Molecular Shape Parameters Research Articles

Theory and Simulation of Cholesteric Film Formation Flows of Dilute Collagen Solutions.

Dilute isotropic collagen solutions are usually flow processed into monodomain chiral nematic thin films for obtaining highly ordered materials by a multistep process that starts with complex inhomogeneous flow kinematics. Here we present rigorous theory and simulation of the initial precursors during flow steps in cholesteric collagen film formation. We first extract the molecular shape parameter and rotational diffusivity from previously reported simple shear data of dilute collagen solutions, where the former leads the reactive parameter (tumbling function) which determines the net effect of vorticity and strain rate on the average orientation and where the latter establishes the intensity of strain required for flow-birefringence, both crucial quantities for controlled film formation flow. We find that the tumbling function is similar to those of rod-like lyotropic liquid crystalline polymers and hence it is predicted that they would tumble in the ordered high concentration state leading to flow-induced texturing. The previously reported experimental data is well fitted with rotational diffusivities whose order of magnitude is consistent to those of other biomacromolecules. We then investigate the response of the tensor order parameter to complex flow kinematics, ranging from pure vorticity, through simple shear, to extensional flow, as may arise in typical flow casting and film flows. The chosen control variable to produce precursor cholesteric films is the director or average orientation, since the nematic order is set close to typical values found in concentrated cholesteric type I collagen solutions. Using the efficient four-roll mill kinematics, we summarize the para-nematic structure-flow process diagram in terms of the director orientation and flow type. Using analysis and computation, we provide a parametric envelope that is necessary to eventually produce well-aligned cholesteric films. We conclude that extensional flow is an essential ingredient of well-ordered film precursors with required Deborah numbers on the order of unity.

Retention behavior of isomeric polycyclic aromatic sulfur heterocycles in reversed-phase liquid chromatography

Retention indices for 70 polycyclic aromatic sulfur heterocycles (PASHs) were determined using reversed-phase liquid chromatography (LC) on a monomeric and a polymeric C18 stationary phase. Molecular shape parameters [length, breadth, thickness (T), and length-to-breadth ratio (L/B)] were calculated for all the compounds studied. Correlations between the retention on the polymeric C18 phase and PASH geometry (L/B and T) were investigated for six specific PASH isomer groups with molecular mass (MM) 184Da, 234Da, 258Da, 284Da, 334Da, and 384Da. Similar to previous studies for polycyclic aromatic hydrocarbons (PAHs), PASH elution order on the polymeric C18 phase was generally found to follow increasing L/B values. Correlation coefficients for retention vs L/B ranged from r=0.45 (MM 184Da) to r=0.89 (MM 284Da). In the case of smaller PASHs (MM≤258Da), the location of the sulfur atom in the bay-region of the structure resulted in later than expected elution of these isomers based on L/B. In the case of the larger PASHs (MM≥284Da), nonplanarity had a significant influence on earlier than predicted elution based on L/B values.

Retention behavior of alkyl-substituted polycyclic aromatic sulfur heterocycles in reversed-phase liquid chromatography

Retention indices for 79 alkyl-substituted polycyclic aromatic sulfur heterocycles (PASHs) were determined by using reversed-phase liquid chromatography (LC) on a monomeric and polymeric octadecylsilane (C18) stationary phase. Molecular shape parameters [length, breadth, thickness (T), and length-to-breadth ratio (L/B)] were calculated for all the compounds studied. Based on separations of isomeric methylated polycyclic aromatic hydrocarbons on polymeric C18 phases, alkyl-substituted PASHs are expected to elute based on increasing L/B ratios. However, the correlation coefficients had a wide range of values from r=0.43 to r=0.93. Several structural features besides L/B ratios were identified to play an important role in the separation mechanism of PASHs on polymeric C18 phases. First, the location of the sulfur atom in a bay-like-region results in alkylated-PASHs being more retentive than non-bay-like-region alkylated-PASHs, and they elute later than expected based on L/B value. Second, the placement of the alkyl group in the k region of the structure resulted in a later elution than predicted by L/B. Third, highly nonplanar methyl-PASHs (i.e., 1-Me and 11-MeBbN12T) elute prior to the parent PASH (BbN12T).

Effect of magnetic field on discotic nematic liquid crystalline polymers under simple shear flow

AbstractThe effect of magnetic field on the discotic nematic liquid crystalline polymers (LCPs) is analyzed with the extended Doi theory, in which the molecular shape parameter (β) is defined at −1.0. The evolution equation for the probability function of the discotic nematic LCP molecules is solved without any closure approximations. The transition among flow‐orientation modes, such as tumbling, wagging, and aligning defined similar to the rodlike LCPs, is strongly affected by the magnetic fields. The new aligning flow‐orientation mode observed for the rodlike LCPs under magnetic fields also can be investigated in the lower shear rate region. On the other hand, the effect of magnetic fields parallel to the x‐ and y‐axis on the time‐averaged first and second normal stress differences ( $\bar N_1^*$, $\bar N_2^*$) are also studied. It can be seen that the shear rate regions of the sign changes of $\bar N_1^*$, $\bar N_2^*$ are completely contrary to those conclusions achieved for the rodlike LCPs. In addition, the absolute values of $\bar \eta ^*$ increase with the magnetic field strength in the lower shear rate range owing to the new aligning flow‐orientation mode. Finally, the flow‐phase diagram versus β is also discussed. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013

Effect of Magnetic Field on Shear Stress of Disklike Nematic Liquid Crystalline Polymer

The effect of magnetic field on shear stress of disklike nematic liquid crystalline polymers (LCPs) is analyzed with the extended Doi theory in which the molecular shape parameter is defined at negative one. The evolution equation for the probability function of the LCP molecules is solved without any closure approximations. It can be seen that the shear rate regions of the sign changes of the time-averaged first normal stress differences are completely contrary with those conclusions achieved for the rodlike LCPs.

Effect of Magnetic Field on Molecular Orientation of Disklike Nematic Liquid Crystalline Polymer

The effect of magnetic field on the flow-phase diagram of discotic nematic liquid crystalline polymers (LCPs) is analyzed with the extended Doi theory in which the molecular shape parameter is defined at negative one. The evolution equation for the probability function of the LCP molecules is solved without any closure approximations. The transition among flow-orientation modes, such as tumbling, wagging and aligning defined similar to the rodlike LCPs, are strongly affected by the magnetic fields parallel to the flow direction.

Effects of magnetic field on shear stress of nematic liquid crystalline polymer under simple shear flow

The effect of magnetic fields on the shear stress of liquid crystalline polymers (LCPs) under shear flows is numerically analyzed using the Doi theory. The evolution equation for the probability density of LCP molecules is directly solved without any closure approximations. When the magnetic field is imposed on the LCPs along the shear flow, the low-shear rate plateau of the time-averaged generalized viscosity disappears, which is due to the manner of the new aligning mode observed by Fu et al. The negative first normal stress difference becomes opposite in all the shear rate regimes with the disappearance of periodic oscillations. For the magnetic field parallel to the velocity gradient direction, the more complicated sign changes of is investigated because of the moment caused by the magnetic field vertical to the one caused by the shear flow. The ratio increases with the increasing magnetic field strength. Finally, when the molecular shape parameter is considered as 0.9, the similar discussions are achieved according to the phase diagram among tumbling, wagging, and aligning modes versus the magnetic field strength. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1919–1926, 2010

Molecular model of biaxial ordering in nematic liquid crystals composed of flat molecules with four mesogenic groups

Relative stability of uniaxial and biaxial nematic phases is analyzed in a model nematic liquid crystal composed of flat molecules of C2h symmetry with four mesogenic groups rigidly linked to the same center. The generalized effective quadrupole mean-field potential is proposed and its constants are evaluated numerically for the pair intermolecular potential based on Gay-Berne interaction between mesogenic groups. The dependencies of the constants on molecular shape parameters are systematically analyzed. Order parameters of the uniaxial and biaxial nematic phases are evaluated by direct minimization of the free energy at different temperatures. The corresponding phase diagrams are obtained enabling one to study the effects of molecular model parameters on the stability regions of uniaxial and biaxial phases. The results are used to clarify the nature of experimentally observed biaxial ordering in nematic liquid crystals composed of tetrapode molecules with the same symmetry.

QSAR Studies on 4-Quinolone Derivatives as High-Affinity Ligands at the Benzodiazepine Site of Brain GABAA Receptors

Quantitative structure activity relationship approach using stepwise regression analysis was applied to a series of 4-quinolone derivatives as high-affinity ligands at the benzodiazepine site of brain GABA(A) receptors. For the purpose 25 compounds were used to develop models. Statistically significant equations were obtained with high squared correlation coefficient (r(2)=0.8761, 0.9295 and 0.8705) and low root mean square error (RMSE=0.4844, 0.3894 and 0.4952). The robustness of the model was confirmed with the help of leave one out cross validation method which exhibited high r(2)(cv) values (r(2)(cv)=0.7875, 0.8263 and 0.7927). A good correlation of various molecular shape parameters, like ovality, Szeged index, and energy of the molecule with the GABA(A) affinity was achieved.

On the flow-phase diagram for nematic liquid crystalline polymer under magnetic field

The effect of magnetic fields on molecular configuration of liquid crystalline polymers under shear flows are numerically analyzed using the extended Doi theory in which a molecular shape parameter is admitted. The evolution equation for the probability density function of the LCP molecules is directly solved without any closure approximations. One case is considered that the magnetic field makes 45° with respect to the flow direction. We can find that the magnetic fields strongly affect on the transition among flow-orientation modes, such as tumbling, wagging, and aligning modes. And a new aligning flow-orientation mode emerges at low shear rate, which is macroscopically same as the ordinary aligning mode, but is microscopically quite different from the ordinary one. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009

Desulfurization characteristics of thermophilic Paenibacillus sp. strain A11-2 against asymmetrically alkylated dibenzothiophenes

The thermophilic bacterium Paenibacillus sp. A11-2, which can utilize dibenzothiophene (DBT) as the sole sulfur source at high temperature (45–55°C), was investigated for its ability to cleave carbon-sulfur bonds in the dibenzothiophene (DBT) ring with asymmetrical alkyl substitution, such as methyl, dimethyl, trimethyl, ethyl and propyl DBTs. The biodesulfurization products of each of these alkylated DBTs (Cx-DBTs) were identified and quantitatively determined. The results suggested that each of the Cx-DBTs was desulfurized at a low rate, then converted to alkylated hydroxybiphenyls containing the isomers, and molar ratios of these metabolic isomers were altered in terms of not only the positions but also the numbers and lengths of the alkyl substituents. Moreover, these ratios were compared with those obtained using the mesophilic desulfurizing bacterium Rhodococcus erythropolis KA2-5-1. Consequently, biodesulfurization reactions of these microbes could be characterized using asymmetrically Cx-DBTs and their molecular shape parameters (length and length-to-breadth ratio), indicating differences in the selectivity of the microbial enzymic systems between the two bacterial strains.

Desulfurization Characteristics of Thermophilic Paenibacillus sp. Strain A11-2 against Asymmetrically Alkylated Dibenzothiophenes

The thermophilic bacterium Paenibacillus sp. A11-2, which can utilize dibenzothiophene (DBT) as the sole sulfur source at high temperature (45-55 degrees C), was investigated for its ability to cleave carbon-sulfur bonds in the dibenzothiophene (DBT) ring with asymmetrical alkyl substitution, such as methyl, dimethyl, trimethyl, ethyl and propyl DBTs. The biodesulfurization products of each of these alkylated DBTs (Cx-DBTs) were identified and quantitatively determined. The results suggested that each of the Cx-DBTs was desulfurized at a low rate, then converted to alkylated hydroxybiphenyls containing the isomers, and molar ratios of these metabolic isomers were altered in terms of not only the positions but also the numbers and lengths of the alkyl substituents. Moreover, these ratios were compared with those obtained using the mesophilic desulfurizing bacterium Rhodococcus erythropolis KA2-5-1. Consequently, biodesulfurization reactions of these microbes could be characterized using asymmetrically Cx-DBTs and their molecular shape parameters (length and length-to-breadth ratio), indicating differences in the selectivity of the microbial enzymic systems between the two bacterial strains.

Theory of Molecular Deformations and Mesomorphic Behavior of Dendrimers

We present a simple statistical theory of anisotropic fluid phases consisting of deformable molecules and we use it to describe the self-organization of liquid crystalline dendrimers in the limit of very densely attached mesogenic units. We perform calculations for model-systems of spherical molecules that can deform into rod-like or disc-like states and we determine their mesomorphic range as a function of molecular shape parameters and intrinsic conformational probability

97/01757 Method and apparatus to improve secondary froth quality within oil and oil extraction process

The thermophilic bacterium Paenibacillus sp. A11-2, which can utilize dibenzothiophene (DBT) as the sole sulfur source at high temperature (45–55°C), was investigated for its ability to cleave carbon-sulfur bonds in the dibenzothiophene (DBT) ring with asymmetrical alkyl substitution, such as methyl, dimethyl, trimethyl, ethyl and propyl DBTs. The biodesulfurization products of each of these alkylated DBTs (Cx-DBTs) were identified and quantitatively determined. The results suggested that each of the Cx-DBTs was desulfurized at a low rate, then converted to alkylated hydroxybiphenyls containing the isomers, and molar ratios of these metabolic isomers were altered in terms of not only the positions but also the numbers and lengths of the alkyl substituents. Moreover, these ratios were compared with those obtained using the mesophilic desulfurizing bacterium Rhodococcus erythropolis KA2-5-1. Consequently, biodesulfurization reactions of these microbes could be characterized using asymmetrically Cx-DBTs and their molecular shape parameters (length and length-to-breadth ratio), indicating differences in the selectivity of the microbial enzymic systems between the two bacterial strains.

A QSAR study of anti-inflammatory N-arylanthranilic acids.

A detailed quantitative structure-activity relationship (QSAR) analysis of a series of 112 anti-inflammatory N-arylanthranilic acids has been performed to determine which physicochemical properties of these compounds are responsible for their anti-inflammatory activity. The results indicate that activity is modelled best by molecular shape parameters. The angle between the planes of the two benzene rings, dictated by the substitution pattern of the compounds, also appears relevant to activity. Dipole moments show some significance, but log P and other physiochemical parameters correlate poorly with activity. The best QSAR obtained was: [equation: see text] where B1 and B3 are Verloop substituent width parameters and mu(bond) is bond dipole (position in parentheses).

Gradient theory of surface tension of pure fluids: Effect of molecular shape and polarity

In this paper, we investigate the effect of molecular shape and multipolarity on interfacial properties using a modified van der Waals theory of interfaces and an equation of state developed by Mohanty and Davis for attracting, nonspherical particles with a rigid, convex core. The equation of state contains, in addition to the classical van der Waals parameters, molecular shape and multipolar parameters. Our results indicate that the dimensionless surface tension of pure fluids varies linearly with the multipolar parameter and exponentially with the molecular shape parameter. The agreement between our predictions and experimental data is good.

ChemInform Abstract: Cross‐Sectional Areas of Alkanoic Acids. A Comparative Study Applying Fractal Theory of Adsorption and Considerations of Molecular Shape.

AbstractTwo independent novel theories are tested against each other by determination of cross‐sectional areas of a series of alkanoic acids (I) and (II): a recently developed method for elucidation of molecular shape parameters; and fractal theory of adsorption.

Quantitative structure-activity relationships in a series of alcohols exhibiting inhibition of cytochrome P-450-mediated aniline hydroxylation

The results of Molecular Orbital (MO) calculations by the MINDO/3 method are reported, together with the results of multiple regression analysis of electronic and structural parameters with inhibition of aniline hydroxylation by a series of 22 alcohols. The most significant correlations show the relationships between molecular length, frontier electron density of the α-carbon and hydroxyl oxygen, nucleophilic superdelocalizability of the hydroxyl hydrogen, energy of the highest occupied MO and biological activity involving binding to microsomal cytochromes P-450. Using the data of Cohen and Mannering (Mol. Pharmacol., 9 (1973) 383), Testa, (Chem.-Biol. Interact., 34 (1981) 287) has shown that the inhibition of aniline hydroxylation by a series of alcohols can be related to their electronic structure and hydrophobicity (measured by log P, the octanol-water partition coefficient). The mode of binding and effect on spin-state equilibria in cytochrome P-450 by alcohols has been elucidated by Testa, whereas an alternative hypothesis based on connectivity correlations has been reported by Sabljic and Sabljic (Mol. Pharmacol., 23 (1983) 213). The present work shows that the biological response can be explained by calculated electronic structure and molecular shape parameters. Also, one compound (the only tertiary alcohol) from the original set that was not included in Testa's calculations and analysis, is included in this work and its activity successfully calculated. The latter authors, Sabljic and Sabljic, were led to exclude the data for this compound and one other (phenyl methanol) in order to achieve a good correlation with their calculated parameters of molecular structure.