CHPI Institute

Tokyo, Japan

CHPI Institute

Tokyo, Japan
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Nishio M.,CHPI Institute | Umezawa Y.,Institute of Microbial Chemistry BIKAKEN Tokyo | Fantini J.,Aix - Marseille University | Weiss M.S.,Helmholtz Center Berlin | Chakrabarti P.,Bose Institute of India
Physical Chemistry Chemical Physics | Year: 2014

This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds-Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community. This journal is © the Partner Organisations 2014.


Umezawa Y.,Institute of Microbial Chemistry BIKAKEN Tokyo | Nishio M.,CHPI Institute
Supramolecular Chemistry | Year: 2013

A crystallographic database study was carried out to investigate the potentiality of guanidinium group acting as an effective CH acceptor (π-donor) of the CH/π hydrogen bond; it has been demonstrated that this group is a good receptor of CH in crystals of arginine and its derivatives. Implication of the present finding to protein biochemistry and rational drug design is suggested. © 2013 © 2013 Taylor & Francis.


Takahashi O.,Hiroshima University | Yamasaki K.,Hiroshima University | Kohno Y.,Yokohama National University | Ueda K.,Yokohama National University | Nishio M.,CHPI Institute
RSC Advances | Year: 2012

Introduction of an axial methyl group to a bridgehead carbon has been known to enhance the circular dichroism (CD) amplitude of exomethylene steroids such as 4- and 6-methylene-5α-estrane, at ca. 200 nm (π/π* transition). To investigate the effect of a methyl group on the rotational strength of these steroids, time-dependent density functional theory (DFT) calculations were carried out at the M06-2X/6-311++G(d,p)//MP2/6-31G(d,p) level. It has been shown that the replacement of the bridgehead hydrogen atom at position 10 of these steroids by a methyl group influenced the CD amplitude at the π/π* transition. Analysis of natural bonding orbital (NBO) charges of relevant atoms has provided data consistent with this finding. In view of this, we suggest that the enhancement of the CD amplitude by methyl substitution β to the carbon-carbon double bond originates from the CH/π hydrogen bond occurring between CH groups and the π-system. © 2012 The Royal Society of Chemistry.


The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm. © the Owner Societies 2011.


Rotational strengths were calculated, by the TD-DFT (time-dependent density functional theory) method, for a series of 5,7-diene steroids, ergosterol, lumisterol, pirocarciferol, isopirocarciferol, as well as structurally related compounds such as 2,4-cholestadiene and levopimaric acid. The results were discussed in the context of the CH/π hydrogen bond; we suggest that the CH/π hydrogen bond plays an important role in the enhancement of CD amplitude of cisoid dienes. © 2013 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.


Takahashi O.,Hiroshima University | Kohno Y.,Yokohama National University | Ueda K.,Yokohama National University | Nishio M.,CHPI Institute
New Journal of Chemistry | Year: 2013

Introduction of methyl group(s) at bridgehead carbons at positions 10 and 5 of steroidal 1,3-dienes has been known to influence the Cotton effect of the π-π* transition at ca. 260 nm. Thus the positive sign of the circular dichroism (CD) curve of 5α-estra-1,3-dien-17β-ol becomes negative in 5α-androsta-1,3-dien-17β-ol, even though the helical sense of the diene chromophore remains practically unchanged. In order to investigate the effect of methyl substitution on the CD of 1,3-diene steroids, we carried out time dependent density functional theory (TD-DFT) calculations at the M06-2X/6-311++G(d,p)//MP2/6-31G(d,p) level. It has been shown that replacement of the bridgehead hydrogen by a methyl group greatly influenced the sign and amplitude of CD spectra of the π-π* transition. We suggest that the change in the CD curves by methyl substitution originates from CH/π hydrogen bonds between the diene π-system and a CH3 group homoallylic to it. © 2013 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.


Takahashi O.,Hiroshima University | Kohno Y.,Yokohama National University | Nishio M.,CHPI Institute
Chemical Reviews | Year: 2010

Researchers conducted investigations to reveal evidence from the latest experimental data and high-level ab initio MO calculations regarding the relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates. The researchers showed that the gauche or folded conformation prevailed in organic compounds bearing at least an electronegative or π-group in the molecule. Evidence gathered from the investigations revealed that the gauche or folded conformation is preferred to describe the relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates. It was demonstrated that weak attractive forces were essential in deciding the conformation of organic compounds and the 3D structure of biomacromolecules. Researchers also gathered evidence that revealed that hydrogen bonds other than the conventional hydrogen bond were ubiquitous.


Nishio M.,CHPI Institute
Journal of Molecular Structure | Year: 2012

The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly. © 2011 Elsevier B.V. All rights reserved.

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