Nature of halogen-centered intermolecular interactions in crystal growth and design: Fluorine-centered interactions in dimers in crystalline hexafluoropropylene as a prototype

The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C₃F₆), upon its interaction with another same molecule to form (C₃F₆)₂ dimers. The existence of σ- and π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C₃F₆ itself and the (C₃F₆)₂ dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C₃F₆)₂ dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C₃F₆)₂ dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt, Angew. Chem. Int. Ed. 2017, 56, 368). © 2019 Wiley Periodicals, Inc.     

π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures

Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called “π-hole interactions” are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about −5 kcal mol⁻¹ for ligand–protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand–protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.     

两个salen型卤代希夫碱Ni(Ⅱ)配合物的合成、晶体结构及Hirshfeld表面分析

通过硝酸镍与卤代希夫碱在甲醇溶液中反应,合成了2个Ni（Ⅱ）希夫碱配合物[Ni（3,5-Cl-salcy）]（1）和[Ni（3-Cl-salcy）]（2）,（3,5-Cl-salcyH₂=N,N′-（±）-双（3,5-二氯水杨基）-1,2-环己二胺; 3-Cl-salcyH₂=N,N′-（±）-双（3-氯水杨基）-1,2-环己二胺）。通过X射线衍射测定了2个配合物的结构。结构分析表明2个配合物的基本单元均为Ni（Ⅱ）离子通过与希夫碱配体的[N₂O₂]原子配位构成相似的平面型单核配合物。Platon软件分析表明配合物1中并不存在任何氢键,配合物2也仅存在非经典氢键。通过Hirshfeld表面分析法对2个配合物晶体结构中弱交换作用的分析结果表明,虽然卤原子构成的氢键相对较弱,但是C-H…X在稳定三维超分子晶体结构中起着非常重要的作用;此外,通过2个配合物的对比发现,配体中卤原子数量的不同对于晶体中弱交换作用的占比可以起到非常重要的影响。     

Recent progress on pure organic room temperature phosphorescence materials based on host-guest interactions

Pure organic room temperature phosphorescence (RTP) has been attracting a lot interest recently. So far, many strategies have succeeded in achieving efficient organic RTP materials by increasing the rate of intersystem crossing (ISC) and suppressing non-radiative transitions. In supramolecular chemistry, the control and regulation of molecular recognition based on the role of the host and guest in supramolecular polymers matrix, has attracted much attention. Recently, researchers have successfully achieved room temperature phosphorescence of pure organic complexes through host-guest interactions. The host molecule specifically includes the phosphorescent guest to reduce non-radiative transitions and enhance room temperature phosphorescence emission. This review aims to describe the developments and achievements of pure organic room temperature phosphorescence systems through the mechanism of host-guest interactions in recent years, and demonstrates the exploration and pursuit of phosphorescent materials of researchers in different fields.     

Terphen[n]arenes and Quaterphen[n]arenes (n=3–6): One‐Pot Synthesis,Self‐Assembly into Supramolecular Gels,and Iodine Capture

Herein, two new classes of macrocyclic compounds, terphen[n]arenes (TPns) (n=3–6) and quaterphen[n]arenes (QPns) (n=3–6), were designed and synthesized by a one‐step condensation reaction in relatively high yields. They comprise 2,2′′‐dimethoxy terphenyl and 2,2′′′‐dimethoxy quaterphenyl monomers, respectively, linked by methylene bridges. Given their long and rigid monomers, TPns and QPns have much larger cavities and better self‐assembly properties than classic macrocycles. More interestingly, the cyclic pentamers and hexamers TP5, TP6, QP5, and QP6 formed supramolecular organogels, which were composed of interwoven fibers, nanosheets, or entangled macropore networks formed by multiple face‐to‐face and edge‐to‐face π???π stacking interactions. The xerogel materials effectively captured volatile iodine, not only in aqueous media but also in the gaseous state, and could be recycled multiple times without obvious loss in performance.     

Tailored Combinatorial Microcompartments through the Self‐Organization of Microobjects: Assembly,Characterization, and Cell Studies

A new concept enables the generation of cell microenvironments by microobject assembly at an water/air interface. As the orientation of 30 μm sized polymer cubes and their capillary force assembly are controlled by the surface wettability, which in turn can be modulated by coating the initially exposed surfaces with gold and self‐assembled monolayers, unique niches in closely packed arrays of cubes with vertex up orientation can be realized. The random assembly of distinctly different cubes, prefunctionalized or surface‐structured exclusively on their top surface, facilitates the parallel generation of different microenvironments in a combinatorial manner, which paves the way to future systematic structure–property relationship studies with cells.     

Theoretical ab Initio Study on Cooperativity Effects between Nitro π-hole and Halogen Bonding Interactions

This article analyzes the interplay between nitro's π-hole and halogen–bonding (XB) interactions in nitroarenes. Remarkable cooperativity effects are observed when π–hole and XB interactions coexist in the same complex. The nitroarene presents two π-holes, one approximately over the N atom of the nitro group and the other over the aromatic ring, being the former more positive. The interplay between both interactions has been analyzed in terms of energetic and geometric features of the complexes, which are computed at the RI-MP2/def2-TZVPD level of theory. Molecular electrostatic potential (MEP) surface calculations have been used to explore the variation of the MEP values at the π-hole upon the formation of halogen bonding interactions between the nitroarene and CF₃X (X=Cl, Br and I) molecules. In addition, the Bader's theory of atoms in molecules” (AIM) is used to characterize the interactions by means of the distribution of bond critical points and bond paths and to analyze their strengthening or weakening depending upon the variation of charge density at critical points. The aforementioned computational methods are adequate to examine how these interactions mutually influence each other. Natural bond orbital (NBO) and noncovalent interaction plot (NCIPlot) computational tools have been also used in some representative complexes to further analyze cooperativity effects. Finally, the Cambridge Structural Database (CSD) is used to provide some experimental evidence.     

A new sequence based encoding for prediction of host–pathogen protein interactions

Pathogen–host interactions are very important to figure out the infection process at the molecular level, where pathogen proteins physically bind to human proteins to manipulate critical biological processes in the host cell. Data scarcity and data unavailability are two major problems for computational approaches in the prediction of pathogen–host interactions. Developing a computational method to predict pathogen–host interactions with high accuracy, based on protein sequences alone, is of great importance because it can eliminate these problems. In this study, we propose a novel and robust sequence based feature extraction method, named Location Based Encoding, to predict pathogen–host interactions with machine learning based algorithms. In this context, we use Bacillus Anthracis and Yersinia Pestis data sets as the pathogen organisms and human proteins as the host model to compare our method with sequence based protein encoding methods, which are widely used in the literature, namely amino acid composition, amino acid pair, and conjoint triad. We use these encoding methods with decision trees (Random Forest, j48), statistical (Bayesian Networks, Naive Bayes), and instance based (kNN) classifiers to predict pathogen–host interactions. We conduct different experiments to evaluate the effectiveness of our method. We obtain the best results among all the experiments with RF classifier in terms of F1, accuracy, MCC, and AUC.