Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

A Cyclotomic Lattice Based Quasi-Orthogonal STBC for Eight Transmit Antennas

In this letter, we propose a lattice-based full diversity design for rate-one quasi-orthogonal space time block codes (QSTBC) to obtain an improved diversity product for eight transmit antennas where the information bits are mapped into 4-D lattice points instead of the common modulation constellations. Particularly, the diversity product of the proposed code is directly determined by the minimum Euclidean distance of the used lattice and can be improved by using the lattice packing. We show analytically and by using simulation results that the proposed code achieves a larger diversity product than the rate-one QSTBCs reported previously.

Study of FT-Raman Spectroscopy on the Effects of Lanthanide Ions and Their Complexes on the Fluidity of Dipalmitoylphosphatidylethanolamine Bilayer

The effects of lanthanide ions and their complexes of citrate and DTPA ligands on the fluidity of dipalmitoylphosphatidylethanolamine (DPPE) bilayers have been studied by FT-Raman spectroscopy. the results show that lanthanide ions of lower concentrationn decrease the fluidity of acyl chains of DPPE bilayers and change the conformation of C C-C backbone from gauche to the trans lanthanide ions of higher concentration, however, increase the fluidity of acyl chains and increase the gauche population of C-C-C backbone. Lanthanide complex of citrate have no effect on the fluidity of acyl chains of DPPE bilayers in the region of experimental concentration, but La-DTPA complex increase slightly the fluidity of acyl chains. the results also indicated that lanthanide ion of lower concentration changed the lattice packing of hydrocarbon chains from hexagonal form to orthorhombic form, but it is still in hexagonal or distorted hexagonal lattice cell in the gel state in the presence of metal ions and lanthanide complexes of higher concentration

Mer and fac isomerism in tris chelate diimine metal complexes

In this perspective, we highlight the issue of meridional (mer) and facial (fac) orientation of asymmetrical diimines in tris-chelate transition metal complexes. Diimine ligands have long been the workhorse of coordination chemistry, and whilst there are now good strategies to isolate materials where the inherent metal centered chirality is under almost complete control, and systematic methodologies to isolate heteroleptic complexes, the conceptually simple geometrical isomerism has not been widely investigated. In systems where the two donor atoms are significantly different in terms of the σ-donor and π-accepting ability, the fac isomer is likely to be the thermodynamic product. For the diimine complexes with two trigonal planar nitrogen atoms there is much more subtlety to the system, and external factors such as the solvent, lattice packing and the various steric considerations play a delicate role in determining the observed and isolable product. In this article we discuss the possibilities to control the isomeric ratio in labile systems, consider the opportunities to separate inert complexes and discuss the observed differences in their spectroscopic properties. Finally we report on the ligand orientation in supramolecular systems where facial coordination leads to simple regular structures such as helicates and tetrahedra, but the ability of the ligand system to adopt a mer orientation enables self-assembled structures of considerable beauty and complexity. 

An Extension of Craig's Family of Lattices

Let p be a prime, and let zeta(p) be a primitive p-th root of unity. The lattices in Craig's family are (p - 1)-dimensional and are geometrical representations of the integral Z[zeta(p)]-ideals < 1 - zeta(p)>(i), where i is a positive integer. This lattice construction technique is a powerful one. Indeed, in dimensions p - 1 where 149 <= p <= 3001, Craig's lattices are the densest packings known. Motivated by this, we construct (p - 1)(q - 1)-dimensional lattices from the integral Z[zeta(pq)]-ideals < 1 - zeta(p)>(i) < 1 - zeta(q)>(j), where p and q are distinct primes and i and fare positive integers. In terms of sphere-packing density, the new lattices and those in Craig's family have the same asymptotic behavior. In conclusion, Craig's family is greatly extended while preserving its sphere-packing properties.

Synthesis, properties and application of polyphenylene phosphonium salts

The central objective of this work was to generate weakly coordinating cations of unprecedented molecular size providing an inherently stable hydrophobic shell around a central charge. It was hypothesized that divergent dendritic growth by means of thermal [4+2] Diels-Alder cycloaddition might represent a feasible synthetic method to circumvent steric constraints and enable a drastic increase in cation size.rnThis initial proposition could be verified: applying the divergent dendrimer synthesis to an ethynyl-functionalized tetraphenylphosphonium derivative afforded monodisperse cations with precisely nanoscopic dimensions for the first time. Furthermore, the versatile nature of the applied cascade reactions enabled a throughout flexible design and structural tuning of the desired target cations. The specific surface functionalization as well as the implementation of triazolyl-moieties within the dendrimer scaffold could be addressed by sophisticated variation of the employed building block units (see chapter 3). rnDue to the steric screening provided by their large, hydrophobic and shape-persistent polyphenylene shells, rigidly dendronized cations proved more weakly coordinating compared to their non-dendronized analogues. This hypothesis has been experimentally confirmed by means of dielectric spectroscopy (see chapter 4). It was demonstrated for a series of dendronized borate salts that the degree of ion dissociation increased with the size of the cations. The utilization of the very large phosphonium cations developed within this work almost achieved to separate the charge carriers about the Bjerrum length in solvents of low polarity, which was reflected by approaching near quantitative ion dissociation even at room temperature. In addition to effect the electrolyte behavior in solution, the steric enlargement of ions could be visualized by means of several crystal structure analyses. Thus an insight into lattice packing under the effect of extraordinary large cations could be gathered. rnAn essential theme of this work focused on the application of benzylphosphonium salts in the classical Wittig reaction, where the concept of dendronization served as synthetic means to introduce an exceptionally large polyphenylene substituent at the -position. The straightforward influence of this unprecedented bulky group on the Wittig stereochemistry was investigated by NMR-analysis of the resulting alkenes. Based on the obtained data a valuable explanation for the origin of the observed selectivity was brought in line with the up-to-date operating [2+2] cycloaddition mechanism. Furthermore, a reliable synthesis protocol for unsymmetrically substituted polyphenylene alkenes and stilbenes was established by the design of custom-built polyphenylene precursors (see chapter 5).rnFinally, fundamental experiments to functionalize a polymer chain with sterically shielded ionic groups either in the pending or internal position were outlined within this work. Thus, inherently hydrophobic polysalts shall be formed so that future research can invesigate their physical properties with regard to counter ion condensation and charge carrier mobility.rnIn summary, this work demonstrates how the principles of dendrimer chemistry can be applied to modify and specifically tailor the properties of salts. The numerously synthesized dendrimer-ions shown herein represent a versatile interface between classic organic and inorganic electrolytes, and defined macromolecular structures in the nanometer-scale. Furthermore the particular value of polyphenylene dendrimers in terms of a broad applicability was illustrated. This work accomplished in an interdisciplinary manner to give answer to various questions such as structural modification of ions, the resulting influence on the electrolyte behavior, as well as the stereochemical control of organic syntheses via polyphenylene phosphonium salts. rn

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study. (c) 2005 Wiley Periodicals, Inc.

Effect of substitution on molecular conformation and packing features in a series of aryl substituted ethyl-6-methyl-4-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylates

The supramolecular structures of eight aryl protected ethyl-6-methyl-4-phenyl-2-thioxo-1,2,3,4 tetrahydropyrimidine-5-carboxyl ates were analyzed in order to understand the effect of variations in functional groups on molecular geometry, conformation and packing of molecules in the crystalline lattice. It is observed that the existence of a short intra-molecular C-H center dot center dot center dot pi interaction between the aromatic hydrogen of the aryl ring with the isolated double bond of the six-membered tetrahydropyrimidine ring is a key feature which imparts additional stability to the molecular conformation in the solid state. The compounds pack via the cooperative involvement of both N-H center dot center dot center dot S=C and N-H center dot center dot center dot O=C intermolecular dimers forming a sheet like structure. In addition, weak C-H center dot center dot center dot O and C-H center dot center dot center dot pi intermolecular interactions provide additional stability to the crystal packing.

Topological analysis off charge density distribution in concomitant polymorphs of 3-acetylcoumarin, a case off packing polymorphism

Detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin in terms of experimental and theoretical densities shows significant differences in the intermolecular features when analyzed based on the topological properties via the quantum theory of atoms in molecules. The two forms, triclinic and monoclinic (Form A and Form B), pack in the crystal lattice via weak C-H---O and C-H---pi interactions. Form A results in a head-to-head molecular stack, while Form B generates a head-to-tail stack. Form A crystallizes in PI (Z' = 2) and Form B crystallizes in P2(1)/n (Z = 1). The electron density maps of the polymorphs demonstrate the differences in the nature of the charge density distribution in general. The charges derived from experimental and theoretical analysis show significant differences with respect to the polymorphic forms. The molecular dipole moments differ significantly for the two forms. The lattice energies evaluated at the HF and DFT (B3LYP) methods with 6-31G** basis set for the two forms clearly suggest that Form A is the thermodynamically stable form as compared to Form B. Mapping of electrostatic potential over the molecular surface shows dominant variations in the electronegative region, which bring out the differences between the two forms.

Insights into conformational and packing features in a series of aryl substituted ethyl-6-methyl-4-phenyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate

The supramolecular structures of eight aryl protected ethyl-6-methyl-4-phenyl-2-oxo-1,2,3,4-tetrahydropyrimidine- 5-carboxylates have been analyzed to determine the role of different functional groups on the molecular geometry, conformational characteristics and the packing of these molecules in the crystal lattice. Out of these the para fluoro substituted compound on the aryl ring exhibits conformational polymorphism, due to the different conformation of the ester moiety. This behaviour has been characterized using both powder and single-crystal X-ray diffraction, optical microscopy and differential scanning calorimetry performed on both these polymorphs. The compounds pack via the cooperative interplay of strong N-H center dot center dot center dot O=C intermolecular dimers and chains forming a sheet like structure. In addition, weak C-H center dot center dot center dot O=C and C-H center dot center dot center dot pi interactions impart additional stability to the crystal packing.

Solid-state photobehaviour and crystal packing of o-chlorobenzylidene-DL-piperitone: influence of molecular topology on photobehaviour

C17H19ClO, M(r) = 274.7, triclinic, P1BAR, a = 11.154 (3), b = 12.685 (2), c = 12.713 (2) angstrom, alpha = 100.68 (1), beta = 113.58 (1), gamma = 104.50 (2)-degrees, V = 1511.1 (6) angstrom3, Z = 4, D(m) = 1.22, D(x) = 1.215 Mg m-3, Cu K-alpha, lambda = 1.5418 angstrom, mu = 2.16 mm-1, F(000) = 584, T = 293 K, R = 0.057 for 3481 observed reflections. The title compound is photostable in the crystalline state and lattice-energy calculations have been employed to rationalize the photobehaviour. The well-known beta-steering ability of the chloro group is not operative in this system as there are no Cl...Cl interactions in the crystal lattice. All five benzylidene-DL-piperitone structures so far studied are alpha-packed and the molecular topology appears to be a deciding factor even in the presence of steering groups.

Intruder detection over sensor placement in a hexagonal lattice

The problem of intrusion detection and location identification in the presence of clutter is considered for a hexagonal sensor-node geometry. It is noted that in any practical application,for a given fixed intruder or clutter location, only a small number of neighboring sensor nodes will register a significant reading. Thus sensing may be regarded as a local phenomenon and performance is strongly dependent on the local geometry of the sensor nodes. We focus on the case when the sensor nodes form a hexagonal lattice. The optimality of the hexagonal lattice with respect to density of packing and covering and largeness of the kissing number suggest that this is the best possible arrangement from a sensor network viewpoint. The results presented here are clearly relevant when the particular sensing application permits a deterministic placement of sensors. The results also serve as a performance benchmark for the case of a random deployment of sensors. A novel feature of our analysis of the hexagonal sensor grid is a signal-space viewpoint which sheds light on achievable performance.Under this viewpoint, the problem of intruder detection is reduced to one of determining in a distributed manner, the optimal decision boundary that separates the signal spaces SI and SC associated to intruder and clutter respectively. Given the difficulty of implementing the optimal detector, we present a low-complexity distributive algorithm under which the surfaces SI and SC are separated by a wellchosen hyperplane. The algorithm is designed to be efficient in terms of communication cost by minimizing the expected number of bits transmitted by a sensor.

Synthesis and an Evaluation of Molecular Conformation and Crystal Packing in Two Substituted 4-Phenylquinolines

The title compounds, namely Methyl 2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (II) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)A degrees in (I), and 79.02 (8)A degrees in (II) respectively. It is the weak C-H center dot center dot center dot O=C H-bond and C-H center dot center dot center dot pi interactions which dictate packing of molecules in (I). In (II), it is C-H center dot center dot center dot N and C-H center dot center dot center dot pi, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, pi center dot center dot center dot pi aromatic stacking interactions involving the quinoline fragment is present in all the molecules. The title compounds, namely methyl-2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (III) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)A degrees in (I), and 79.02 (8)A degrees in (II) respectively. It is the weak C-H center dot center dot center dot O=C H-bond and C-H center dot center dot center dot pi interactions which dictate packing of molecules in (I). In (II), it is C-H center dot center dot center dot N and C-H center dot center dot center dot pi, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, pi center dot center dot center dot pi aromatic stacking interactions involving the quinoline fragment is present in all the molecules.

Crystal packing of poly(ether ketone ketone)

The crystal structure of poly(ether ketone ketone) (PEKK) is predicted by using Cerius2 software according to the wide angle X-ray diffraction (WAXD) experiment result. The predicted structure has a planar zigzag chain conformation between ether oxygen and ketone carbons in an orthorhombic lattice. Average zigzag angle is 126 degrees and average torsion angle is 30.32 degrees. The WAXD powder pattern calculated from the crystal packing model is in good agreement with the experiment result.

Structural characterization of a new crystal form of the four-way Holliday junction formed by the DNA sequence d(CCGGTACCGG)2: sequence versus lattice?

DNA-strand exchange is a vital step in the recombination process, of which a key intermediate is the four-way DNA Holliday junction formed transiently in most living organisms. Here, the single-crystal structure at a resolution of 2.35 Å of such a DNA junction formed by d(CCGGTACCGG)2, which has crystallized in a more highly symmetrical packing mode to that previously observed for the same sequence, is presented. In this case, the structure is isomorphous to the mismatch sequence d(CCGGGACCGG)2, which reveals the roles of both lattice and DNA sequence in determining the junction geometry. The helices cross at the larger angle of 43.0° (the previously observed angle for this sequence was 41.4°) as a right-handed X. No metal cations were observed; the crystals were grown in the presence of only group I counter-cations.