Apparent Molecular Length Research Articles

Optical and X-ray studies of a four component cyano liquid crystal mixture: Comparison of properties with that of a similar mixture

Optical and X-ray studies have been conducted on a four component liquid crystal mixture (code name 2013) with cyano–end groups in all the four components and a lateral substitution of fluorine atom in one of them. The variations in the optical birefringence with temperature, have been investigated and the thermal dependence of polarisability anisotropy and orientational order parameter have been evaluated. X-ray studies have been conducted to determine the effective molecular characteristics such as apparent molecular length and inter molecular distance and their variations with temperature. From nature of molecular alignment as envisaged from X-ray photographs the order parameter variation with temperature has been determined and compared with macroscopic order parameter variation as determined from birefringence studies. The results have been compared with these obtained for another structurally similar four-component liquid crystal mixture (code name 2014) with isothiocyanato end group in place of cyano.

Orientational order parameter determination of the liquid crystal: 4 propyl paraethoxy phenyl cyclohexyl carboxylate by X-ray studies

ABSTRACTThe compound 4 propyl paraethoxy phenyl cyclohexyl carboxylate (code name D302) is a member of a homologous series and exhibits liquid crystalline (nematic) behavior in the temperature range 48°C to 78°C. An experiment has been set up for conducting X-ray studies of liquid crystal samples at various temperatures. From X-ray studies conducted at different temperatures on D302, the apparent molecular length and inter-molecular distance and their temperature dependence have been determined. The variation of the orientational-order parameter <P2>xray has been determined from the intensities of the scanned X-ray photographs taken at different temperatures. The results have been compared with the<P2>opt values obtained by us from birefringence studies.

On the Nature of Molecular Associations, Static Permittivity and Dielectric Relaxation in a Uniaxial Nematic Liquid Crystal

One fluorinated terphenyl compound was studied by polarizing microscopy, x-ray diffraction and dielectric spectroscopy. It exhibits the nematic phase over a range of 107.80. The average intermolecular distance was observed to be more than in systems without any lateral fluorine substitution. Apparent molecular length was found to be more than the molecular model length, suggesting presence of antiparallel molecular associations. Optimized geometry, obtained by molecular modeling, yielded a dipole moment of 6.68 D. The observed principal dielectric constants are consistent with respective components of dipole moments and show quite a high value of dielectric anisotropy. The threshold voltage and the splay elastic constant have also been determined. Flip-flop mode dielectric relaxation frequency is found to increase with temperature, and the activation energy for the process is found to be 35.53 kJ mol–1.

Determination of Orientational Order Parameters of Two Tri-Component Mixtures from Optical Birefringence and X-Ray Diffraction Measurements

Two tri-component mixtures as base mixtures for vertically aligned mode LCD’s were prepared. The eutectic compositions were theoretically estimated and experimentally verified from differential scanning calorimetry studies. A room temperature nematic mixture with fairly broad operating range emerged from each of the tri-component mixtures. The optical birefringence of these mixtures at the eutectic composition was measured as a function of temperature. X-ray diffraction measurements were done on these mixtures to obtain the orientational order parameters as a function of temperature. The order parameter values were also determined from birefringence measurements and the results were compared with mean field theory. Structural parameters like intermolecular distance and apparent molecular length have also been determined.

Physical Properties of Three Liquid Crystals with Negative Dielectric Anisotropy from X-Ray Diffraction and Optical Birefringence Measurements

In this work, we report the results of x-ray diffraction, density and birefringence measurements on three fluorinated liquid crystalline compounds having negative dielectric anisotropy. Small angle x-ray diffraction data from aligned samples have been analyzed to determine the orientational order parameter as a function of temperature. The order parameter values were also determined from birefringence measurements and the results were compared with mean field theory. Structural parameters like intermolecular distance and layer thickness (in smectic B phase), apparent molecular length (in nematic phase) have been determined and the order of the phase transition in these compounds has been discussed.

Orientational order and molecular parameters of two nematogenic mixtures from X-ray studies: confirmation of electro-optical results

This study entails the report of X-ray studies conducted on two nematogenic mixtures (code names ZLI 1221 and ZLI 1291) containing identical moieties: phenyl cyclohexane, biphenyl cyclohexane and cyclohexyl benzoate, but exhibiting different mesogenic ranges and properties. X-ray studies have been undertaken with a view to investigate the difference in the mesogenic behaviour of the said mixtures at the molecular level. The average apparent molecular length ‘l ’ and intermolecular distance ‘D’ of the two mixtures and their variations with temperature have been determined from X-ray data. The orientational order parameters ⟨P 2⟩ and ⟨P 4⟩ and their thermal variations have also been obtained. Comparison has been made with the ⟨P 2⟩ values obtained from X-ray study with those obtained from optical study. The average apparent molecular lengths of the two mixtures corroborate the findings regarding the relative molecular weights of the two samples obtained from optical and dielectric data.

X‐ray diffraction and optical birefringence studies on four nematogenic difluorobenzene derivatives

The results of optical microscopy, DSC, X‐ray diffraction and optical birefringence studies on four nematogenic difluorobenzene derivatives are presented. The thermal stability of the compounds increases substantially as greater flexibility is introduced into the core structure. Average intermolecular distances, obtained from X‐ray data, are found to increase when a comparatively rigid planar phenyl ring is substituted by a flexible non‐planar cyclohexyl ring in the core structure. From the values of apparent molecular lengths in the nematic phase, a short range antiferroelectric type of association is found to exist between neighbouring molecules. Density values suggest that the molecular packing is less efficient with increasing flexibility either in chain‐ or in core‐structure. All the refractive indices exhibit normal dispersive behaviour, and a positive optical anisotropy is observed in all the compounds which decreases quickly with temperature. Temperature dependences of orientational order parameters, determined from both X‐ray and optical birefringence studies, are presented. Variations of different physical properties with order parameters are discussed.

Phase Transitions and Physical Properties of a Binary Mixture of Bicyclohexane Compounds, II: X-ray Diffraction Measurements

X-ray diffraction data from a binary mixture of two isomeric nonpolar bicyclohexane compounds containing alkenyl side chains have been analyzed to determine the bond orientational order (BOO), orientational order parameters (OOP), layer thickness (in Smectic B phase), apparent molecular length (in nematic phase), and lateral molecular distance, D, as a function of temperature. The phase diagram shows the presence of a two-phase smectic B–nematic co-existing region. The orientational order parameter (OOP) values drop sharply with an increase in temperature within the co-existing phase, which is because the observed OOP value is the weighted mean OOP of the two phases. Interestingly, the BOO values are found to increase with an increase in temperature in the co-existing smectic, B–nematic phase. The transverse correlation lengths in the smectic, co-existing, and nematic phases have also been estimated. These values are found to diverge as the co-existing smectic B–nematic phase region is approached, indicating a second-order phase transition. This result has also been supported by entropy, density, refractive index, and OOP measurements.

AFM-Based Single Molecule Force Spectroscopy of End-Grafted Poly(acrylic acid) Monolayers

AFM-based single molecule force spectroscopy has been applied to study the detachment of poly(acrylic acid) (PAA) chains preadsorbed onto a silicon nitride tip surface at varied pH. In particular, monolayers of end-grafted chains prepared by nitroxide-mediated polymerization initiated from silica substrates were brought into close contact with the silicon nitride tip of an AFM. The detachment of PAA chains from the tip surface is reflected by a set of constant-force plateaus in the AFM force spectra. From those, comprehensive information about the molecular length distribution of surface-grafted polymers, about their conformation, and about their interaction with the tip as a function of pH is deduced. At neutral pH, the plateau-length distribution well reproduces the molecular weight distribution of the grafted polymers as obtained by GPC. At high pH, increasing electrostatic repulsion between PAA and the tip surface reduces the strength of adsorption, which is manifested in a decrease of average plateau lengths and measured detachment forces. At low pH, complex force spectra and a bimodal distribution of apparent molecular lengths are obtained, reflecting the poor solubility of protonated PAA chains in water as well as polymer−substrate interactions.

X-ray diffraction, optical birefringence, dielectric and phase transition properties of the long homologous series of nematogens 4-(trans -4′- n -alkylcyclohexyl) isothiocyanatobenzenes

The temperature dependence of density, refractive indices, apparent molecular length and intermolecular distance of 11CHBT, are reported, together with the static dielectric permittivities, ε∥, ε┴, ε iso of 11CHBT and 12CHBT; the effect of chain length on various physical properties of the CHBT series is also discussed. All the temperatures T m, T NI and T NCr show an odd-even (OE) effect, but transition enthalpies ΔH m and ΔH c show no such behaviour. T m, T NI and T NCr and ΔH m are found to increase with chain length, while ΔH c shows a maxima at n = 6. At the common reduced temperature T* = 0.98 TNI, the density of the compounds are found to decrease with increasing chain length while the polarizability parameters αe, αo and α increase. However, the volume expansion coefficient, polarizability anisotropy and normalized polarizability anisotropy show a distinct OE effect. Similarly, n e decreases smoothly with chain length but n o and Δn show an OE effect like ε┴ and Δε. The ratio ln ⟨P 2⟩ /ln ⟨ P 4⟩ remains closer to Faber theory than MS theory. Effective dipole moments are found to be approximately constant in the series; antiparallel association is observed in all the members. Kirkwood correlation factors g┴ and Δg are found to exhibit an OE effect like ε∥ and ε∥, but g∥ and ε∥ show no such effect. The effects of substitution in the core and end polar group on these properties are also discussed.

Small Angle X-Ray Diffraction Study for the Determination of Structural Parameters of Two Mesomorphic Compounds Having Smectic C Phase

X-ray diffraction study was carried out for the pentyl and octyl members of the series 4-n-alkoxy phenyl 4′-n octyloxy benzoate (PPOB and OPOB in short). The first shows SC, SA and N phases while the second compound has only SC and N phases. The transition temperatures were determined by studying texture under polarizing microscope. Apparent molecular length in nematics, layer line spacings in smectics, tilt angle in SC, inter molecular distances and orientational order parameters were determined from X-ray diffraction patterns of aligned samples at different temperatures. Temperature variation of the orientational order parameters agree fairly well with Maier-Saupe theory in the nematic phase and with McMillan's theory in the smectic phase with tilt angle correction in SC. Discontinuities of <P2>and <P4>- at SAN in PPOB and at SC -N transitions indicate that the transitions are of the first order.

Study of Physical Properties of Binary Mixtures of Two Nematogens

We have reported different physical parameters of binary mixtures of p-ethoxyphenyl trans-4-butylcyclohexane carboxylate and 4′-n-pentyloxy-4-cyanobiphenyl, the two nematogenic compounds. The mixtures are prepared in four different compositions with X50CB=0.213, 0.434, 0.626 and 0.818. Transition temperatures are determined by studying textures under a polarizing microscope. For all the compounds schlieren textures are observed. X-ray diffraction, optical birefringence study and density measurements have been carried out throughout the mesomorphic range. Only one mixture shows a cybotactic nematic phase. Apparent molecular lengths and order parameters are determined from X-ray studies and n0, ne and Δn from optical studies. Variation of all the parameters with temperature and concentration is discussed. Order parameters are compared with theoretical values.

Aminoglycoside binding in the major groove of duplex RNA: the thermodynamic and electrostatic forces that govern recognition

We use a combination of spectroscopic, calorimetric, viscometric and computer modeling techniques to characterize the binding of the aminoglycoside antibiotic, tobramycin, to the polymeric RNA duplex, poly(rI)·poly(rC), which exhibits the characteristic A-type conformation that is conserved among natural and synthetic double-helical RNA sequences. Our results reveal the following significant features: (i) CD-detected binding of tobramycin to poly(rI)·poly(rC) reveals an apparent site size of four base-pairs per bound drug molecule; (ii) tobramycin binding enhances the thermal stability of the host poly(rI)·poly(rC) duplex, the extent of which decreases upon increasing in Na + concentration and/or pH conditions; (iii) the enthalpy of tobramycin-poly(rI)·poly(rC) complexation increases with increasing pH conditions, an observation consistent with binding-induced protonation of one or more drug amino groups; (iv) the affinity of tobramycin for poly(rI)·poly(rC) is sensitive to both pH and Na + concentration, with increases in pH and/or Na + concentration resulting in a concomitant reduction in binding affinity. The salt dependence of the tobramycin binding affinity reveals that the drug binds to the host RNA duplex as trication. (v) The thermodynamic driving force for tobramycin-poly(rI)·poly(rC) complexation depends on pH conditions. Specifically, at pH⩽6.0, tobramycin binding is entropy driven, but is enthalpy driven at pH > 6.0. (vi) Viscometric data reveal non-intercalative binding properties when tobramycin complexes with poly(rI)·poly(rC), consistent with a major groove-directed mode of binding. These data also are consistent with a binding-induced reduction in the apparent molecular length of the host RNA duplex. (vii) Computer modeling studies reveal a tobramycin-poly(rI)·poly(rC) complex in which the drug fits snugly at the base of the RNA major groove and is stabilized, at least in part, by an array of hydrogen bonding interactions with both base and backbone atoms of the host RNA. These studies also demonstrate an inability of tobramycin to form a stable low-energy complex with the minor groove of the poly(rI)·poly(rC) duplex. In the aggregate, our results suggest that tobramycin-RNA recognition is dictated and controlled by a broad range of factors that include electrostatic interactions, hydrogen bonding interactions, drug protonation reactions, and binding-induced alterations in the structure of the host RNA. These modulatory effects on tobramycin-RNA complexation are discussed in terms of their potential importance for the selective recognition of specific RNA structural motifs, such as asymmetric internal loops or hairpin loop-stem junctions, by aminoglycoside antibiotics and their derivatives.

Small Angle X-Ray Diffraction Studies on the Homologous Series of Mesogenic 4-(trans-4′-n-Alkylcyclohexyl)Isothiocyanatobenzenes

The compounds of the series (nCHBT in short, n=4–9) show only nematic phase with supercooling effect. 4CHBT and 5CHBT show monotropic transition. X-ray diffraction studies of magnetically oriented samples have been done in the entire nematic range which indicate that all the members possess ordinary nematic phase. The average intermolecular distance is found to be ∼5.1Å for all of them. The apparent molecular length, 1 varies from 22.3A for 4CHBT to 29.3Å for 9CHBT at 0.98TNI. Temperature dependence of these parameters has been discussed. Average values of apparent molecular lengths in their nematic range are found to be ∼1.1 times of their respective molecular model lengths indicating the presence of bimolecular association. The orientational order parameters, <P2> were found to be slightly higher than Maier-Saupe theoretical values and lower than the values obtained from refractive index studies; whereas <P4> values were found to be comparable with Maier-Saupe values. The results have been discussed in relation to three other similar homologous series.

Physical properties of three bicyclohexane compounds possessing smectic B phase. I: X-ray diffraction studies

Abstract Small angle X-ray diffraction data from aligned samples of three bicyclohexane compounds in smectic B and nematic phase have been analysed to determine the bond orientational order (BOO), orientational order parameters (OOP), transtational order parameter (TOP), layer thickness (in smectic B phase), apparent molecular length (in nematic phase), and lateral molecular distance as a function of temperature. Correlation lengths in the smectic layer plane have also been estimated. The experimental OOP and TOP values are compared with McMillan's theory.

Structure of the liquid crystalline state in hexakis (4-(4′-alkyloxy)biphenoxy)cyclotriphosphazenes

Abstract X-ray measurements on hexakis(4-(4′-alkyloxy)biphenoxy)cyclotriphosphazenes [PN-(OC6H4C6H4OC n H2n + 1)2]3 (HACP, n = 7–9), confirm the previous mesophase identification. The apparent molecular length measured in the mesophase compares to twice the length of an alkyloxybiphenyl side group. Specific features are added to the usual features of the nematic and smectic diffraction patterns which show that the molecular arrays in directions parallel and perpendicular to the director both reflect the peculiar shape of the cyclotriphosphazenes.

Small Angle X-ray Scattering Studies on Smectic and Nematic Phases of a Toluidine Compound

Abstract X-ray diffraction studies on N,N′-Bis (p-butoxybenzylidine) -α, α′ -bi -p toluidine [BEBT] in smectic and nematic phases have been reported. Apparent molecular length, average intermolecular distance in both the phases have been determined. Molecular organizations in the smectic phase has been discussed in relation to its packing in the crystalline state.

The role of repetitive DNA sequences in the size variation of Epstein--Barr virus (EBV) nuclear antigens, and the identification of different EBV isolates using RFLP and PCR analysis

The six Epstein-Barr virus (EBV) nuclear antigen proteins (EBNA-1-6) show characteristic size variations between different virus isolates; this is a feature that has been used to identify the source of virus isolates in epidemiological studies (Ebnotyping). We have now studied the correlation between restriction fragment length polymorphisms (RFLPs) within exons coding for the EBNAs and the molecular masses of the respective proteins. The B95-8 EBV strain was used as the prototype virus. The variation in apparent molecular mass of EBNA-1, -3 and -6 correlated positively with the size of RFLP coding for repeat sequences in these polypeptides. For EBNA-2, no correlation between apparent molecular mass and length of the repetitive sequences was found. The EBNA-4 protein showed virtually no variation in apparent molecular mass and RFLP size across the repeat sequence. Based on the strong correlation between apparent molecular mass and RFLP size for EBNA-6, we developed an EBNA-6 PCR assay that discriminated between different isolates of EBV. This assay offers the advantage of EBV characterization using uncultured material (e.g. throat washings, blood or biopsies), thus avoiding the selection against poorly transforming strains that occurs during establishment of lymphoblastoid cell lines required for Ebnotyping at the protein level.

Study of the physical properties of an ester/biphenyl mixture, exhibiting an injected smectic phase, by small-angle x-ray diffraction

Abstract Small angle x-ray diffraction intensities from binary mixtures of 4-n-pentyl 4′cyanobiphenyl (5CB) and 4-n pentyl phenyl 4-n′ hexyloxy benzoate (ME60.5), which show an injected smectic phase, have been analysed to determine the orientational order parameters (P 2) and (P 4), the translational order parameter, the layer thickness in the smectic phase, and the apparent molecular length in the nematic phase. The order parameters have been fitted satisfactorily to those calculated from McMillan's theory by varying the potential parameters α and [sgrave]. The experimental variation of the layer thickness with mole fraction of 5CB has been explained fairly well by assuming the presence of both homo dimers (5CB + 5CB) and hetero dimers (5CB + ME 60.5) in the mixture. Orientational order parameters, layer thickness, and packing fraction all exhibit minima at about 50% molar concentration of 5CB.

Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping.

A light microscope-based technique for rapidly constructing ordered physical maps of chromosomes has been developed. Restriction enzyme digestion of elongated individual DNA molecules (about 0.2 to 1.0 megabases in size) was imaged by fluorescence microscopy after fixation in agarose gel. The size of the resulting individual restriction fragments was determined by relative fluorescence intensity and apparent molecular contour length. Ordered restriction maps were then created from genomic DNA without reliance on cloned or amplified sequences for hybridization or analytical gel electrophoresis. Initial application of optical mapping is described for Saccharomyces cerevisiae chromosomes.