Temperature and entropy in molecular system

The irreversibility, temperature, and entropy are identified for an atomic system of solid material. Thermodynamics second law is automatically satisfied in the time evolution of molecular dynamics (MD). The irreversibility caused by an atom spontaneously moves from a non-stable equilibrium position to a stable equilibrium position. The process is dynamic in nature associated with the conversion of potential energy to kinetic energy and the dissipation of kinetic energy to the entire system. The forward process is less sensitive to small variation of boundary condition than reverse process, causing the time symmetry to break. Different methods to define temperature in molecular system are revisited with paradox examples. It is seen that the temperature can only be rigorously defined on an atom knowing its time history of velocity vector. The velocity vector of an atom is the summation of the mechanical part and the thermal part, the mechanical velocity is related to the global motion (translation, rotation, acceleration, vibration, etc.), the thermal velocity is related to temperature and is assumed to follow the identical random Gaussian distribution for all of its [Formula: see text], [Formula: see text] and [Formula: see text] component. The [Formula: see text]-velocity (same for [Formula: see text] or [Formula: see text]) versus time obtained from MD simulation is treated as a signal (mechanical motion) corrupted with random Gaussian distribution noise (thermal motion). The noise is separated from signal with wavelet filter and used as the randomness measurement. The temperature is thus defined as the variance of the thermal velocity multiply the atom mass and divided by Boltzmann constant. The new definition is equivalent to the Nose–Hover thermostat for a stationary system. For system with macroscopic acceleration, rotation, vibration, etc., the new definition can predict the same temperature as the stationary system, while Nose–Hover thermostat predicts a much higher temperature. It is seen that the new definition of temperature is not influenced by the global motion, i.e., translation, rotation, acceleration, vibration, etc., of the system. The Gibbs entropy is calculated for each atom by knowing normal distribution as the probability density function. The relationship between entropy and temperature is established for solid material.

Can boron form coordination complexes with diffuse electrons? Evidence for linked solvated electron precursors

Density functional theory and ab initio multi-reference calculations are performed to examine the stability and electronic structure of boron complexes that host diffuse electrons in their periphery. Such complexes (solvated electron precursors or SEPs) have been experimentally identified and studied theoretically for several s- and d-block metals. For the first time, we demonstrate that a p-block metalloid element can form a stable SEP when appropriate ligands are chosen. We show that three ammonia and one methyl ligands can displace two of the three boron valence electrons to a peripheral 1s-type orbital. The shell model for these outer electrons is identical to previous SEP systems (1s, 1p, 1d, 2s). Further, we preformed the first examination of a molecular system consisting of two SEPs bridged by a hydrocarbon chain. The electronic structure of these dimers is very similar to that of traditional diatomic molecules forming bonding and anti-bonding σ and π orbitals. Their ground state electronic structure resembles that of two He atoms, and our results indicate that the excitation energies are nearly independent of the chain length for four carbon atoms or longer. These findings pave the way for the development of novel materials similar to expanded metals and electrides.

3-oxo-C12:2-HSL, Quorum Sensing Molecule from Human Intestinal Microbiota, Inhibits Pro-inflammatory Pathways in Immune Cells via Bitter Taste Receptors

In the gut ecosystem, microorganisms regulate group behaviour and interplay with the host via a molecular system called quorum sensing (QS). The QS molecule 3-oxo-C12:2-HSL, first identified in human gut microbiota, exerts anti-inflammatory effects and could play a role in inflammatory bowel diseases where dysbiosis has been described. Our aim was to identify which signalling pathways are involved in this effect. We observed that 3-oxo-C12:2-HSL decreases expression of pro-inflammatory cytokines such as, Interleukine-1β (-3 %) and Tumor Necrosis Factor-α (TNFα) (40 %) by stimulated immune RAW264.7 cells and decreased TNF secretion by stimulated PBMC in a dose-dependent manner, between 25 µM to 100 µM. Transcriptomic analysis of RAW264.7 cells exposed to 3-oxo-C12:2-HSL, in a pro-inflammatory context, highlighted JAK-STAT, NF-κB and TFN signalling pathways and we confirmed that 3-oxo-C12:2-HSL inhibited JAK1 and STAT1 phosphorylation. We also showed through a screening assay that 3-oxo-C12:2-HSL interacted with several human bitter taste receptors. Its anti-inflammatory effect involved TAS2R38 as shown by pharmacologic inhibition and led to an increase in intracellular calcium levels. We thus unravelled the involvement of several cellular pathways in the anti-inflammatory effects exerted by the QS molecule 3-oxo-C12:2-HSL.

FeSi2: a two-dimensional ferromagnet containing planar hexacoordinate Fe atoms

As an unconventional bonding pattern different from conventional chemistry, the concept of planar hypercoordinate atom was first proposed in the molecular system, and it has been recently extended to 2D...

Excellent Ultracold Molecular Candidates From Group VA Hydrides: Whether Do Nearby Electronic States Interfere?

By means of highly accurate ab initio calculations, we identify two excellent ultracold molecular candidates from group VA hydrides. We find that NH and PH are suitable for the production of ultracold molecules, and the feasibility and advantage of two laser cooling schemes are demonstrated, which involve different spin-orbit states (A3Π2 and X3Σ1− ). The internally contracted multireference configuration interaction method is applied in calculations of the six low-lying Λ-S states of NH and PH with the spin-orbit coupling effects included, and excellent agreement is achieved between the computed and experimental spectroscopic data. We find that the locations of crossing point between the A3Π and Σ−5 states of NH and PH are higher than the corresponding v′ = 2 vibrational levels of the A3Π state indicating that the crossings with higher electronic states would not affect laser cooling. Meanwhile, the extremely small vibrational branching loss ratios of the A3Π2 → a1Δ2 transition for NH and PH (NH: 1.81 × 10–8; PH: 1.08 × 10–6) indicate that the a1Δ2 intermediate electronic state will not interfere with the laser cooling. Consequently, we construct feasible laser-cooling schemes for NH and PH using three lasers based on the A3Π2 → X3Σ1− transition, which feature highly diagonal vibrational branching ratio R00 (NH: 0.9952; PH: 0.9977), the large number of scattered photons (NH: 1.04×105; PH: 8.32×106) and very short radiative lifetimes (NH: 474 ns; PH: 526 ns). Our work suggests that feasible laser-cooling schemes could be established for a molecular system with extra electronic states close to those chosen for laser-cooling.

Primary Amine Nucleophilic Addition to Nitrilium Closo-Dodecaborate [B12H11NCCH3]–: A Simple and Effective Route to the New BNCT Drug Design

In the present work, a convenient and straightforward approach to the preparation of borylated amidines based on the closo-dodecaborate anion [B12H11NCCH3NHR]–, R=H, Alk, Ar was developed. This method has two stages. A nitrile derivative of the general form [B12H11NCCH3]− was obtained, using a modified technique, in the first stage. On the second stage the resulting molecular system interacted with primary amines to form the target amidine products. This approach is characterised by a simple chemical apparatus, mild conditions and high yields of the final products. The mechanism of the addition of amine to the nitrile derivative of the closo-dodecaborate anion was studied, using quantum-chemical methods. The interaction between NH3 and [B12H11NCCH3]− ammonia was chosen as an example. It was found that the structure of the transition state determines the stereo-selectivity of the process. A study of the biological properties of borylated amidine sodium salts indicated that the substances had low toxicity and could accumulate in cancer cells in significant amounts.

Generation of long range and short range potentials

The general particle transfer (GPT) potential generates not only the Yukawa-type potential but also the 1⁄r^n-type potential in the hadron system, where the mass dependence of the transferred particle is clarified. The GPT potential from the atom-molecular system to the quark-gluon system was transversally studied, where the pico-meter physics could be highlighted. It was found that the long range three-body Efimov potential is connected with the short range three-body force potential.

Electrodynamic approach for description of mass transfer phenomena

Based on the equations of macroscopic electrodynamics, the article considers the most important consequences from the point of view of practical application for condensed matter. It has been theoretically shown that a virtual molecular filter with a fairly high degree of selectivity can be used for them. The theoretical substantiation of mass transfer processes in condensed systems is presented for cases of external influence on them when solving problems of technological change of macroscopic properties of a molecular system. Monitoring problems are indicated when moving the minimum amount of substance in the case of mass transfer for processes: diffusion, adsorption, capillary filtration. The functioning of the filter is based on the theory of macroscopic electrodynamics, namely, on how the space charge density is distributed in the sample under study. The results obtained make it possible to evaluate the physicochemical changes that occur in a condensed medium under external technological influence. The presented theoretical research results can serve as the basis for improving the methods of electrometric monitoring of gaseous and liquid media of unknown qualitative and quantitative composition.

Intra-Molecular Electrical Field Regulated Nonlinear Catalyst Charge Transfer in the Organic Conjugated Molecular System

The application of organic conjugated molecular systems to photocatalysis is based on the charge transition with different electronegative substituents and the electron–hole separation behavior of charge transfer under light excitation. In this work, the relationship between the intra-molecular electrical field and molecular second-order nonlinear optical properties is investigated theoretically by the sum-of-states (SOS) method. We use substituents with different electron affinity energy to construct internal electric fields with different properties in similar conjugated systems. The studies of these systems reveal the intra-molecular electric field strength and mode regulation of nonlinear optical coefficients and explain its physical mechanism. The intra-molecular charge recombination caused by the electrostatic potential multipole field of different substituents changes the transition behavior of one-photon, resulting in the enhancement of nonlinear optical properties (second-harmonic generation and sum-frequency coefficient) greater than 104.

Anharmonicity and Spectra–Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K3) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600–2600 cm−1. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000–3600 and 2800–1800 cm−1 ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.