N-2-(4-Methyl-2-quinolyl)phenyl]acetamide: a P1 structure with Z=4

The title compound, C18H16N2O, crystallizes in the triclinic space group P1, with four independent molecules in the asymmetric unit wherein two molecules have an irregular -ac, -ac, +ap conformation (ap, antiperiplanar; ac, anticlinal), while the other molecules exhibit a different, +ac, +ac, +ap conformation. The planar (r.m.s. deviation = 0.006 A in each of the four molecules) quinoline ring systems of the four molecules are oriented at dihedral angles of 32.8 (2), 33.4 (2), 31.7 (2) and 32.3 (2)degrees with respect to the benzene rings. Intramolecular N-H...N interactions occur in all four independent molecules. The crystal packing is stabilized by intermolecular N-H...O and C-H...O hydrogen bonds, and are further consolidated by C-H...pi and pi-pi stacking interactions centroid-centroid distances = 3.728 (3), 3.722 (3), 3.758 (3) and 3.705 (3) A].

1-(3,5-Diethyl-1H-pyrazol-1-yl)-3-phenylisoquinoline

In the title molecule, C22H21N3, the isoquinoline ring is almost planar maximum deviation = 0.046 (1) A] and makes dihedral angles of 52.01 (4) and 14.61 (4)degrees with the pyrazole and phenyl rings, respectively. The phenyl ring and the pyrazole ring are twisted by 44.20 (6)degrees with respect to each other. The terminal C atoms of both of the ethyl groups attached to the pyrazole ring are disordered over two sites with occupancy ratios of 0.164 (7):0.836 (7) and 0.447 (16):0.553 (16). A weak intramolecular C-H...N contact may influence the molecular conformation. The crystal structure is stabilized by C-H...pi contacts involving the phenyl and pyrazole rings, and by pi-pi stacking interactions involving the pyridine and benzene rings centroid-centroid distance = 3.5972 (10) A].

Crystallographic characterization of the conformation of the 1-aminocyclohexane-1-carboxylic acid residue in simple derivatives and peptides

The crystal structures of 1-aminocyclohexane-1-carboxylic acid (H-Acc6-OH) and six derivatives (including dipeptides) have been determined. The derivatives are Boc-Acc6-OH, Boc-(Acc6)2-OH, Boc-L-Met-Acc6-OMe, ClCH2CO-Acc6-OH, p-BrC6H4CO-Acc6-OH oxazolone, and the symmetrical anhydride from Z-Acc6-OH, [(Z-Acc6)2O]. The cyclohexane rings in all the structures adopt an almost perfect chair conformation. The amino group occupies the axial position in six structures; the free amino acid is the only example where the carbonyl group occupies an axial position. The values determined for the torsion angles about the N–Cα(φ) and Cα–CO (ψ) bonds correspond to folded, potentially helical conformations for the Acc6 residue.

Crystallographic identification of a ‘stepped-cubane’ structure for the Cu4O4 core in [Cu4L2(bipy)4(µ3-OH)2][ClO4]4(HL = 5-hydroxy-6-methylpyridine-,4-dimethanol, bipy = 2,2′-bipyridine)

The structure of [Cu4L2(bipy)4(µ3-OH)2][ClO4]4 containing a Vitamin B6 ligand, pyridoxine (5-hydroxy-6-methylpyridine-3,4-dimethanol, HL), and 2,2′-bipyridine (bipy) has been determined by single-crystal X-ray analysis. This is the first report on a copper(II) complex having a ‘stepped-cubane’ structure. The compound crystallizes in the triclinic space group P[1 with combining macron](Z= 1) with a= 11.015(3), b= 11.902(1), c= 13.142(2)Å, α= 105.07(1), β= 102.22(1) and γ= 99.12(1)°; R= 0.054). The co-ordination geometry around each copper is trigonally distorted square pyramidal. Two of the basal sites are occupied by bipyridyl nitrogens in a bidentate fashion. The remaining basal positions for Cu(1) are filled by a phenolic oxygen and a 4-hydroxymethyl oxygen of the L moiety, whereas for Cu(2) they are occupied by two µ3-OH oxygens. The axial sites are occupied by a µ3-OH oxygen and the 4-hydroxymethyl oxygen of the same pyridoxine for Cu(1) and Cu(2), respectively. Both the bridging nature of the 4-hydroxymethyl oxygen of the L moiety and the unsymmetrical bridging nature of the µ3-OH groups with axial–equatorial bridging are novel features. The structure is discussed in relation to stepped-cubane structures reported in the literature. A comparative study is also made with µ3-hydroxo-bridged copper(II) complexes. Both the plasticity effect of CuII and the stacking interactions between the various rings appear to be important in stabilizing this unusual structure.

Conformational properties of hybrid peptides containing alpha and omega-amino acids

This review briefly surveys the conformational properties of guest omega-amino acid residues when incorporated into host alpha-peptide sequences. The results presented focus primarily on the use of beta- and gamma-residues in alphaomega sequences. The insertion of additional methylene groups into peptide backbones enhances the range of accessible conformations, introducing additional torsional variables. A nomenclature system, which permits ready comparisons between alpha-peptides and hybrid sequences, is defined. Crystal structure determination of hybrid peptides, which adopt helical and beta-hairpin conformations permits the characterization of backbone conformational parameters for beta- and gamma-residues inserted into regular alpha-polypeptide structures. Substituted beta- and gamma-residues are more limited in the range of accessible conformation than their unsubstituted counterparts. The achiral beta,beta-disubstituted gamma-amino acid, gabapentin, is an example of a stereochemically constrained residue in which the torsion angles about the C-beta-C-gamma (theta(1)) and C-alpha-C-beta (theta(2)) bonds are restricted to the gauche conformation. Hybrid sequences permit the design of novel hydrogen bonded rings in peptide structures.

MNDO study of coupled strained hydrocarbons: Additivity of exocyclic C---C bond contraction induced by different ring systems

MNDO geometry optimizations were carried out on a series of symmetrically and unsymmetrically coupled strained ring hydrocarbons, R1-R1 and R1–R2 (R1=methyl, cyclopropyl, 1-bicyclo[1.1.0]butyl, 1-bicyclo[1.1.1]pentyl, prismyl, cubyl, 6-tricyclo [3.1.1.03,6]heptyl, and tetrahedryl groups; R2=methyl and cyclopropyl). The remarkable contraction of the C---C bond connecting the strained rings found experimentally in a few cases was reproduced correctly by the calculations. A linear correlation was found between the bond length shortening and the bond angle widening at the corresponding carbon atoms for all the structures considered. The reduction in C---C bond lengths due to various ring systems is additive. The additivity indicates that inter-ring interactions which effect the central bond length are absent and confirms the common electronic origin of bond contraction in these systems, viz. enhanced s-character in the exocyclic bonds of strained rings.

Computational Methods for Studies of Quantum Dots and Boson Condensates

This thesis presents ab initio studies of two kinds of physical systems, quantum dots and bosons, using two program packages of which the bosonic one has mainly been developed by the author. The implemented models, \emph{i.e.}, configuration interaction (CI) and coupled cluster (CC) take the correlated motion of the particles into account, and provide a hierarchy of computational schemes, on top of which the exact solution, within the limit of the single-particle basis set, is obtained. The theory underlying the models is presented in some detail, in order to provide insight into the approximations made and the circumstances under which they hold. Some of the computational methods are also highlighted. In the final sections the results are summarized. The CI and CC calculations on multiexciton complexes in self-assembled semiconductor quantum dots are presented and compared, along with radiative and non-radiative transition rates. Full CI calculations on quantum rings and double quantum rings are also presented. In the latter case, experimental and theoretical results from the literature are re-examined and an alternative explanation for the reported photoluminescence spectra is found. The boson program is first applied on a fictitious model system consisting of bosonic electrons in a central Coulomb field for which CI at the singles and doubles level is found to account for almost all of the correlation energy. Finally, the boson program is employed to study Bose-Einstein condensates confined in different anisotropic trap potentials. The effects of the anisotropy on the relative correlation energy is examined, as well as the effect of varying the interaction potential.}

Protein Hydration and Water Structure: X-ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content

Low-humidity monoclinic lysozyme, resulting from a water-mediated transformation, has one of the lowest solvent contents (22% by volume) observed in a protein crystal. Its structure has been solved by the molecular replacement method and refined to an R value of 0.175 for 7684 observed reflections in the 10–1.75 Å resolution shell. 90% of the solvent in the well ordered crystals could be located. Favourable sites of hydration on the protein surface include side chains with multiple hydrogen-bonding centres, and regions between short hydrophilic side chains and the main-chain CO or NH groups of the same or nearby residues. Major secondary structural features are not disrupted by hydration. However, the free CO groups at the C terminii and, to a lesser extent, the NH groups at the N terminii of helices provide favourable sites for water interactions, as do reverse turns and regions which connect β-structure and helices. The hydration shell consists of discontinuous networks of water molecules, the maximum number of molecules in a network being ten. The substrate-binding cleft is heavily hydrated, as is the main loop region which is stabilized by water interactions. The protein molecules are close packed in the crystals with a molecular coordination number of 14. Arginyl residues are extensively involved in intermolecular hydrogen bonds and water bridges. The water molecules in the crystal are organized into discrete clusters. A distinctive feature of the clusters is the frequent occurrence of three-membered rings. The protein molecules undergo substantial rearrangement during the transformation from the native to the low-humidity form. The main-chain conformations in the two forms are nearly the same, but differences exist in the side-chain conformation. The differences are particularly pronounced in relation to Trp 62 and Trp 63. The shift in Trp 62 is especially interesting as it is also known to move during inhibitor binding.

A porphyrin bearing tetrahydrothiophene pickets; co-ordination behaviour and electron transfer

A novel ‘picket-fence’ porphyrin, 5,10,15,20-tetrakis[o-(tetrahydro-2-thenoylamino)phenyl]porphyrin (H2L) with ligating tetrahydrothiophene rings disposed perpendicular to the porphyrin plane has been synthesised. Its zinc(II) derivative, [ZnL], binds two silver(I) ions co-operatively with a dissociation constant of 4.8 × 10–8 dm3 mol–1. Time-resolved fluorescence lifetime measurements reveal the presence of intramolecular photoexcited electron transfer in this donor–acceptor system.

Can equipartition fields produce the tilts of bipolar magnetic regions?

The effect of turbulence on the nonaxisymmetric flux rings of equipartition field strength in bipolar magnetic regions is studied on the basis of the small-scale momentum exchange mechanism and the giant cell drag combined with the Kelvin-Helmholtz drag mechanism. It is shown that the giant cell drag and small-scale momentum exchange mechanism can make equipartition flux loops emerge at low latitudes, in addition to making them exhibit the observed tilts. However, the sizes of the flux tubes have to be restricted to a couple of hundred kilometers. An ad hoc constraint on the footpoints of the flux loops is introduced by not letting them move in the phi direction, and it is found that equipartition fields of any size can be made to emerge at sunspot latitudes with the observed tilts by suitably adjusting the footpoint separations.

Molecular structure of Lantadene-B&C, triterpenoids ofantana camara, red variety: Lantadene-B, 22β-angeloyloxy-3-oxoolean-12-en-28-oic acid; Lantadene-C, 22 β-(S)-2′-methyl butanoyloxy-3-oxoolean-12-en-28-oic acid

(I)Lantadene-B: C35H52O5,M r =552.80, MonoclinicC2,a=25.65(1),b=6.819(9),c=18.75(1) Å,beta=100.61(9),V=3223(5) Å3,Z=4,D x =1.14 g cm–3 CuKagr (lambda=1.5418A),mgr=5.5 cm–1,F(000)=1208,R=0.118,wR=0.132 for 1527 observed reflections withF o ge2sgr(F o ). (II)Lantadene-C: C35H54O5·CH3OH,Mr=586.85, Monoclinic,P21,a=9.822(3),b=10.909(3),c=16.120(8)Å,beta=99.82(4),V=1702(1)Å3,Z=2,D x =1.145 g cm–3, MoKagr (lambda=0.7107Å), mgr=0.708 cm–1 F(000)=644,R=0.098, wR=0.094 for 1073 observed reflections. The rings A, B, C, D, and E aretrans, trans, trans, cis fused and are in chair, chair, sofa, half-chair, chair conformations, respectively, in both the structures. In the unit cell the molecules are stabilized by O-HctdotO hydrogen bonds in both the structures, however an additional C-HctdotO interaction is observed in the case of Lantadene-C.

Raman spectral studies of borate glasses

Raman spectroscopic measurements in borate glasses have been reviewe. The review shows that the technique is useful in identifying the structural groups present in the borate on the basis of the Krogh-Moe hypothesis. Vitreous B2O3 and alkali borates are extensvvely studied and a satisfactory assignment of bands is possible by a careful consideration of the literature. A cation effect on the borate netwoork is observed. Availaable measurements on binary borates other than alkali borates and on ternary borates are limited and more work is required to identify the structural modifications that take place with composition. Mixed alkali effect is reported only lithium-caesium borade and shows the formation of non-bridging oxygens, destroying the six-membered rings when Li2O is replaced by Cs2O. Fast ionic glasses (alkali borates containing alkali halides) yield the same Raman spectra as the alkali borates, except when the alkali is a fluoride.

Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Structure of a steriod fungal metabolite

3a,7a, 14a-Trihydroxypregn-16-en-20-one, C21H3204, M r = 348.48, orthorhombic, P212121, a = 9.211 (1), b = 13.201 (1), c = 16.031 (1),~, V = 1949.28 (29)/~3, Z = 4, Dx = 1.187 g cm -3, A(Cu Ka), = 1.5418 ,~,/z = 6.07 cm-l, F(000) = 760, T= 293 K, R = 0.061 for 1337 observations. The A, B and C rings adopt normal chair conformations with the D ring in a 14a-envelope conformation. The molecules are held together by two hydrogen bonds [0(3)..'0(20) = 2.879 and O(7).--O(14)= 2.612 A,].

Structure of pregna-4,16-diene-7[alpha],14[alpha]-diol-3,20-dione

7a,14a-Dihydroxypregna-4,16-diene-3,20- dione, C21H2804, M r = 344.45, orthorhombic, P212121, a = 7.136 (1), b = 12.342 (1), c = 20.049 (3)/k, V= 1765.7 (3)/k 3, Z = 4, Dx = 1.295 g cm -3, A(Cu Kte) = 1.5418/k, /z = 6.7 cm- a, F(000) = 744, T = 293 K, R = 0.048 for 1345 observations. The A ring may be described as in a l a,2flhalf- chair conformation or a l a-sofa conformation. The B and C rings adopt normal chair conformations and the D ring has a 14a-envelope conforma tion. The molecules are held together by a hydrogen bond [0(3)...0(7)= 2.767 A].