Valence energy correction for electron reactive force field

Reactive force fields (ReaxFF) are a classical method to describe material properties based on a bond-order formalism, that allows bond dissociation and consequently investigations of reactive systems. Semiclassical treatment of electrons was introduced within ReaxFF simulations, better known as electron reactive force fields (eReaxFF), to explicitly treat electrons as spherical Gaussian waves. In the original version of eReaxFF, the electrons and electron–holes can lead to changes in both the bond energy and the Coulomb energy of the system. In the present study, the method was modified to allow an electron to modify the valence energy, therefore, permitting that the electron\u27s presence modifies the three-body interactions, affecting the angle among three atoms. When a reaction path involving electron transfer is more sensitive to the geometric configuration of the molecules, corrections in the angular structure in the presence of electrons become more relevant; in this case, bond dissociation may not be enough to describe a reaction path. Consequently, the application of the extended eReaxFF method developed in this work should provide an improved description of a reaction path. As a first demonstration this semiclassical force field was parametrized for hydrogen and oxygen interactions, including water and water\u27s ions. With the modified methodology both the overall accuracy of the force field but also the description of the angles within the molecules in presence of electrons could be improved

Density Functional Theory Studies on Sulfur-Polyacrylonitrile as a Cathode Host Material for Lithium-Sulfur Batteries

Cyclized polyacrylonitrile, which can be obtained by vulcanization of polyacrylonitrile with sulfur, is an electron-conductive polymer that can be used as a host material in lithium–sulfur batteries. Using density functional theory, we investigated the interaction between a surrounding electrolyte and the polymeric sulfur–polyacrylonitrile (SPAN) electrode. In particular, we focused on different configurations, where the system contains 1,3-dioxane as a solvent and can have (i) polysulfide (PS) solvated in the electrolyte, (ii) a PS attached to the polymer backbone, (iii) lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) as a salt dissolved in the electrolyte, and (iv) both PS and LiTFSI dissolved in the electrolyte. We found that the polymer, when having a hydrogen vacancy at a carbon atom (undercoordinated carbon) of the polymer backbone, is able to not only capture a PS from the electrolyte but also decompose and bind to the solvent and/or remove lithium from the PS. During this capturing process, the polysulfide might undergo S–S bond cleavage and recombination, accompanied by a charge transfer between the polysulfide and polymer. Thus, cyclized polyacrylonitrile not only is an interesting host material but also acts as an active material, together with sulfur, by capturing Li from the polysulfide

Potential‐Dependent Pt(111)/Water Interface: Tackling the Challenge of a Consistent Treatment of Electrochemical Interfaces**

The interface between an electrode and an electrolyte is where electrochemical processes take place for countless technologically important applications. Despite its high relevance and intense efforts to elucidate it, a description of the interfacial structure and, in particular, the dynamics of the electric double layer at the atomic level is still lacking. Here we present reactive force-field molecular dynamics simulations of electrified Pt(111)/water interfaces, shedding light on the orientation of water molecules in the vicinity of the Pt(111) surface, taking into account the influence of potential, adsorbates, and ions simultaneously. We obtain a shift in the preferred orientation of water in the surface oxidation potential region, which breaks with the previously proclaimed strict correlation to the free charge density. Moreover, the characterization is complemented by course of the entropy and the intermolecular ordering in the interfacial region complements the characterization. Our work contributes to the ongoing process of understanding electric double layers and, in particular, the structure of the electrified Pt(111)/water interface, and aims to provide insights into the electrochemical processes occurring there

Effect of Guest Solvents on the Ionic Conductivity and Electrochemical Performance of Metal‐Organic Framework‐Based Magnesium Semi‐Solid Electrolytes

Developing suitable electrolytes is crucial for the advancement of rechargeable magnesium batteries. Recently, metal-organic frameworks (MOFs) have shown a great interest in the field of solid electrolytes for metal ion batteries. However, the ionic conductivity as well as the electrolyte stability in the presence of Mg electrodes are shown to be strongly dependent on the guest solvent used to solvate Mg salts in MOFsSEs. Our measurements showed that full evacuation of the MOF structure before semi-solid electrolytes (sSEs) preparation is crucial for achieving relatively low Mg overpotentials regardless of the ionic conductivity values. Moreover, the behavior of the anode/MOFsSEs interfaces (MOF: α-Mg$_3$[HCOO]$_6$; Mg salt : MgCl$_2$-Mg[TFSI]$_2$ (1 : 1 wt %); guest solvent: acetone, DMF, DEG, DME and tetraglyme) was investigated by EIS, CV and galvanostatic measurements. The current comparative study of the electrochemical deposition processes of magnesium from MOFsSEs revealed that magnesium deposition/dissolution reactions vary depending on the MOF structure, the guest anion species as well as the nature of the guest solvents

Conformational States of the CXCR4 Inhibitor Peptide EPI-X4—A Theoretical Analysis

EPI-X4, an endogenous peptide inhibitor, has exhibited potential as a blocker of CXCR4—a G protein-coupled receptor. This unique inhibitor demonstrates the ability to impede HIV-1 infection and halt CXCR4-dependent processes such as tumor cell migration and invagination. Despite its promising effects, a comprehensive understanding of the interaction between EPI-X4 and CXCR4 under natural conditions remains elusive due to experimental limitations. To bridge this knowledge gap, a simulation approach was undertaken. Approximately 150,000 secondary structures of EPI-X4 were subjected to simulations to identify thermodynamically stable candidates. This simulation process harnessed a self-developed reactive force field operating within the ReaxFF framework. The application of the Two-Phase Thermodynamic methodology to ReaxFF facilitated the derivation of crucial thermodynamic attributes of the EPI-X4 conformers. To deepen insights, an ab initio density functional theory calculation method was employed to assess the electrostatic potentials of the most relevant (i.e., stable) EPI-X4 structures. This analytical endeavor aimed to enhance comprehension of the inhibitor’s structural characteristics. As a result of these investigations, predictions were made regarding how EPI-X4 interacts with CXCR4. Two pivotal requirements emerged. Firstly, the spatial conformation of EPI-X4 must align effectively with the CXCR4 receptor protein. Secondly, the functional groups present on the surface of the inhibitor’s structure must complement the corresponding features of CXCR4 to induce attraction between the two entities. These predictive outcomes were based on a meticulous analysis of the conformers, conducted in a gaseous environment. Ultimately, this rigorous exploration yielded a suitable EPI-X4 structure that fulfills the spatial and functional prerequisites for interacting with CXCR4, thus potentially shedding light on new avenues for therapeutic development

Causes and Consequences of Coronavirus Spike Protein Variability

Coronaviruses are a large family of enveloped RNA viruses found in numerous animal species. They are well known for their ability to cross species barriers and have been transmitted from bats or intermediate hosts to humans on several occasions. Four of the seven human coronaviruses (hCoVs) are responsible for approximately 20% of common colds (hCoV-229E, -NL63, -OC43, -HKU1). Two others (SARS-CoV-1 and MERS-CoV) cause severe and frequently lethal respiratory syndromes but have only spread to very limited extents in the human population. In contrast the most recent human hCoV, SARS-CoV-2, while exhibiting intermediate pathogenicity, has a profound impact on public health due to its enormous spread. In this review, we discuss which initial features of the SARS-CoV-2 Spike protein and subsequent adaptations to the new human host may have helped this pathogen to cause the COVID-19 pandemic. Our focus is on host forces driving changes in the Spike protein and their consequences for virus infectivity, pathogenicity, immune evasion and resistance to preventive or therapeutic agents. In addition, we briefly address the significance and perspectives of broad-spectrum therapeutics and vaccines