Organic chemists tend to consider the conformation of compounds as a consequence of repulsive steric interactions. In other words, “the steric effect” means “repulsive” in many cases. Thus, folded conformations observed in organic molecules have been often regarded as unusual, while the reason remained undecided. However, accurate determinations by modern spectroscopic methods, recent crystallographic data, and high-level ab initio MO calculations have demonstrated that the folded conformation is by no means exceptional. We will show that the gauche or folded conformation prevails in organic compounds bearing at least an electronegative or π-group in the molecule. We consider that the above phenomenon finds its origin, in most cases, in nonconventional hydrogen bonds such as the CH/X (X ) O, halogen, etc.) and the XH/π (X ) O, N, C, etc.) hydrogen bonds. * To whom correspondence should be addressed. E-mail: shu@ hiroshima-u.ac.jp. ‡ Hiroshima University. § Yokohama National University. ⊥ The CHPI Institute. Chem. Rev. 2010, 110, 6049–6076 6049

Relevance of Weak Hydrogen Bonds in the Conformation of Organic Compounds and Bioconjugates: Evidence from Recent Experimental Data and High-Level ab Initio MO Calculations

This treatise is an update to a preceding highlight (CH/π hydrogen bonds in crystals) published in this journal 5 years ago (M. Nishio, CrystEngComm, 2004, 6, 130–156). After the introductory part (sections 1 and 2), we survey recent results (mostly since 2004) relevant to the CH/π hydrogen bond: crystal conformation, packing and host/guest chemistry (section 3). Section 4 summarizes the results obtained by crystallographic database (CSD and PDB) analyses. In section 5, several topics in related fields (selectivity in organic reactions, surface chemistry, structural biology, drug design and high-level ab initio calculations of protein/substrate complexes and natural organic compounds) are introduced, and in the final part we comment on the prospects of this emerging field of chemistry.

CH/π hydrogen bonds in organic and organometallic chemistry

N‐Heterocyclic Carbene Ligands: Coordination Chemistry, Reactivity, and Applications Steṕhane Bellemin-Laponnaz*,†,‡ and Samuel Dagorne* †IPCMS (Institut de Physique et Chimie des Mateŕiaux de Strasbourg), CNRS-Universite ́ de Strasbourg, 23 rue du Loess BP 43, F-67034 Strasbourg, France ‡University of Strasbourg Institute for Advanced Study (USIAS), 5 alleé du Geńeŕal Rouvillois, F-67083 Strasbourg, France Institut de Chimie de Strasbourg, CNRS-Universite ́ de Strasbourg, 1 rue Blaise Pascal, F-67000 Strasbourg, France

Group 1 and 2 and Early Transition Metal Complexes Bearing N-Heterocyclic Carbene Ligands: Coordination Chemistry, Reactivity, and Applications

Using ab initio metadynamics we have computed the conformational free energy landscape of β-d-glucopyranose as a function of the puckering coordinates. We show that the correspondence between the free energy and the Stoddard's pseudorotational itinerary for the system is rather poor. The number of free energy minima (9) is smaller than the number of ideal structures (13). Moreover, only six minima correspond to a canonical conformation. The structural features, the electronic properties, and the relative stability of the predicted conformers permit the rationalization of the occurrence of distorted sugar conformations in all the available X-ray structures of β-glucoside hydrolase Michaelis complexes. We show that these enzymes recognize the most stable distorted conformers of the isolated substrate and at the same time the ones better prepared for catalysis in terms of bond elongation/shrinking and charge distribution. This suggests that the factors governing the distortions present in these complexes are...

The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases.

Carbohydrate-active enzymes such as glycoside hydrolases (GHs) and glycosyltransferases (GTs) are of growing importance as drug targets. The development of efficient competitive inhibitors and chaperones to treat diseases related to these enzymes requires a detailed knowledge of their mechanisms of action. In recent years, sophisticated first-principles modeling approaches have significantly advanced in our understanding of the catalytic mechanisms of GHs and GTs, not only the molecular details of chemical reactions but also the significant implications that just the conformational dynamics of a sugar ring can have on these mechanisms. Here we provide an overview of the progress that has been made in the past decade, combining molecular dynamics simulations with density functional theory to solve these sweet mysteries of nature.

http://pubs.acs.org/doi/pdf/10.1021/jacs.5b01156

Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations

An investigation of the pyranose ring interconversion path of α-L-idose calculated using density functional theory

The conformation of alkyl cyclohexanones and terpenic ketones. Interpretation for the ‘alkylketone effect’ based on the CH/π(CO) hydrogen bond

Twisted coordination mode of bis(N-heterocyclic carbene) ligands in octahedral geometry of group 6 transition metal complexes: Synthesis, structure, and reactivity

In this work, three different types of acetylacetonato-based pincer-type nickel(ii) complexes (2) were prepared. Complex 2a possessed the tridentate ONN ligand, which was constructed by the condensation reaction of acetylacetone with N,N-diethylethylenediamine. Complex 2b contained the PPh2 donor group in contrast to the NEt2 group in 2a, i.e., an ONP ligand framework. Complex 2c was composed of the NNN ligand, which was prepared by the reaction of 4-((2,4,6-trimethylphenyl)amino)pent-3-en-2-one with N,N-diethylethylenediamine. In addition to X-ray diffraction analysis, these complexes were characterized spectroscopically. Their catalytic activity for a cross-coupling reaction of aryl halides with aryl Grignard reagents was also evaluated. Among these complexes, 2b acted as an effective catalyst for the cross-coupling reaction using aryl chlorides as electrophiles. The electronic properties of these Ni(ii) complexes were investigated by cyclic voltammetry and density functional theory calculations.

/pdf/acetylacetonato-based-pincer-type-nickel-ii-complexes-2ska5424n4.pdf

Acetylacetonato-based pincer-type nickel(ii) complexes: synthesis and catalysis in cross-couplings of aryl chlorides with aryl Grignard reagents.

A β‐Diketiminato‐Based Pincer‐Type Nickel(II) Complex: Synthesis and Catalytic Performance in the Cross‐Coupling of Aryl Fluorides with Aryl Grignard Reagents

Youji Kurihara

Papers

An investigation of the pyranose ring interconversion path of α-L-idose calculated using density functional theory

The conformation of alkyl cyclohexanones and terpenic ketones. Interpretation for the ‘alkylketone effect’ based on the CH/π(CO) hydrogen bond

Twisted coordination mode of bis(N-heterocyclic carbene) ligands in octahedral geometry of group 6 transition metal complexes: Synthesis, structure, and reactivity

Acetylacetonato-based pincer-type nickel(ii) complexes: synthesis and catalysis in cross-couplings of aryl chlorides with aryl Grignard reagents.

A β‐Diketiminato‐Based Pincer‐Type Nickel(II) Complex: Synthesis and Catalytic Performance in the Cross‐Coupling of Aryl Fluorides with Aryl Grignard Reagents