Sei Tsuboyama

CH/π hydrogen bonds in organic and organometallic chemistry

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.

CHπ interaction in the conformation of organic compounds. A database study

Abstract A study was carried out, with use of the Cambridge Structural Database, to examine the role of CH π interaction in the conformation of organic compounds. A number of short intramolecular CH π distances have been disclosed in the crystal structure of these compounds. The structure was inspected to know whether the crystal conformation is a consequence of the so-called packing forces, or the CH π interaction plays a role. The result has demonstrated that the CH π interaction plays an appreciable role in controlling the conformation of organic compounds.

CH/π Interactions as Demonstrated in the Crystal Structure of Host/Guest Compounds. A Database Study

Abstract Crystal structures deposited in the Cambridge Structural Database (CSD) were examined, by use of our program CHPI, for several kinds of clathrates in order to know the role of the CH/π interaction in host/guest chemistry. These include cyclodextrin complexes, calix[4]arene complexes, cryptophane complexes and pseudorotaxanes. A number of short CH/π distances have been shown in the crystal structure of these compounds. The result was discussed in view of the role of the CH/π interaction in controlling the specific structure of supramolecules.

CH/π Interactions Implicated in the Crystal Structure of Transition Metal Compounds − A Database Study

A statistical study was carried out to investigate the role of the CH/π interaction in the crystal structure of transition metal compounds. Thus, short CH/π distances were surveyed in crystal structures deposited in the Cambridge Structural Database. Among organometallic entries bearing C6 or C5 aromatic rings, a substantial part of the structures has been found to have intermolecular CH/π contacts shorter than the van der Waals distance. Further, in many structures short intramolecular CH/π contacts have been found. Interligand and intraligand CH/π interactions were also surveyed in coordination compounds bearing the typical ligands 1,10-phenanthroline, 2,2′-bipyridine, and 2,2′:6′,2′′-terpyridine, as well as triphenylphosphane complexes of ruthenium, rhenium, and rhodium. The results were discussed in the context of the CH/π interaction in controlling the crystal packing and the molecular structure of transition metal compounds. The compact structure with CH/π interactions is a general aspect in coordination and organometallic chemistry. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)

CH/π interaction in the conformation of peptides. A database study

A study was carried out, with use of the Cambridge Structural Database, to examine the role of the CH/pi interaction in the conformation of peptides. A number of short intramolecular CH/pi distances have been shown in the crystal structure of peptides bearing at least an aromatic residue in the sequence. The molecular structure in the crystal was inspected individually to know whether the conformation is merely a consequence of the so-called packing forces, or the CH/pi interaction plays a role. It has been demonstrated that the CH/pi interaction constitutes one of the key factors in controlling the conformation of peptides.

Spectroscopic studies on copper(II) complexes of chiral cyclens: [CuN4Cl] chromophores varying from square pyramidal to trigonal bipyramidal stereochemistry

A series of five copper(II) complexes with four geometrically isomeric ligands of 1,4,7,10-tetrabenzyl-2,5,8,11-tetraethyl-1,4,7,10-tetraazacyclododecane and with (2R,5R,8R,11R)-2,5,8,11-tetraethyl-1,4,7,10-tetraazacyclododecane has been investigated by means of ESR, CD and MCD in solution. X-ray studies reported separately had shown that the [CuN4Cl] chromophores were distorted to varying extents from square pyramidal to trigonal bipyramidal geometry. The stability and rigidity of the molecular structure have enabled us to carry out a complementary study of the crystalline state and solution chemistry. The ground state Kramers doublets varied from 3dx2−y2 to 3dz2 type with increasing distortion around the copper ion. The orbital sequence of the 3d1 positive hole, dx2−y2<dz2<dyz,xz<dxy, has been obtained for the C4v complexes. The 3dxy orbital is also the highest in energy for the complex with the 3dz2 type ground state doublet. This complex exhibited superhyperfine splitting in the gz region due to the chlorine nucleus, which implies the principal z axis of the g tensor is along the CuCl bond. The sign of the copper hyperfine tensors was determined by means of Swalens treatment. The changing values of the orbital coefficients decreasing for the 3dx2−z2 and increasing for the 3dz2, 3dxz and 3dyz in the ground state doublets have been attributed to concomitant elongation of the in-plane CuN bond and reduction of the out-of-plane CuCl bond length with the increasing distortion around the copper ions.

Chiral recognition of α-amino acids by an optically active (2S,5S,8S,11S)-2,5,8,11-tetraethyl cyclen cobalt(III) complex.

The optically active cobalt(III) complex with chiral cyclen, (2S,5S,8S,11S)-2,5,8,11-tetraethyl-1,4,7,10-tetraazacyclododecane, preferentially binds to D-phenylglycine (D-Phg) or D-t-leucine (D-t-Leu) rather than L-Phg or L-t-Leu, respectively, with 20% de in dimethyl sulfoxide at 293 K. Comparative studies on the crystal structures of cobalt(III) complexes with d-Phg and l-Phg revealed that the diastereoselectivity is due to the difference in the steric hindrance that should occur between the amino group of Phg and the ethyl group of cyclen.

Structural studies on metal complexes of chiral cyclen. III. The structure of chloro[(2R,5S,8R,11S)-1,4,7,10-tetrabenzyl-2,5,8,11-tetraethyl-1,4,7,10-tetraazacyclododecane]copper(II) chloride chloroform solvate

[Cu(C44H60N4)C1]C1.2CHCI 3 is triclinic, P[, with a = 14.297 (13), b = 14.542 (18), c = 12.960 (9)A, a = 99.81 (8), fl = 108.33 (7), y = 85.67(10) °, U = 2520 (4)/I,3, Z = 2, D m = 1.324, D c = 1.342 Mg m -3. The structure was refined to a final R of 6.4% for 4646 independent reflections. The 12-membered tetramine ring is coordinated to Cu tl as a quadridentate ligand, and takes a rectangular form. The Cu H atom forms an approximate trigonal bipyramid with five coordination. The observed Cu-CI distance, 2.354 (3)A, is shorter than those found in the cyclen complexes of Cu with a square-pyramidal conformation.

Stereochemical Properties of Copper(II) Complexes of (S)-3-Aminohexahydroazepine. Crystal and Molecular Structure of Bromobis[(S)-3-aminohexahydroazepine]copper(II)Perchlorate [CuBr(S-ahaz)2]ClO4

A series of copper(II) complexes of (S)-3-aminohexahydroazepine (abbreviated as S-ahaz) were prepared. The molecular structure of bromobis[(S)-3-aminohexahydroazepine]copper(II) perchlorate, [CuBr(S-ahaz)2]ClO4, was determined using single-crystal X-ray diffraction method. The complex crystallizes is space group P212121 with a=13.449(6), b=17.411(11), c=7.937(2) A, and Z=4. The structure was solved by the direct method and refined by the least squares to R value of 0.068 for 1853 unique reflections. The Cu2+ ion has the square-pyramidal five-coordination geometry with four nitrogen atoms as basal donors and a bromide as an apical donor. The structures of other copper(II) complexes of S-ahaz were assigned on the basis of the above X-ray analysis result, together with electronic spectral and conductivity measurements. The complexes having the formula Cu(S-ahaz)2X(ClO4) (X−=CI−, I−, NCS−, ONO−) were assigned to have square-pyramidal five-coordinated structures. The S-ahaz complexes Cu(S-ahaz)2X2 (X−=Cl−, Br−...

Cobalt(III) complex of (2R, 5R, 8R, 11R)-tetraethyl-1,4,7,10-tetraazacyclododecane

Abstract Preparation and property of Co(III) complex of an optically active 12-membered macrocyclic lignad (tecyclen) are reported.