Although it is widely accepted that the local structure of liquid water has tetrahedral arrangements of molecules ordered by hydrogen bonds, the mechanism by which water molecules switch hydrogen-bonded partners remains unclear. In this mechanism, the role of nonhydrogen-bonded configurations (NHBs) between adjacent molecules is of particular importance. A molecule may switch hydrogen-bonding p...

Saturated acyclic four-atom groups closed with a classic intramolecular hydrogen bond, generating planar five-membered rings (hydrogen-bridged quasi-rings), in which at least one of the ring atoms is bonded to other non-ring atoms that are not in the ring plane and, thus, capable to form intermolecular interactions, were studied in this work, in order to find the preferred mutual positions of t...

Codeposition of two molecular species [copper phtalocyanine (CuPc, donor) and perfluoropentacene (PFP, acceptor)] on noble metal (111) surfaces leads to the self-assembly of an ordered mixed layer with a maximized donor-acceptor contact area. The main driving force behind this arrangement is assumed to be the intermolecular C-H ⋯ F hydrogen-bond interactions. Such interactions would be maximize...

Two-dimensional Raman-terahertz (THz) spectroscopy is presented as a multidimensional spectroscopy directly in the far-IR regime. The method is used to explore the dynamics of the collective intermolecular modes of liquid water at ambient temperatures that emerge from the hydrogen-bond networks water forming. Two-dimensional Raman-THz spectroscopy interrogates these modes twice and as such can ...

Chemical feature based pharmacophore models were generated for Toll-like receptors 7 (TLR7) agonists using HypoGen algorithm, which is implemented in the Discovery Studio software. Several methods tools used in validation of pharmacophore model were presented. The first hypothesis Hypo1 was considered to be the best pharmacophore model, which consists of four features: one hydrogen bond accepto...

A computer program has been developed to survey a set of crystal structures for hydrogen-bond motifs. Possible ring and chain motifs are generated automatically from a user-defined list of interacting molecular fragments and intermolecular interactions. The new program was used to analyse the hydrogen-bond networks in the crystals of 52 zwitterionic alpha-amino acids. All the possible chain mot...

The structure of the ortho-, meta- and para- hybrid diindolylmethane-phenylboronic acids and their interactions were optimized with by a quantum chemical method, using density functional theory at the (DFT) level. Thus, infrared bands were assigned based on the scaled theoretical wavenumbers by correlating the respective experimental data of the molecules. In addition, the corresponding ¹H-/13C...

The aim of this work is to investigate polymer[middle dot][middle dot][middle dot]substrate interactions for a polymer nanocomposite material: poly(ethylene oxide) (PEO) confined in graphite oxide (GO). Six discrete and simplified models (one for PEO and five for GO) have been chosen in order to reproduce the most likely PEO···GO interactions. Twelve potential interaction energy curves have bee...

Anhydrous Hydrogen Fluoride (HF) at high temperatures and pressures is used to process manufacture nuclear fuel. As HF often directly with uranium, correct neutron thermal scattering cross sections are crucial criticality safety applications. Classical molecular dynamics (CMD) simulation of the flexible system was create law (TSL) sections. The initial 2-site model in LAMMPS, it can not capture...

It is generally accepted that the distinctive properties of water can be ascribed to hydrogen bonding [1]. The fundamental dynamical process of the liquid is the making and breaking of hydrogen bonds. This dynamics, however, is far from being completely understood. Experiments such as infrared absorption and Raman scattering [2], depolarized light scattering [3], and inelastic neutron scatterin...