Classification of So-Called Non-Covalent Interactions Based on VSEPR Model

The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.     

The Nature of Activated Non‐classical Hydrogen Bonds: A Case Study on Acetylcholinesterase–Ligand Complexes

Molecular recognition events in biological systems are driven by non‐covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH???Y type involving electron‐deficient CH donors using dispersion‐corrected density functional theory (DFT) calculations applied to acetylcholinesterase–ligand complexes. The strengths of CH???Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non‐activated CH???Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH???Y interactions when analysing protein–ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.     

A comprehensive conformational analysis of tryptophan,its ionic and dimeric forms

Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan ( W ) and its ionized counterparts cations (WC) , anions (WA) , and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH‐π, NH‐π, CH‐π, CH‐O, and π‐π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH‐O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T‐shaped orientations (CH‐π interactions) are more prevalent, while stacked orientations (π‐π interactions) are predominant at a smaller distance. © 2013 Wiley Periodicals, Inc.     

Opposing Phase‐Segregation and Hydrogen‐Bonding Forces in Supramolecular Polymers

Phase segregation between different macromolecules and specific weak interactions are the basis of molecular organization in many biological systems, which are held together by attractive hydrogen bonds (H‐bonds) and dissociated by phase segregation. We report significant changes in the association behavior of covalent H‐bonds by the phase of attached polymer chains. Depending on the aggregation state, we observed either intact H‐bonds despite segregation of the phases, or macrophase separation with a larger amount of H‐bonding dissociation.     

Cross bridging proteins in nature and their utilization in bio- and nanotechnology

Cross-linking and cross-bridging are highly versatile methods of creating composite protein structures with desired mechanical properties such as deformation endurance, elasticity, extensibility, and stability under intensive and repetitive sheering forces. Cross-linking and cross-bridging are distinguished by the bonds that hold the structural components together. Cross-linking implies a covalent association, whereas cross-bridging depends on biological recognition, in which hydrogen bonding, ionic, and hydrophobic interactions predominate. Cross-bridged structures are found in all living systems. Cytoskeletal interaction, cell invasion by pathogens, fertilization, and cellulosomal degradation of cellulose are all examples of biological processes in which cross-bridging proteins play a key role. This article will review the different types of biological cross-bridging proteins that are known and discuss their emerging nano- and biotechnological applications.     

Recent Advances in Luminescent Recognition and Chemosensing of Iodide in Water

This Minireview covers the latest developments of chemosensors based on transition‐metal receptors and organic fluorophores with specific binding sites for the luminescent detection and recognition of iodide in aqueous media and real samples. In all selected examples within the last decade (made‐post 2010), the iodide sensing and recognition is probed by monitoring real‐time changes of the fluorescence or phosphorescence properties of the chemosensors. This review highlights effective strategies to iodide sensing from a structural approach where the iodide recognition/sensing process, through supramolecular interactions as coordination bonds, hydrogen bonds, halogen bonds and electrostatic interactions, is transduced into an optical change easily measurable. The selective iodide sensing is an active field of research with global interest due to the importance of iodide in biological, medicinal, industrial, environmental and chemical processes.     

Tunable Orthogonal Reversible Covalent (TORC) Bonds: Dynamic Chemical Control over Molecular Assembly

Dynamic assembly of macromolecules in biological systems is one of the fundamental processes that facilitates life. Although such assembly most commonly uses noncovalent interactions, a set of dynamic reactions involving reversible covalent bonding is actively being exploited for the design of functional materials, bottom‐up assembly, and molecular machines. This Minireview highlights recent implementations and advancements in the area of tunable orthogonal reversible covalent (TORC) bonds for these purposes, and provides an outlook for their expansion, including the development of synthetically encoded polynucleotide mimics.     

Ab initio investigation of the complexes between bromobenzene and several electron donors: some insights into the magnitude and nature of halogen bonding interactions

Halogen bonding, a specific intermolecular noncovalent interaction, plays crucial roles in fields as diverse as molecular recognition, crystal engineering, and biological systems. This paper presents an ab initio investigation of a series of dimeric complexes formed between bromobenzene and several electron donors. Such small model systems are selected to mimic halogen bonding interactions found within crystal structures as well as within biological molecules. In all cases, the intermolecular distances are shown to be equal to or below sums of van der Waals radii of the atoms involved. Halogen bonding energies, calculated at the MP2/aug-cc-pVDZ level, span over a wide range, from -1.52 to -15.53 kcal/mol. The interactions become comparable to, or even prevail over, classical hydrogen bonding. For charge-assisted halogen bonds, calculations have shown that the strength decreases in the order OH- > F- > HCO2- > Cl- > Br-, while for neutral systems, their relative strengths attenuate in the order H2CS > H2CO > NH3 > H2S > H2O. These results agree with those of the quantum theory of atoms in molecules (QTAIM) since bond critical points (BCPs) are identified for these halogen bonds. The QTAIM analysis also suggests that strong halogen bonds are more covalent in nature, while weak ones are mostly electrostatic interactions. The electron densities at the BCPs are recommended as a good measure of the halogen bond strength. Finally, natural bond orbital (NBO) analysis has been applied to gain more insights into the origin of halogen bonding interactions.     

Metal-catalyzed nucleophilic carbon-heteroatom (C-X) bond formation: the role of M-X intermediates

Many important reactions that lead to carbon-heteroatom bond formation involve attack of anionic heteroatom nucleophiles, such as hydroxides, alkoxides, amides, thiolates and phosphides, at carbon. Related catalytic transformations are mediated by late transition metal complexes of these groups, which remain nucleophilic on metal coordination as a result of repulsive filled-filled interactions between the heteroatom lone pairs and metal d-orbitals and/or of polarization of the bonds Mdelta+-Xdelta-. This Perspective presents examples of catalytic nucleophilic C-X bond formation in both biological and synthetic systems and describes how changes in the metal, ancillary ligands and X groups may be used to tune nucleophilic reactivity.     

Experimental measurement of carbohydrate-aromatic stacking in water by using a dangling-ended DNA model system

Protein-carbohydrate recognition is of fundamental importance for a large number of biological processes; carbohydrate-aromatic stacking is a widespread, but poorly understood, structural motif in this recognition. We describe, for the first time, the measurement of carbohydrate-aromatic interactions from their contribution to the stability of a dangling-ended DNA model system. We observe clear differences in the energetics of the interactions of several monosaccharides with a benzene moiety depending on the number of hydroxy groups, the stereochemistry, and the presence of a methyl group in the pyranose ring. A fucose-benzene pair is the most stabilizing of the studied series (-0.4 Kcal mol(-1)) and this interaction can be placed in the same range as other more studied interactions with aromatic residues of proteins, such as Phe-Phe, Phe-Met, or Phe-His. The noncovalent forces involved seem to be dispersion forces and nonconventional hydrogen bonds, whereas hydrophobic effects do not seem to drive the interaction.     

Structural and thermodynamic studies on cation-Pi interactions in lectin-ligand complexes: high-affinity galectin-3 inhibitors through fine-tuning of an arginine-arene interaction

The high-resolution X-ray crystal structures of the carbohydrate recognition domain of human galectin-3 were solved in complex with N-acetyllactosamine (LacNAc) and the high-affinity inhibitor, methyl 2-acetamido-2-deoxy-4-O-(3-deoxy-3-[4-methoxy-2,3,5,6-tetrafluorobenzamido]-beta-D-galactopyranose)-beta-D-glucopyranoside, to gain insight into the basis for the affinity-enhancing effect of the 4-methoxy-2,3,5,6-tetrafluorobenzamido moiety. The structures show that the side chain of Arg144 stacks against the aromatic moiety of the inhibitor, an interaction made possible by a reorientation of the side chain relative to that seen in the LacNAc complex. Based on these structures, synthesis of second generation LacNAc derivatives carrying aromatic amides at 3'-C, followed by screening with a novel fluorescence polarization assay, has led to the identification of inhibitors with further enhanced affinity for galectin-3 (K(d) > or = 320 nM). The thermodynamic parameters describing the binding of the galectin-3 C-terminal to selected inhibitors were determined by isothermal titration calorimetry and showed that the affinity enhancements were due to favorable enthalpic contributions. These enhancements could be rationalized by the combined effects of the inhibitor aromatic structure on a cation-Pi interaction and of direct interactions between the aromatic substituents and the protein. The results demonstrate that protein-ligand interactions can be significantly enhanced by the fine-tuning of arginine-arene interactions.     

Unusual Changes of C−H Bond Lengths in Chiral Zinc Complexes Induced by Noncovalent Interactions

In order to better understand the effect of non-covalent weak interactions on molecules, we have explored a variety of weak interactions, such as improper H-bonding (HB), tetrel bonds (TBs) and halogen bonds, in fluorinated chiral zinc complexes. High resolution neutron diffraction studies revealed a methylene carbon-hydrogen bond elongation and shortening due to TB and improper HB interactions, respectively. To show the accumulative effects of multiple weak interactions on the C−H bond, three types of tetrel bonds have been carefully examined. We have also shown how C−H bond elongation can be easily offset by forming an improper HB with the H atom from this C−H bond. Non-covalent interaction and electrostatic potential analysis investigations have been used to affirm the nature of the interactions based on density functional theory (DFT) and other related calculations.     

Combined effect of stacking and solvation on the spontaneous mutation in DNA

In DNA, base pairs are involved in two reciprocal interactions: interbase hydrogen bonds and stacking. Furthermore, base pairs also undergo the effects of the external entities present in the biological environment, such as water molecules and cations. In this contribution, the double spontaneous mutation has been studied with hybrid theoretical tools in a DNA-embedded guanine-cytosine model accounting for the impact of the first hydration shell. According to our findings, the combination of the neighboring base pairs and surrounding water molecules plays a crucial role in the double proton transfer. Indeed, as a consequence of these interactions, the double proton transfer (DPT) mechanism is altered: on the one hand, stacking and hydration strongly affect the geometry of base pairs, and, on the other hand, vicinal water molecules may play an active role in the tautomeric equilibrium by catalyzing the proton transfer reaction.     

Quantifying the Bonding Strength of Gold‐Chalcogen Bonds in Block Copolymer Systems

Gold‐chalcogen interactions are ubiquitous in gold biological and medicinal systems. Understanding the nature of these interactions can provide the basis for regulating their structures and functionalities, and a reasonable way to interpret the differences in various properties. However, the relative strength of gold‐chalcogen bonds remains controversial, and the conclusions of many related works are inconsistent. Thus, in this work, we successfully quantified the relative strength of Au‐X (X=S, Se, and Te from chalcogenide‐containing A‐B‐A type block copolymers) interactions at the single‐molecule level through single‐molecule force spectroscopy (SMFS) from a kinetic point of view and quantum chemical studies from a thermodynamic point of view. Both sets of results suggested that the strength of the Au‐X bonds decreases as Au‐Te>Au‐Se>Au‐S. Our findings unveiled the relative strength and nature of gold‐chalcogen interactions, which may help expand their application in electronics, catalysis, medicine and many other fields.     

配位交联的NBR/PVC合金的制备及表征

橡胶通常是通过共价键将线型高分子交联成三维网状结构,而交联过的橡胶不溶不熔,很难再生利用,对环境造成严重污染,为了解决橡胶材料再生利用问题,许多人尝试将一些非共价键用于橡胶的交联,如热塑性弹性体(物理交联)、离子弹性体Ⅲ及通过氢键交联的橡胶,然而由于上述非共价键作用较弱,导致材料力学性能较差及高温使用性能下降,配位键是所有非共价键中最强的键,     

Identification of bismuth-thiolate-carboxylate clusters by electrospray ionization mass spectrometry

The known thermal and hydrolytic stability of bismuth-sulfur bonds indicates that biological targets for bismuth likely involve thiol or thiolate functionalities, such as in L-cysteine. Complexes of bismuth with cysteine or other thiol-carboxylic acid ligands have been isolated and characterized providing a preliminary view of the potential participation of these functional groups in the biochemical mechanisms involving bismuth. A broader assessment of bismuth-thiolate interactions has been possible using electrospray ionization mass spectrometry (ESI-MS). A wide range of complexes has been observed containing mercaptosuccinic acid, 2-mercaptopropionic acid, 3-mercaptopropionic acid, and/or 2-amino-3-mercaptopropionic acid (cysteine). The identification of various multibismuth multiligand cluster ions defines new chemistry for bismuth.     

金属卟啉对杂环及DNA分子识别研究进展

介绍了近几年国内外关于组装金属卟啉对杂环分子、DNA碱基以及RNA的分子识别的研究进展, 并简述了本课题组对金属卟啉与杂环及药物分子复合物的理论研究工作. 金属卟啉广泛存在于自然界和生物体中, 此识别过程对研究和模拟生命体中各种细胞之间的相互作用具有重要意义. 组装后的金属卟啉可通过轴向配位、氢键及π-π堆积作用等识别杂环分子. 金属卟啉对DNA的识别主要有四种作用方式, 而金属卟啉对DNA以及RNA分子的识别主要靠疏水作用力、静电力以及自堆叠作用. 卟啉阳离子与DNA的结合位点受主体侧链取代基的空间结构影响. 金属卟啉对药物分子的识别靠配位键和氢键进行, 以配位键结合的复合物通常具有更高的结合能.     

Conformation analysis of nucleic acids and proteins adsorbed on single-shell carbon nanotubes

This paper presents a concise review of the experimental and calculated data reported in the literature on the noncovalent interactions of DNA and proteins with the nonfunctionalized carbon nanotubes. Our Raman scattering and electron microscopy data on carbon nanotubes and SEIRA spectral data on changes in the conformational state of the main biological polymers (DNA, Poly, BSA, and RNase) in reactions with single-shell carbon nanotubes allowed us to define the character of noncovalent interactions in the tube biomolecule system. An analysis of the data showed that reactions of DNA with nanotubes lead to the binding on the surface of the nanotube and form stable complexes with van der Waals interactions, in which stacking plays the major role and which changes the hydrogen bonds in the biological molecule with structure rearrangements. Albumin and RNase are presumably adsorbed at the conventional binding sites of these proteins on the nanotube with participation of hydrophobic interaction and π stacking, as indicated by structure rearrangements in proteins.     

Binding of genistein to the estrogen receptor based on an experimental electron density study

In a continuing effort to determine a relationship between the biological function and the electronic properties of steroidal and nonsteroidal estrogens by analysis of the submolecular properties, an experimental charge density study has been pursued on the nonsteroidal phytoestrogen, genistein. X-ray diffraction data were obtained using a Rigaku R-Axis Rapid high-power rotating anode diffractometer with a curved image plate detector at 20(1) K. The total electron density was modeled using the Hansen-Coppens multipole model. Genistein packs in puckered sheets characterized by intra- and intermolecular hydrogen bonds while weaker intermolecular hydrogen bonds (O...H-C) exist between the sheets. A topological analysis of the electron density of genistein was then completed to characterize all covalent bonds, three O...H-O and four O...H-C intermolecular hydrogen bonds. Two O...H-O hydrogen bonds are incipient (partially covalent) type bonds, while the other O...H-O hydrogen bond and O...H-C hydrogen bonds are of the pure closed-shell interaction type. In addition, two intermolecular H...H interactions have also been characterized from the topology of the electron density. The binding of genistein to the estrogen receptor is discussed in terms of the electrostatic potential derived from the electron density distribution.