Neutral Molecules Research Articles

Spontaneous bilayer wrapping of virus particles by a phospholipid Langmuir monolayer

We report here the spontaneous formation of lipid-bilayer-wrapped virus particles, following the injection of “naked” virus particles into the subphase of a Langmuir trough with a liquid monolayer of lipids at its air–water interface. The virus particles are those of the well-studied cowpea chlorotic mottle virus, CCMV, which are negatively charged at the pH 6 of the subphase; the lipids are a 9:1 mix of neutral DMPC and cationic CTAB molecules. Before adding CCMV particles to the subphase we establish the mixed lipid monolayer in its liquid-expanded state at a fixed pressure (17.5 mN/m) and average area-per-molecule of (41Å2). Keeping the total area fixed, the surface pressure is observed to decrease at about 15 h after adding the virus particles in the subphase; by 37 h it has dropped to zero, corresponding to essentially all the lipid molecules having been removed from the air–water interface. By collecting particles from the subphase and measuring their sizes by atomic force microscopy, we show that the virus particles have been wrapped by lipid bilayers (or by two lipid bilayers). These results can be understood in terms of thermal fluctuations and electrostatic interactions driving the wrapping of the anionic virus particles by the cationic lipids.Graphical Spontaneous acquisition by a virus particle of, first, a hydrophobic lipid monolayer envelope and, then, a hydrophilic lipid bilayer envelope, as it interacts from the subphase with an oppositely charged Langmuir monolayer

Simulation of filamentation dynamics of microwave discharge in nitrogen

The present study deals with numerical simulations of microwave (MW) discharges in nitrogen based on extended fluid-dynamic model. The set of governing equations for non-equilibrium gas-discharge plasma includes conservation equations for species number densities, electron energy density, Poisson equation for the electric field coupled to the multi-temperature Navier–Stokes fluid-dynamic equations taking into account thermal nonequilibrium; the power transmitted from MW radiation to electrons is determined from the Helmholtz equation. The kinetic scheme includes 61 reactions involving neutral molecules and atoms in the ground and electronically excited states, ions and electrons. The set of equations is solved for a two-dimensional problem under conditions of experiments at a pressure of 40 and 50 Torr and different electromagnetic wave frequencies and pulse duration. The dynamics of discharge formation and transition from the diffuse to the filament form is studied. The results are compared with experimental data, and a good agreement is shown for the time larger than 10 µs. The possible reasons for discrepancies at a shorter time are discussed and the effect of small oxygen impurities on the quantitative characteristics of the discharge are evaluated. The presence of a small oxygen impurity and seed electrons in the region of discharge formation yields a better agreement between numerical and experimental data.

Unusual Dynamics and Vibrational Fingerprints of van der Waals Dimers Formed by Linear Molecules and Rare-Gas Atoms.

Detailed structural, dynamical, and vibrational analyses have been performed for systems composed of linear triatomic molecules solvated by a single rare-gas atom, He, Ne, or Ar. Among the chromophores of these van der Waals (vdW) dimers, there are four neutral molecules (CO2, CS2, N2O, and OCS) and six molecular cations (HHe2+, HNe2+, HAr2+, HHeNe+, HHeAr+, and HNeAr+), both of apolar and polar nature. Following the exploration of bonding preferences, high-level four-dimensional (4D) potential energy surfaces (PESs) have been developed for 24 vdW dimers, keeping the two intramonomer bond lengths fixed. For these 24 complexes, over 1500 bound vibrational states have been obtained via quasi-variational nuclear-motion computations, employing exact kinetic-energy operators together with the accurate 4D PESs and their 2D/3D cuts. The reduced-dimensional (2D to 4D) dimer models have been compared with full-dimensional (6D) ones in the cases of the neutral CO2·Ar and charged HHe2+·He dimers, corroborating the high accuracy of the 2D to 4D vibrational energies. The reduced-dimensional models suggest that (a) while the equilibrium structures are T-shaped and planar, the effective ground-state structures are nonplanar, (b) certain bound states belong to collinear molecular structures, even when they are not minima, (c) the vdW vibrations are heavily mixed and many states have amplitudes corresponding to both the T-shaped and collinear structures, (d) there are a few dimers, for which even some of the vdW fundamentals lie above the first dissociation limit, and (e) the vdW vibrations are almost fully decoupled from the intramonomer bending motion.

Quaternization cross-linking of hyperbranched polyethylene-graft-poly(diethylaminoethyl methacrylate) as antimicrobial separation layer of molecular sieving membrane

Positively charged composite membranes with polyethylene-based antimicrobial separation layers are conveniently developed herein for precise molecular sieving. Quaternization cross-linking between hyperbranched polyethylene-graft-poly(diethylaminoethyl methacrylate) and 1,2-dibromoethane constructs porous networks with abundant quaternary ammonium groups. Modified membranes exhibit different interception capabilities for anions, cations, and neutral molecules. We explain the possible sieving mechanisms with respect to size exclusion, the Donnan effect, and the intrapore energy barrier. A strongly positively charged separation layer introduces the electrostatic interaction which has different effects on cationic, anionic, and neutral molecules during filtration. Membranes prepared by the simple quaternization cross-linking strategy can efficiently separate molecular mixtures with different dimensions or charges. Moreover, the plentiful quaternary ammonium groups endow the membranes with favorable antimicrobial activity against Gram-positive E. coli and Gram-negative S. aureus.

Modulation of the NLO properties of p-coumaric acid by the solvent effects and proton dissociation

Solute-solvent interactions and deprotonation effects have been related to second-order nonlinear optical response modulators. This work takes advantage of sequential Monte Carlo/Quantum mechanics together with Time-Dependent Density Functional Theory, Coupled Cluster methods, and the hyper-Rayleigh scattering formalism to investigate how these effects influence the stability and optical response of p-coumaric acid (pCA) and its anionic and diionic forms. The solvent influences the chromophores in different ways, inducing bathochromic and hypsochromic solvatochromism so for the neutral pCA molecule as for its deprotonated derivatives. The results indicate a high sensitivity of the nonlinear optics (NLO) parameters with relation to proton dissociation. Ionization of the carboxyl group produces the lowest values of the first frequency-dependent hyperpolarizability (βHRS), while phenolic deprotonation leads to the highest values. The results show that proton removal can be used as a switch that modulates the NLO response within a wide range of values (159.15≤βHRS≤4393.97 au) greater than those reported for reference NLO chromophores like urea (37.3 au) and p-nitroaniline (74.3 au). Thermochemical analysis of enthalpies and Gibbs free energies indicate that both monoionic forms of the pCA molecule are the most stable in gas or water solvents. Furthermore, these structures represent the limits of NLO modulation in the gas and solvent phases. Analysis of the projected density of states and mapping of the molecular electrostatic potential indicate that increased contributions from conduction electrons found in the aromatic ring are the mechanism by which deprotonation enhances the NLO response. All the results show that ionic pCA forms are promising in the functionalization of optoelectronic devices.

Gas-phase ion chemistry of [B12X12]2− (X = F, Cl, Br, I, CN). A brief review of twelve years of researching twelve−vertexed dianions and their fragments

The closo-dodecaborate dianions [B12X12]2− (X = halogen, CN) have been recognized in recent years for their outstanding physical and chemical properties. Gas-phase ion chemistry and spectroscopy have contributed to the understanding and further development of their record stability, which is applied to stabilize highly reactive cations. Fragment ions generated by collision induced dissociation provide access to a large variety of boron-based structures previously not available in the condensed phase and have challenged common chemical concepts (e.g., the discovery of “superelectrophilic anions”). This has opened new avenues for noble gas chemistry and direct functionalization of alkyl groups with covalently bound “charge tags”. Furthermore, the interactions with neutral molecules in the gas phase, e.g., host-guest chemistry, complements the fundamental understanding of solvation effects in solution and association with large neutral molecules, which is highly relevant for the biochemical applications of these compounds. Future perspectives, in particular the special role of these ions and their fragments in preparative mass spectrometry, are discussed.

Simple Composite Approach to Efficiently Estimate Basis Set Limit CCSD(T) Harmonic Frequencies and Reaction Thermochemistry.

We introduce a simple strategy that combines the G3(MP2) composite method and explicitly correlated coupled cluster CCSD(T)-F12 method to efficiently estimate complete basis set CCSD(T) molecular geometries and harmonic vibrational frequencies at the cost of a double-ζ basis set calculation. Based on a large test set of 61 neutral, ionic, and open-shell molecules, and additionally 31 molecules in the HFREQ2014 data set, we demonstrate that this composite strategy has an average accuracy of 2 cm-1 or better relative to complete basis set CCSD(T) values. Using this approach, we estimated 696 CCSD(T)/CBS reaction energies of small to medium-sized systems containing up to 6 heavy atoms and confirmed existing approximations that use small basis set density functional theory methods [e.g., M06-2X/6-31+G(d)] to calculate thermal contributions to reaction enthalpies and Gibbs free energies that are accurate to within 0.2 kcal mol-1 on average.

Nanocomposite HKUST-1@polysulfone membrane for the adsorptive removal of tetracyclines in waters

To mitigate the presence of tetracyclines in water, it is essential to implement proper wastewater treatment processes that can effectively remove these compounds. In this work we develop a polymeric filtration membrane functionalized with nanocrystals of a metallic organic framework, designated by HKUST-1. The membrane was evaluated for the remotion of oxytetracycline (OTC), tetracycline (TC), and chlortetracycline (CTC) in water samples. The membrane was fabricated using polysulfone (PSU), polyethyleneglycol (PEG), MOF (HKUST-1), and N-methyl-2-pyrrolidone (NMP) through the nonsolvent induced phase separation (NIPS) method. The membrane that presents the best antibiotic rejection characteristics was prepared with 15 % (w/w) PSU, 3 % (w/w) PEG, 1 % (w/w) HKUST-1, and 81 % (w/w) N-methyl-2-pyrrolidone (NMP). This membrane exhibited a pure water flux of up to 76.2 L.m−2.h−1, approximately 40 times more than the one achieved for pristine membranes. Once determined the best membrane composition, a physical–chemical characterization of membrane was done. A high antibiotic rejection rate was obtained for OTC, TC, and CTC, around 91 %, 91 %, and 99 % respectively. The pH of solutions has a strong influence on membrane rejection. The results suggest that intermolecular forces such as π-π type interactions and hydrogen bonds exist between the neutral molecules of tetracyclines (pH > pKa1 and < pKa2) and HKUST-1@PSU MMM, which are greater than the electrostatic forces at pH < pKa1 or pH > pKa2. Furthermore, FTIR spectra demonstrate the formation of a Cu-tetracycline complex as another adsorption mechanism. Finally, the interaction of the tetracyclines in the mixture on the removal performance was evaluated. The study revealed that chlortetracycline (CTC) exhibited superior removal performance, even over extended periods of time, despite having a lower initial concentration in the mixture. This innovative membrane represents a new generation of highly efficient filter systems specifically designed for water purification purposes.

On the electron impact cross-section maxima for dissociative and non-dissociative single ionization of molecules and radicals

Determining absolute electron impact ionization cross-sections for atoms and molecules, whether through experimental or theoretical means, poses a formidable challenge and is typically limited to a narrow selection of species. In this paper, by using measured cross-sections and polarizability data, it was obtained empirical scaling laws for total single ionization and non-dissociative single ionization cross-section maximum of neutral molecules by collisions with electrons. It is found that the total single ionization cross-sections scale linearly with the target electric static polarizability, while the non-dissociate cross-sections exhibit a saturation effect for large target polarizabilities. This saturation effect is interpreted as the increasing role of fragmentation with polarizability.

Design and characterization of an optical-fiber-coupled laser-induced desorption source for gas-phase dynamics experiments.

Preparation of neutral non-volatile molecules intact in the gas phase for mass spectrometry or chemical dynamics experiments remains a challenge for many classes of molecules. Here, we report the design and characterization of a fiber-coupled laser-based thermal desorption source capable of preparing intact neutral molecules at high molecular densities in the gas phase for use in velocity-map imaging experiments. Within this source, the sample is deposited onto a thin tantalum foil. Irradiation of the foil from the reverse side by a focused laser beam leads to highly localized heating of the sample, resulting in desorption of a plume of molecules into the gas phase. The fiber-coupled design simplifies the alignment of the desorption laser beam, and the ability to rotate the foil relative to the fixed laser beam allows the sample to be continually refreshed under vacuum. We use 118nm photoionization of three test molecules-uracil, adenine, and phenylalanine-to characterize the source and to demonstrate various aspects of its performance. These include the dependence of the velocity-map imaging performance on the size of the interaction region and the dependence of the laser-induced desorption source emission on desorption laser power and heating time. Signal levels recorded in these measurements are comparable to those we typically obtain in similar experiments using a pulsed supersonic molecular beam, and we, therefore, believe that the source has considerable potential for use in a wide range of chemical dynamics and other experiments.

Determination of the Effective Collision Frequency of Electrons in the E and D Regions of the High-Latitude Ionosphere from Analysis of Radio Occultation Measurements

Collisions between electrons and neutral molecules are of special interest for the physics of the Earth’s ionosphere, in particular, for determining the ionospheric conductivity and current systems in the lower ionosphere of the planet, as well as elucidating the role they play in attenuating radio waves propagating inside the D and E regions of the ionosphere. The effective collision frequency of electrons can be estimated from laboratory studies of electron mobility in atmospheric gases in combination with rocket measurements of temperature and particle density in the Earth’s upper atmosphere, or it can be determined independently from analysis of radio occultation data. We have developed a method for reconstructing the vertical profiles of the absorption coefficient of decimeter (wavelength ~19 cm) radio waves by solving the inverse problem of signal absorption in the D and E regions of the Earth’s ionosphere. Based on the analysis of radio occultation data from the FORMOSAT-3/COSMIC satellites, the altitude profiles of the absorption coefficient of decimeter (DM) radio waves in the planet’s ionosphere during the geomagnetic storm on June 22–23, 2015, were determined. It is known that the absorption coefficient at a given fixed frequency is directly proportional to both the electron density and the collision frequency of electrons with ions and neutrals. Using the data on the vertical profiles of the absorption coefficient of DM radio waves and the electron density reconstructed from the analysis of FORMOSAT-3/COSMIC radio occultations, we estimated the effective collision frequency of electrons in the D and E regions of the Earth’s high-latitude ionosphere. The practical significance of studying the frequency of electron collisions and the effects of radio wave absorption in the D and E regions of the planet’s ionosphere is associated with maintaining the uninterrupted operation of space radio communication and navigation systems.

Dinityrosyl Iron Complexes with Thiol-Containg Ligands as a Funcionally Active “Working Form” of Nitric Oxide System in Living Organisms

The experimental data are summarized which allow to suggest that dinitrosyl iron complexes (DNIC) with thiol-containing ligands can be considered as an endogenous “working form” of nitric oxide (NO) system in living organisms. The complexes can function as donors of both neutral NO molecules as well as nitrosonium cations (NO+) which exert respectively positive (regulatory) or negative (cytotoxic) effect on human and animal organisms. A special attention is paid to DNIC capacity to block (especially in combination with dithiocarbamate derivatives) coronavirus SARS-CoV-2 infection in Syrian hamsters.

Crystal structure of 2-methyl-1H-imidazol-3-ium 3,5-di-carb-oxy-benzoate.

The structure of the title salt, C4H7N2 +·C9H5O6 - (1), is reported. The compound is built from a protonated 2-methyl-imidazole and a singly deprotonated trimesic acid. Detailed analysis of bond distances and angles for both ions reveals subtle differences compared with their neutral mol-ecule counterpart. Analysis of the crystal packing in compound 1 reveals the formation of undulating chains by the ions through hydrogen bonding. The chains stack along the b axis through π-π inter-actions and inter-connect with other chains in an out-of-phase arrangement along the ac plane through further hydrogen-bonding inter-actions.

Spodium Bonds Involving Methylmercury and Ethylmercury in Proteins: Insights from X-ray Analysis and Computations.

In this study, the stability, directionality, and physical nature of Spodium bonds (SpBs, an attractive noncovalent force involving elements from group 12 and Lewis bases) between methylmercury (MeHg) and ethylmercury (EtHg) and amino acids (AAs) have been analyzed from both a structural (X-ray analysis) and theoretical (RI-MP2/def2-TZVP level of theory) point of view. More in detail, an inspection of the Protein Data Bank (PDB) reported evidence of noncovalent contacts between MeHg and EtHg molecules and electron-rich atoms (e.g., O atoms belonging to the protein backbone and S atoms from MET residues or the π-systems of aromatic AAs such as TYR or TRP). These results were rationalized through a computational study using MeHg coordinated to a thiolate group as a theoretical model and several neutral and charged electron-rich molecules (e.g., benzene, formamide, or chloride). The physical nature of the interaction was analyzed from electrostatics and orbital perspectives by performing molecular electrostatic potential (MEP) and natural bonding orbital (NBO) analyses. Lastly, the noncovalent interactions plot (NCIplot) technique was used to provide a qualitative view of the strength of the Hg SpBs and compare them to other ancillary interactions present in these systems as well as to shed light on the extension of the interaction in real space. We believe that the results derived from our study will be useful to those scientists devoted to protein engineering and bioinorganic chemistry as well as to expanding the current knowledge of SpBs among the chemical biology community.

Critical Assessment of pH-Dependent Lipophilicity Profiles of Small Molecules: Which One Should We Use and In Which Cases?

Lipophilicity is a physicochemical property with wide relevance in drug design, computational biology, and food, environmental and medicinal chemistry. Lipophilicity is commonly expressed as thepartition coefficientfor neutral molecules, whereas for molecules with ionizable groups, the distribution coefficient (D) at a given pH is used. The logDpH is usually predicted using a pH correction, while often ignoring the apparent ionic partition [[EQUATION]]. In this work, we studied the impact of [[EQUATION]] on the prediction of both the experimental lipophilicity of small molecules and experimental lipophilicity-based applications and metrics such as lipophilic efficiency (LipE), distribution of spiked drugs in milk products, and pH-dependent partition of water contaminants in synthetic passive samples such as silicones. Our findings show that better predictions are obtained by considering the apparent ionic partition.In this context, we developed machine learning algorithms to determine the cases that [[EQUATION]] should be considered. The results indicate that small, rigid, and unsaturated molecules with logPN close to zero, which present a significant proportion of ionic species in the aqueous phase, were better modeled using the apparent ionic partition [[EQUATION]]). Finally, our findings can serve as guidance to the scientific community working in early-stage drug design, food, and environmental chemistry.

Dye-Derived Red-Emitting Carbon Dots for Lasing and Solid-State Lighting.

Carbon dots are carbon-based nanoparticles renowned for their intense light-emitting capabilities covering the whole visible light range. Achieving carbon dots emitting in the red region with high efficiency is extremely relevant due to their huge potential in biological applications and in optoelectronics. Currently, photoluminescence in such an energy interval is often associated with polyheterocyclic molecular domains forming during the synthesis that, however, present low emission efficiency and issues in controlling the optical features. Here, we overcome these problems by solvothermally synthesizing carbon dots starting from Neutral Red, a common red-emitting dye, as a molecular precursor. As a result of the synthesis, such molecular fluorophore is incorporated into a carbonaceous core while retaining its original optical properties. The obtained nanoparticles are highly luminescent in the red region, with a quantum yield comparable to that of the starting dye. Most importantly, the nanoparticle carbogenic matrix protects the Neutral Red molecules from photobleaching under ultraviolet excitation while preventing aggregation-induced quenching, thus allowing solid-state emission. These advantages have been exploited to develop a fluorescence-based color conversion layer by fabricating polymer-based highly concentrated solid-state carbon dot nanocomposites. Finally, the dye-based carbon dots demonstrate both stable Fabry-Perot lasing and efficient random lasing emission in the red region.

Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions.

A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.

High- dose nitric oxide gas inhalation for HIV infection

Therapeutic effect of high-dose nitric oxide gas inhalation (NO concentration was not less than than 1000 ppm) on two patients with HIV infection was shown. Inhaled NO therapy led to a rapid decrease in viral load to an undetectable level which was persistent even after analytical treatment interruption. It is suggested that HIV infection is controlled by nitrosonium (NO+) cations, the oxidized form of neutral NO molecules that enter the blood. Subsequent conversion of NO+ cations into nitrite anions due to a reaction with hydroxyl ions is inhibited by the binding of NO+ cations and chloride anions leading to the formation of nitrosyl chloride in the blood. Further entry of nitrosyl chloride into cells and tissues ensures NO+ transfer to them. Interaction between nitrosyl chloride and thiols requires the appearance of relevant S-nitrosothiols as NO donors in cells and tissues.

Quantum scattering cross-sections for O(3P) + N2 collisions for planetary aeronomy

ABSTRACT ‘Hot atoms’, atoms in their excited states, transfer their energy to the surrounding atmosphere through collisions. This process (known as thermalization) plays a crucial role in various astrophysical and atmospheric processes. Thermalization of hot atoms is mainly governed by the amount of species present in the surrounding atmosphere and the collision cross-sections between the hot atoms and surrounding species. In this work, we investigated the elastic and inelastic collisions between hot oxygen atoms and neutral N2 molecules, relevant to oxygen gas escape from the Martian atmosphere and for characterizing the chemical reactions in hypersonic flows. We conducted a series of quantum scattering calculations between various isotopes of O(3P) atoms and N2 molecules across a range of collision energies (0.3–4 eV), and computed both their differential and collision cross-sections using quantum time-independent coupled-channel approach. Our differential cross-section results indicate a strong preference for forward scattering over sideways or backward scattering, and this anisotropy in scattering is further pronounced at higher collision energies. By comparing the cross-sections of three oxygen isotopes, we find that the heavier isotopes consistently have larger collision cross-sections than the lighter isotopes. As a whole, this study contributes to a better understanding of the energy distribution and thermalization processes of hot atoms within atmospheric environments. Specifically, the cross-sectional data presented in this work is directly useful in improving the accuracy of energy relaxation modelling of O and N2 collisions over the Mars and Venus atmospheres.

Characterizing the multi-dimensional reaction dynamics of dihalomethanes using XUV-induced Coulomb explosion imaging.

Site-selective probing of iodine 4d orbitals at 13.1nm was used to characterize the photolysis of CH2I2 and CH2BrI initiated at 202.5nm. Time-dependent fragment ion momenta were recorded using Coulomb explosion imaging mass spectrometry and used to determine the structural dynamics of the dissociating molecules. Correlations between these fragment momenta, as well as the onset times of electron transfer reactions between them, indicate that each molecule can undergo neutral three-body photolysis. For CH2I2, the structural evolution of the neutral molecule was simultaneously characterized along the C-I and I-C-I coordinates, demonstrating the sensitivity of these measurements to nuclear motion along multiple degrees of freedom.