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

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.

Orientational relaxation in a random dipolar lattice: Wave-number and frequency dependence

In order to understand the role of translational modes in the orientational relaxation in dense dipolar liquids, we have carried out a computer ''experiment'' where a random dipolar lattice was generated by quenching only the translational motion of the molecules of an equilibrated dipolar liquid. The lattice so generated was orientationally disordered and positionally random. The detailed study of orientational relaxation in this random dipolar lattice revealed interesting differences from those of the corresponding dipolar liquid. In particular, we found that the relaxation of the collective orientational correlation functions at the intermediate wave numbers was markedly slower at the long times for the random lattice than that of the liquid. This verified the important role of the translational modes in this regime, as predicted recently by the molecular theories. The single-particle orientational correlation functions of the random lattice also decayed significantly slowly at long times, compared to those of the dipolar liquid.

Proton spin lattice relaxation in lithium ammonium sulphate LiNH4SO4

Lithium ammonium sulphate (LAS) undergoes a phase transition at TC1=459.5K from a paraelectric phase (phase I) to a ferroelectric phase (phase II) and again at TC2=283K to a polar ferroelastic phase (phase III). Proton spin lattice relaxation time measured at 10 MHz in powdered LAS in the temperature range 480 to 77K shows discontinuous changes at the two transitions.

Mean-field results of a lattice-gas model of multilayer adsorption

A lattice-gas model of multilayer adsorption has been solved in the mean-field approximation by a different numerical method. Earlier workers obtained a single solution for all values of temperature and pressure. In the present work, multiple solutions have been obtained in certain regions of temperature and pressure which give rise to bysteresis in the adsorption isotherm. In addition, we have obtained a parameter which behaves like an order parameter for the transition. The potential-energy function shows a double minimum in the region of bysteresis and a single maximum elsewhere.

Studies in Nonlinear Optical Materials: Structure of Methyl 2-(4-Ethyl-5-methyl- 2-thioxo-2,3-dihydro-l,3-thiazol- 3-yl) propionate

CIoH15NO282, Mr=245"0, orthorhombic, P21212 ~, a = 6.639 (2), b = 8.205 (2), c = 22.528(6)A, V= I227.2(6)A 3, z=4, Dm= 1.315, Dx= 1.326gem -3, MoKa, 2=0.7107A, 12= 3.63 cm -1, F(000) = 520, T= 293 K, R = 0.037 for 1115 significant reflections. The second-harmonicgeneration (SHG) efficiency of this compound is only 1/10th of the urea standard. The observed low second-order nonlinear response may be attributed to the unfavourable packing of the molecules in the crystal lattice.

Hantzsch 1,4-dihydropyridine esters and analogs: candidates for generating reproducible one-dimensional packing motifs

Examination of the symmetric Hantzsch 1,4-dihydropyridine ester derivatives of the prototypical nifedipine molecule indicates the tendency of this class of molecule to form a common packing motif. Crystal structure analysis of 2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylic diesters and analogs reveals that they form extended chains, characterized as the C(6) packing motif, via intermolecular (amine) N-H...O=C (C3,C5 carbonyl) hydrogen bonds. In addition, all the prepared derivatives also satisfy the basic structural requirements for their high binding efficiency to the receptor. The reproducible C(6) packing motif observed among these compounds has a use in the design of solid-state materials.

On states, on a lattice, with half-integral charge

In certain molecular models, and related one-dimensional field theories, localized objects appear with half-integral expectation values of charge. We consider whether these states are eigenstates of charge, with half-integral eigenvalue. We find that it is indeed so for a suitably diffuse definition of the charge operator in question. This diffuse charge operator has a spectrum which approaches a continuum. The analysis is made on a lattice, to avoid divergence ambiguities, and on a finite length, which is only subsequently made large. The half-integral charge phenomenon is not tied to solitons, but can also arise as an end effect.

Proline ring conformations corresponding to a bistable jump model from 13C spin-lattice relaxation times

A formalism for extracting the conformations of a proline ring based on the bistable jump model of R. E. London [(1978) J. Am. Chem. Soc. 100, 2678-2685] from 13C spin-lattice relaxation times (T1) is given. The method is such that the relaxation data are only partially used to generate the conformations; these conformations are constrained to satisfy the rest of the relaxation data and to yield acceptable ring geometry. An alternate equation for T1 of 13C nuclei to that of London is given. The formalism is illustrated through an example.

Finite volume TVD formulation of lattice Boltzmann simulation on unstructured mesh

A numerical scheme is presented for accurate simulation of fluid flow using the lattice Boltzmann equation (LBE) on unstructured mesh. A finite volume approach is adopted to discretize the LBE on a cell-centered, arbitrary shaped, triangular tessellation. The formulation includes a formal, second order discretization using a Total Variation Diminishing (TVD) scheme for the terms representing advection of the distribution function in physical space, due to microscopic particle motion. The advantage of the LBE approach is exploited by implementing the scheme in a new computer code to run on a parallel computing system. Performance of the new formulation is systematically investigated by simulating four benchmark flows of increasing complexity, namely (1) flow in a plane channel, (2) unsteady Couette flow, (3) flow caused by a moving lid over a 2D square cavity and (4) flow over a circular cylinder. For each of these flows, the present scheme is validated with the results from Navier-Stokes computations as well as lattice Boltzmann simulations on regular mesh. It is shown that the scheme is robust and accurate for the different test problems studied.