-proven polymers for the development of porous membranes is cellulose acetate (CA). This paper is devoted to the study of the influence of different parameters on ultrafiltration CA membrane formation and their transport properties, such as the variation in coagulation bath temperature, membrane shrinkage (post-treatment at 80 °C), introduction to casting CA solution of polymers (polyethylene glycol (PEG), polysulfone (PS), and Pluronic F127 (PL)) and carbon nanoparticles (SWCNTs, MWCNTs, GO, and C60). The structural and physicochemical properties of developed membranes were studied by scanning electron and atomic force microscopies, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, and contact angle measurements. The transport properties of developed CA-based membranes were evaluated in ultrafiltration of bovine serum albumin (BSA), dextran 110 and PVP K-90. All developed membranes rejected 90% compounds with a molecular weight from ~270,000 g/mol. It was shown that the combination of modifications (addition of PEG, PS, PL, PS-PL, and 0.5 wt% C60) led to an increase in the fluxes and BSA rejection coefficients with slight decrease in the flux recovery ratio. These changes were due to an increased macrovoid number, formation of a more open porous structure and/or thinner top selective, and decreased surface roughness and hydrophobization during C60 modification of blend membranes. Optimal transport properties were found for CA-PEG+C60 (the highest water—394 L/(m2h) and BSA—212 L/(m2h) fluxes) and CA-PS+C60 (maximal rejection coefficient of BSA—59%) membranes. [ABSTRACT FROM AUTHOR]

Recently, we have demonstrated a method to record the longitudinal phase-space distribution of a pulsed cryogenic buffer gas cooled beam of barium fluoride molecules with high resolution. In this paper, we use this method to determine the influence of various source parameters. Besides the expected dependence on temperature and pressure, the forward velocity of the molecules is strongly correlated with the time they exit the cell, revealing the dynamics of the gas inside the cell. Three observations are particularly noteworthy: (1) The velocity of the barium fluoride molecules increases rapidly as a function of time, reaches a maximum 50–200 µ s after the ablation pulse and then decreases exponentially. We attribute this to the buffer gas being heated up by the plume of hot atoms released from the target by the ablation pulse and subsequently being cooled down via conduction to the cell walls. (2) The time constant associated with the exponentially decreasing temperature increases when the source is used for a longer period of time, which we attribute to the formation of a layer of isolating dust on the walls of the cell. By thoroughly cleaning the cell, the time constant is reset to its initial value. (3) The velocity of the molecules at the trailing end of the molecular pulse depends on the length of the cell. For short cells, the velocity is significantly higher than expected from the sudden freeze model. We attribute this to the target remaining warm over the duration of the molecular pulse giving rise to a temperature gradient within the cell. Our observations will help to optimize the source parameters for producing the most intense molecular beam at the target velocity. [ABSTRACT FROM AUTHOR]

The Wiener index is one of the most classic and widely used indicators in topology. It reflects the average distance of any node pair in the graph. It not only makes the boundaries of given graphs clearer but also continuously generates topological indices that are more suitable for new fields, such as the Gutman index. The Wiener index and Gutman index are two important topological indices, which are commonly used to describe the characteristics of molecular structure. They are closely related to the physical and chemical properties of molecular compounds. And they are widely used to predict the physical and chemical properties and biological activity of molecular compounds. In this paper, we study the vertex Gutman index and Gutman index and describe the structural characteristics of all cases of two simple cycles intersecting. We comprehensively analyze the Gutman index and vertex Gutman index in these cases in detail by means of classification discussion and analogical reasoning and characterize their maximum and minimum accordingly. [ABSTRACT FROM AUTHOR]

Revealing the interaction mechanisms between anticancer drugs and target DNA molecules at the single-molecule level is a hot research topic in the interdisciplinary fields of biophysical chemistry and pharmaceutical engineering. When fluorescence imaging technology is employed to carry out this kind of research, a knotty problem due to fluorescent dye molecules and drug molecules acting on a DNA molecule simultaneously is encountered. In this paper, based on self-made novel solid active substrates NpAA/(ZnO-ZnCl2)/AuNPs, we use a surface-enhanced Raman spectroscopy method, inverted fluorescence microscope technology, and a molecular docking method to investigate the action of the fluorescent dye YOYO-1 and the drug DOX on calf thymus DNA (ctDNA) molecules and the influencing effects and competitive relationships of YOYO-1 on the binding properties of the ctDNA-DOX complex. The interaction sites and modes of action between the YOYO-1 and the ctDNA-DOX complex are systematically examined, and the DOX with the ctDNA-YOYO-1 are compared, and the impact of YOYO-1 on the stability of the ctDNA-DOX complex and the competitive mechanism between DOX and YOYO-1 acting with DNA molecules are elucidated. This study has helpful experimental guidance and a theoretical foundation to expound the mechanism of interaction between drugs and biomolecules at the single-molecule level. [ABSTRACT FROM AUTHOR]

Carbon nanotubes filled with organic molecules can serve as chemical nanoreactors. Recent experimental results show that, by introducing cyclic hydrocarbon molecules inside carbon nanotubes, they can be transformed into nanoribbons or inner tubes, depending on the experimental conditions. In this paper, we present our results obtained as a continuation of our previous molecular dynamics simulation work. In our previous work, the initial geometry consisted of independent carbon atoms. Now, as an initial condition, we have placed different molecules inside a carbon nanotube (18,0): C5H5 (fragment of ferrocene), C5, C5+H2; C6H6 (benzene), C6, C6+H2; C20H12 (perylene); and C24H12 (coronene). The simulations were performed using the REBO-II potential of the LAMMPS software package, supplemented with a Lennard-Jones potential between the nanotube wall atoms and the inner atoms. The simulation proved difficult due to the slow dynamics of the H abstraction. However, with a slight modification of the parameterization, it was possible to model the formation of carbon nanoribbons inside the carbon nanotube. [ABSTRACT FROM AUTHOR]

Many industrial processes, several natural processes involving non-living matter, and all the processes occurring within living organisms take place in solution. This means that the molecules playing active roles in the processes are present within another medium, called solvent. The solute molecules are surrounded by solvent molecules and interact with them. Understanding the nature and strength of these interactions, and the way in which they modify the properties of the solute molecules, is important for a better understanding of the chemical processes occurring in solution, including possible roles of the solvent in those processes. Computational studies can provide a wealth of information on solute–solvent interactions and their effects. Two major models have been developed to this purpose: a model viewing the solvent as a polarisable continuum surrounding the solute molecule, and a model considering a certain number of explicit solvent molecules around a solute molecule. Each of them has its advantages and challenges, and one selects the model that is more suitable for the type of information desired for the specific system under consideration. These studies are important in many areas of chemistry research, from the investigation of the processes occurring within a living organism to drug design and to the design of environmentally benign solvents meant to replace less benign ones in the chemical industry, as envisaged by the green chemistry principles. The paper presents a quick overview of the modelling approaches and an overview of concrete studies, with reference to selected crucial investigation themes. [ABSTRACT FROM AUTHOR]

This correction notice addresses inaccuracies in an article about two products used in the animal breeding industry in China. The names of the products and a picture were incorrectly used, and the term "impurity" should be replaced with "trace components." The correction provides the accurate names of the products and clarifies their use as safe and effective Chinese veterinary medicine. Additionally, errors in figures and sample preparation information are corrected. The scientific conclusions of the article remain unaffected by these changes. [Extracted from the article]

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]

Let G be a graph and R = {r1, r2, ..., rk} be an ordered subset of vertices of G, if every two vertices of G have different representation r (v|R) = (d (v, r1) , d (v, r2) , ..., d (v, rk)) with respect to R, then R is said to be a metric-based resolving parameter or resolving set of G and its minimum cardinality is called the metric dimension of graph G. Metric dimension is considered as an important applied concept of graph theory especially in the localization of a network and also in the chemical graph theoretical study of molecular compounds. Therefore, it is hot topic to study for different families of graphs as well. Convex polytopes play an important role both in various branches of mathematics and in applied areas, most notably in linear programming. In this paper, we determine the metric-based resolving parameter of line graph of a convex polytope Sn, and conclude that it has constant metric dimension but vary with the parity of n. This article presents a measurement of the line graph of a convex polytope, denoted as ( S n). The subsequent section provides the metric dimension of the resulting graph. There are two scenarios pertaining to the metric dimension of a selected graph with respect to the metric dimension. The metric dimension of even cycle-based convex polytopes is three, whereas for other values, the metric dimension is four. [ABSTRACT FROM AUTHOR]

The natural product Desmosdumotin D (hereafter referred to as Des-D), isolated from the plant Desmos dumosus, showed potent anti-HIV activity. However, the subsequent pharmacological activity and clinical studies are limited due to the low content of Des-D in the plant. Therefore, the total synthesis path of Des-D was optimized in this paper, and the total yield was increased from 4.4% to 11.9%. Additionally, twelve analogues were obtained following the synthesis route of Des-D. The anti-HIV activity evaluation results in vitro showed that Des-D had the highest activity, with an IC50 value of 13.6 μM, and compounds 17 and 11 had the lowest anti-HIV activity, with IC50 values of 101.3 μM and 161.0 μM, respectively. Through the molecular docking of compounds Des-D and 17 with HIV-IN, the results show that phenolic hydroxyl groups and two benzene rings interact with HIV-IN and are possible pharmacodynamic groups. [ABSTRACT FROM AUTHOR]

Context. The G31.41+0.31 Unbiased ALMA sPectral Observational Survey (GUAPOS) project targets the hot molecular core (HMC) G31.41+0.31 (G31) to reveal the complex chemistry of one of the most chemically rich high-mass star-forming regions outside the Galactic center (GC). Aims. In the third paper of the project we present a study of nine O-bearing (CH3OH, 13CH3OH, CH318OH , CH3CHO, CH3OCH3, CH3COCH3, C2H5OH, aGg′-(CH2OH)2, and gGg′-(CH2OH)2) and six N-bearing (CH3CN,13CH3CN, CH313CN, C2H3CN, C2H5CN, and C2H513CN) complex organic molecules toward G31. The aim of this work is to characterize the abundances in G31 and to compare them with the values estimated in other sources. Moreover, we searched for a possible chemical segregation between O-bearing and N-bearing species in G31, which hosts four compact sources as seen with higher angular resolution data. In the discussion we also include the three isomers of C2H4O2 and the O- and N-bearing molecular species NH2CHO, CH3NCO, CH3C(O)CH2, and CH3NHCHO, which were analyzed in previous GUAPOS papers. Methods. Observations were carried out with the interferometer ALMA and cover the entire Band 3 from 84 to 116 GHz (~32 GHz bandwidth) with an angular resolution of 1.2″ × 1.2″ (~4400 au × 4400 au) and a spectral resolution of ~0.488 MHz (~1.3–1.7 km s−1). The transitions of the 14 molecular species were analyzed with the tool SLIM of MADCUBA to determine the physical parameters of the emitting gas. Moreover, we analyzed the morphology of the emission of the molecular species. Results. The values of abundances with respect to H2 in G31 range from 10−6 to 10−10 for the different species. We compared the abundances with respect to methanol of O-bearing, N-bearing, and O- and N-bearing COMs in G31 with 27 other sources, including other hot molecular cores inside and outside the GC, hot corinos, shocked regions, envelopes around young stellar objects, and quiescent molecular clouds, and with chemical models. Conclusions. From the comparison with other sources there is not a unique template for the abundances in hot molecular cores, pointing toward the importance of the thermal history for the chemistry of the various sources. The abundances derived from the chemical models are in good agreement, within a factor of 10, with those of G31. From the analysis of the maps we derived the peak positions of all the molecular species toward G31. Different species peak at slightly different positions, and this, together with the different central velocities of the lines obtained from the spectral fitting, point to chemical differentiation of selected O-bearing species. [ABSTRACT FROM AUTHOR]

In this paper, a series of coordination polymers, {[Zn(adb)(L1)2]·solvent}n (L1 = solvent = N,N-dimethylacetamide, Hui-3-DMA; L1 = N,N-dimethylformamide and no solvent, Hui-3-DMF; L1 = N,N-diethylformamide and no solvent, Hui-3-DEF) have been synthesized by hydrothermal reactions of Zn(NO3)3·6H2O and 4,4′-(anthracene-9,10-diyl)dibenzoic acid (H2adb). These compounds show similar one-dimensional (1D) zig-zag chain structures, which are limited by the end-coordination of the solvent molecules. Interestingly, these compounds all show blue-emission properties, which could be easily modulated by using different solvents. Among them, Hui-3-DMA presents an excellent quantum yield performance, as high as to 54.1%, which is very promising for blue-emission materials. Moreover, various-temperature fluorescence studies reveal good linear or exponential decline trends for their emission intensity as temperature increases, demonstrating the potential of these compounds as fluorescent thermometers. [ABSTRACT FROM AUTHOR]

The article discusses the debate surrounding the mechanism of sum frequency generation (SFG) signals emitted by liquid benzene. The authors argue that the main signal comes from local modes generated by symmetry breaking, while another paper challenges this view and suggests that the dominant mechanism is the interfacial electric quadrupole. The authors refute this argument, stating that their previous paper considered both symmetry breaking and the electric quadrupole in their calculations, while the opposing paper did not properly examine the effect of symmetry breaking. The authors present evidence of symmetry breaking through computational evaluations and the reversal of symmetry breaking at the silica-benzene interface. They recommend that the opposing authors consider these evidences before drawing their conclusion. [Extracted from the article]

Stimulated Raman Adiabatic Passage (STIRAP) and its variants, such as M-type chainwise-STIRAP, allow for efficiently transferring the populations in a multilevel system and have widely been used to prepare molecules in their rovibrational ground state. However, their transfer efficiencies are generally imperfect. The main obstacle is the presence of losses and the requirement to make the dynamics adiabatic. To this end, in the present paper, a new theoretical method is proposed for the efficient and robust creation and detection of deeply bound molecules in three-level Λ-type and five-level M-type systems via "Invariant-based shortcut-to-adiabaticity." In the regime of large detunings, we first reduce the dynamics of three- and five-level molecular systems to those of effective two- and three-level counterparts. By doing so, the major molecular losses from the excited states can be well suppressed. Consequently, the effective two-level counterpart can be directly compatible with two different "Invariant-based Inverse Engineering" protocols; the results show that both protocols give a comparable performance and have a good experimental feasibility. For the effective three-level counterpart, by considering a relation among the four incident pulses, we show that this model can be further generalized to an effective Λ-type one with the simplest resonant coupling. This generalized model permits us to borrow the "Invariant-based Inverse Engineering" protocol from a standard three-level Λ-type system to a five-level M-type system. Numerical calculations show that the weakly bound molecules can be efficiently transferred to their deeply bound states without strong laser pulses, and the stability against parameter variations is well preserved. Finally, the detection of ultracold deeply bound molecules is discussed. [ABSTRACT FROM AUTHOR]

This paper demonstrates the performance of our previously suggested property-energy consistent method on the example of the generation of effective basis sets, pecS-1 and pecS-2, suited for the calculation of hydrogen, carbon, nitrogen, and oxygen chemical shifts. The new basis sets were successfully approbated in the GIAO-DFT calculations of the chemical shifts of 35 molecules using six different functionals. The pecS-1 basis set demonstrated very good accuracy, which makes this small basis set an effective means for the large-scale computations. At the same time, the pecS-2 basis set also gave very accurate results, thus putting it on a par with the other commensurate basis sets suited for the chemical shifts calculations. [ABSTRACT FROM AUTHOR]

Systems biology analysis of intracellular signaling networks has tremendously expanded our understanding of normal and diseased cell behaviors and has revealed paths to finding proper therapeutic molecular targets. When it comes to neurons in the human brain, analysis of intraneuronal signaling networks provides invaluable information on learning, memory and cognition-related disorders, as well as potential therapeutic targets. However, neurons in the human brain form a highly complex neural network that, among its many roles, is also responsible for learning, memory formation and cognition. Given the impairment of these processes in mental and psychiatric disorders, one can envision that analyzing interneuronal processes, together with analyzing intraneuronal signaling networks, can result in a better understanding of the pathology and, subsequently, more effective target discovery. In this paper, a hybrid model is introduced, composed of the long-term potentiation (LTP) interneuronal process and an intraneuronal signaling network regulating CREB. LTP refers to an increased synaptic strength over a long period of time among neurons, typically induced upon occurring an activity that generates high-frequency stimulations (HFS) in the brain, and CREB is a transcription factor known to be highly involved in important functions of the cognitive and executive human brain such as learning and memory. The hybrid LTP-signaling model is analyzed using a proposed molecular fault diagnosis method. It allows to study the importance of various signaling molecules according to how much they affect an intercellular phenomenon when they are faulty, i.e. dysfunctional. This paper is intended to suggest another angle for understanding the pathology and therapeutic target discovery by classifying and ranking various intraneuronal signaling molecules based on how much their faulty behaviors affect an interneuronal process. Possible relations between the introduced hybrid analysis and the previous purely intracellular analysis are investigated in the paper as well. [ABSTRACT FROM AUTHOR]

The theory of adiabatic electron transport in a correlated condensed-matter system is rooted in a seminal paper by Niu and Thouless [J. Phys. A: Math. Gen. 17, 2453 (1984)]; I adopt here an analogous logic in order to retrieve the known expression for the adiabatic electronic flux in a molecular system [L. A. Nafie, J. Chem. Phys. 79, 4950 (1983)]. Its derivation here is considerably simpler than those available in the current quantum-chemistry literature; it also explicitly identifies the adiabaticity parameter, in terms of which the adiabatic flux and the electron density are both exact to first order. It is shown that the continuity equation is conserved to the same order. For the sake of completeness, I also briefly outline the relevance of the macroscopic electronic flux to the physics of solids and liquids. [ABSTRACT FROM AUTHOR]

Calcite is widely used in many fields. The synthesis of calcite is strongly influenced by solvents and additives. In this paper, the adsorption of water and formic acid molecules on the (104) surface of calcite was systematically studied on the atomic scale using the density functional theory (DFT) method. The results show that both molecules can be adsorbed on the calcite surface by occupying the top position of Ca. The results of differential charge density and the projected crystal orbital Hamiltonian population show that the adsorption is controlled by the charge transfer from the oxygen atom to the surface calcium. Formic acid has a carbonyl oxygen and it plays a greater role in stabilizing the surface than water. Moreover, the adsorption of two molecules can be further stabilized by hydrogen bonds formed between the hydrogen atom in the adsorbed molecules and the oxygen in calcite. This work provides a clear understanding of the stabilization of the calcite surface by adsorbing different molecules and also provides the possibility of tuning the synthesis of calcite by choosing a suitable solvent and additives. [ABSTRACT FROM AUTHOR]

Watson-Crick automata are belonging to the natural computing paradigm as these finite automata are working on strings representing DNA molecules. Watson-Crick automata have two reading heads, and in the 5' → 3' models these two heads start from the two extremes of the input. This is well motivated by the fact that DNA strands have 5' and 3' ends based on the fact which carbon atoms of the sugar group is used in the covalent bonds to continue the strand. However, in the two stranded DNA, the directions of the strands are opposite, so that, if an enzyme would read the strand it may read each strand in its 5' to 3' direction, which means physically opposite directions starting from the two extremes of the molecule. On the other hand, enzymes may not have inner states, thus those Watson-Crick automata which are stateless (i.e. have exactly one state) are more realistic from this point of view. In this paper these stateless 5' → 3' Watson-Crick automata are studied and some properties of the language classes accepted by their variants are proven. We show hierarchy results, and also a "pumping", i.e., iteration result for these languages that can be used to prove that some languages may not be in the class accepted by the class of stateless 5' → 3' Watson-Crick automata. [ABSTRACT FROM AUTHOR]

Organic molecular composition of marine aerosol samples collected during the MALINA cruise in the Arctic Ocean was investigated by gas chromatography/mass spectrometry. More than 110 individual organic compounds were determined in the samples and were grouped into different compound classes based on the functionality and sources. The concentrations of total quantified organics ranged from 7.3 to 185 ngm-3 (mean 47.6 ngm-3), accounting for 1.8-11.0% (4.8%) of organic carbon in the marine aerosols. Primary saccharides were found to be dominant organic compound class, followed by secondary organic aerosol (SOA) tracers formed from the oxidation of biogenic volatile organic compounds (VOCs) such as isoprene, α-pinene and β-caryophyllene. Mannitol, the specific tracer for airborne fungal spores, was detected as the most abundant organic species in the samples with a concentration range of 0.052-53.3 ngm-3(9.2 ngm-3), followed by glucose, arabitol, and the isoprene oxidation products of 2-methyltetrols. Biomass burning tracers such as levoglucosan are evident in all samples with trace levels. On the basis of the tracer-based method for the estimation of fungal-spore OC and biogenic secondary organic carbon (SOC), we estimate that an average of 10.7%(up to 26.2%) of the OC in the marine aerosols was due to the contribution of fungal spores, followed by the contribution of isoprene SOC (mean 3.8%) and α-pinene SOC (2.9%). In contrast, only 0.19% of the OC was due to the photooxidation of β-caryophyllene. This study indicates that primary organic aerosols from biogenic emissions, both from long-range transport of mid-latitude aerosols and from sea-to-air emission of marine organics, as well as secondary organic aerosols formed from the photooxidation of biogenic VOCs are important factors controlling the organic chemical composition of marine aerosols in the Arctic Ocean. [ABSTRACT FROM AUTHOR]

The article presents a study on the principles of water absorption and desorption in cellulosic materials. It discusses the attributes of water which focuses on its physical interaction forces that operate between water molecules and other materials. It highlights selected scientific principles of water interactions relevant to water damage focusing on water absorption of cellulose and the mechanisms and side effects of drying strategies for cellulosic materials.

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]

Physical and chemical properties of plasma-polymerized SiOCH films were investigated using ring-type siloxane monomers with several kinds of side-chain chemicals, and a design principle of the material and plasma-process was derived to obtain a porous SiOCH film of k < 2.5 with sub-nanometer-scaled porous structure framed by the original ring siloxane backbone. Here, the backbone siloxane structure is fixed as a six-membered Si-O ring of the 0.35 nmΦ, and no progen gas and no post-cure-process were utilized. It was found that unsaturated hydrocarbon side chains such as vinyl increase the deposition rate, and the original monomer structure tends to be kept, reducing the dielectric constant with the porous structure. Large alkyl groups increase the hydrocarbon content in the film as well as the deposition rate. The low radio-frequency power plasma with high precursor concentration also helps the original chemical structure to be preserved. The best solution is to use the ring-type siloxane with both of the vinyl (unsaturated hydrocarbon) and the large alkyl (saturated hydrocarbon) under the low-power plasma condition with the high partial pressure of the precursor. The plasma-polymerized porous SiOCH film is a strong candidate for the low-k film in scale-down 45/32 nm node ultralarge-scaled integrated interconnects featured by the simple and low-cost fabrication processes. [ABSTRACT FROM AUTHOR]

Theoretical analysis and computer simulations (Monte Carlo and numerical integration of differential equations) indicate that the statistical effect of a small number of reacting molecules is affected by transfer of reagent molecules between nanoreactors (droplets in this study). As a model reaction, a simple reversible association A + B ⇆ C was chosen, which was studied previously without reagent transfer processes. For sufficiently fast exchange of reactant molecules and a sufficiently high number of nanoreactors, the studied systems virtually do not differ from large volume systems if overall kinetics and thermodynamics of the chemical process are concerned. However, if either reagent molecule exchange is not fast or the number of exchanging nanoreactors is low, then the stochastic effect is clearly visible, influencing the kinetics of reaching reaction equilibrium. In systems with a low number of nanoreactors, the apparent (average) equilibrium constant is affected as well. The distribution of reactant molecules in the nanoreactors is governed by stochastic processes, dependent on stochastic rate constants of all processes, chemical as well as physical (transfer of molecules outside and into droplets). When accumulation of reactant molecules in the continuous phase cannot be neglected, then the partition coefficients of reactants between the continuous and dispersed phases have to be taken into account. Distributions of reactant molecules described in the paper for systems composed of few nanoreactors can be especially important for some biochemical processes in living cells or devised corresponding artificial reactors. If the reactant molecules predominate in a continuous phase, then the kinetics and overall conversion of reversible association may be significantly affected by the presence of the dispersed phase and its catalytic behavior can be observed. It has been shown that Monte Carlo simulations, applying a devised simple algorithm, give reliable results, allowing theoretical studies of nanoscale-droplet systems. [ABSTRACT FROM AUTHOR]

The article comments on an article which deals with the behavior of cellulose molecules in aqueous environments, by researchers Fumio Tanaka and Noriko Fukui, published in the March 2004 issue of the journal "Cellulose." The said article presents molecular dynamics simulations of five cellulose chains, each with 30 glucose units, in both aqueous and non-aqueous environments. Tanaka and Fukui focus instead on the properties of the individual chains and their evolving interactions. Then, they comment on some long-time controversies, including chain-folding, the strain caused by taking a two-fold screw axis conformation and the forces responsible for the solid state structures.

The variational approach detailed in the previous paper (Paper I) for the treatment of the Renner–Teller effect in linear tetra-atomic molecules including all degrees of freedom and couplings between angular momenta is applied for HCCH+. The accurate six-dimensional potential energy surfaces of the X 2Πu electronic state, presented in Paper I is incorporated in the variational treatment in order to obtain all rovibronic levels including the spin-orbit coupling for 1/2≤J≤7/2 and up to 2600 cm-1 above the global zero point energy. The “pure” stretching levels are calculated up to 11 000 cm-1 from the stretching zero point energy. The calculated rovibronic energies are compared with previous theoretical and experimental data. The mean agreement with the zero kinetic energy photoelectron measurements of Tang et al. [J. Chem. Phys. 125, 133201 (2006)] is of 16.7 cm-1. The Renner–Teller parameters have been determined at νtrans=690.0 cm-1, εtrans=0.30, νcis=715.0 cm-1, and εcis=-0.063. A detailed analysis of the rovibronic Hund’s cases is presented and the rotational structures of some vibronic bands recorded by Yang and Mo [J. Phys. Chem. A 110, 11001 (2006)] are given. [ABSTRACT FROM AUTHOR]

This paper presents new results for the modeling of isolated line shapes from the Doppler to the collisional regime, thus including the effects of confinement (Dicke narrowing) and of the speed dependence of collisional parameters. They are obtained within a classical description of the time evolution of the autocorrelation function of the optical transition moment, combined with the use of the Keilson and Storer model for the changes in the radiator translational velocity. A purely numerical solution to the subsequent differential equations, which uses discretized grids for the radiating-molecule velocity vector, is first described. An alternative approach, using projections onto generalized Laguerre polynomials (for the velocity modulus) and spherical harmonics (for the velocity orientation), is also presented. A first test of these approaches is made in the particular case of the Q(1) Raman line of the fundamental band of pure H2 at room temperature (others will be presented in paper II). It is shown that the two models lead to exactly the same results, as expected, and to satisfactory agreement with measured values of the linewidth at various densities. [ABSTRACT FROM AUTHOR]

Previous work testing density functionals for use in calculating high-spin–low-spin energy differences, ΔEHL, for iron(II) spin-crossover transitions has tended to conclude that only properly reparametrized hybrid functionals can predict ΔEHL since it seems to depend critically on a correct description of the electron pairing energy governed by the exchange term. Exceptions to this rule are the previous three papers (I, II, and III in the present series of papers) where it was found that modern generalized gradient approximations (GGAs) and meta-GGAs could do as well as hybrid functionals, if not better, for this type of problem. In the present paper, we extend these previous studies to five more molecules which are too large to treat with high-quality ab initio calculations, namely, the series [Fe(L)(‘NHS4’)], where NHS4=2.2′-bis(2-mercaptophenylthio)diethylamine dianion, and L=NH3, N2H4, PMe3, CO, and NO+. Since we know of no reliable experimental estimate of ΔEHL, we content ourselves with a comparison against the experimentally determined ground-state spin symmetry including, in so far as possible, finite-temperature effects. Together with the results of Papers I, II, and III, this paper provides a test of a large number of functionals against the high-spin/low-spin properties of a diverse set of Fe(II) compounds, making it possible to draw some particulary interesting conclusions. Trends among different classes of functionals are discussed and it is pointed out that there is at least one functional, namely, the OLYP generalized gradient approximation, which is able to give a reasonably good description of the delicate spin energetics of Fe(II) coordination compounds without resorting to hybrid functionals which require the relatively more expensive calculation of a Hartree–Fock-type exchange term. [ABSTRACT FROM AUTHOR]

The Dirac–Coulomb equation with positive-energy projection is solved using explicitly correlated Gaussian functions. The algorithm and computational procedure aims for a parts-per-billion convergence of the energy to provide a starting point for further comparison and further developments in relation with high-resolution atomic and molecular spectroscopy. Besides a detailed discussion of the implementation of the fundamental spinor structure, permutation, and point-group symmetries, various options for the positive-energy projection procedure are presented. The no-pair Dirac–Coulomb energy converged to a parts-per-billion precision is compared with perturbative results for atomic and molecular systems with small nuclear charge numbers. Paper II [D. Ferenc, P. Jeszenszki, and E. Mátyus, J. Chem. Phys. 156, 084110 (2022).] describes the implementation of the Breit interaction in this framework. [ABSTRACT FROM AUTHOR]