Differences In Molecular Conformation Research Articles

Elution Behavior of Protein and Pullulan in Asymmetrical Flow Field-flow Fractionation (AsFlFFF)

An AsFlFFF channel was designed and built, and then tested for analysis of pullulans and proteins. Pullulans and proteins having various nominal molecular weights were injected at various conditions of the cross-flow rate (<TEX>$F_c$</TEX>) and the channel-out flow rate (<TEX>$F_{out}$</TEX>). The retention (measured by the retention ratio R) and the zone broadening (measured by the plate height H) were measured, and then compared with theory. When the incoming flow rate, <TEX>$f_{in}$</TEX> (and thus <TEX>$F_{out}$</TEX>) was varied with <TEX>$F_c$</TEX> fixed at 2.5 mL/min, the plate height measured for the pullulan with nominal molecular weight (M) of about 100,000 showed the trend expected by the longitudinal diffusion theory (H decreases with increasing flow rate). In contrast, when <TEX>$F_{out}$</TEX> was varied with the flow rate ratio, <TEX>$F_c/F_{out}$</TEX>, fixed constant at 5, the plate height measured for the same sample showed the trend expected from the non-equilibrium theory (H increases with increasing flow rate). Calibration plots (log D vs. log M) obtained with pullulans and proteins were not coincide, probably due to the difference in molecular conformation, suggesting the analysis of pullulans and proteins using AsFlFFF requires independent calibration. It was found that the linearity of the protein-calibration plot was improved by using a buffer solution as the carrier.

Adsorption and flocculation behaviors of polydiallyldimethylammonium (PDADMA) salts: Influence of counterion

Two modified polymer flocculants of PDADMA salts, PDADMA nitrate (PDADMAN) and PDADMA sulfate (PDADMAS), were prepared from the most widely used commercial product of polydiallyldimethylammonium chloride (PDADMAC). Solution properties such as conductivity and viscosity were investigated, showing that the conductivity follows the order of PDADMAS > PDADMAC > PDADMAN, while the reduced viscosity increases in the order of PDADMAS < PDADMAC < PDADMAN. The results indicate that, compared with PDADMAC, PDADMAN has a more cationic density and a more extended polymer chain, whereas PDADMAS exhibits a smaller coiled polymer size because of the stronger charge affinity of sulfate ion to the polycation of PDADMA. Flocculation experiments were performed on kaolin suspensions. It was found that PDADMAN is the most efficient in turbidity removal, while PDADMAS has wider optimum dosages, larger floc size and more rapid settling rate. Atomic force microscopy (AFM) was employed for imaging the adsorption structures of the three polymers on the negatively charged mica surface. Remarkable differences in molecular conformation were observed. Compared with the pearl necklace-like aggregation of hemispheroids of PDADMAC polymer, PDADMAN takes a sponge-like thin layer structure and PDADMAS exhibits a uniform hemispherical structure. The above differences in both the solution property and the adsorption and flocculation behaviors are attributable to counterion effects. Different counterions may lead to different adsorption and flocculation mechanisms that PDADMAN adopts a flat and layer–layer adsorption without loops and tails extended from the surface, implying that a charge neutralization mechanism plays more roles, while adsorbed PDADMAS is in the form of coiled spheres with loops and tails so that a bridging mechanism is more involved. Namely, it is the adsorption structure and morphology of the polymer flocculants that is the main factor influencing the flocculation mechanism.

Keto forms in Schiff bases of salicylaldehydes: structural and theoretical aspects

Schiff Bases of Salicylaldehydes undergo enol-keto tautomerism involving proton transfer from the hydroxylic oxygen to the imino nitrogen atom [1]. The difference in molecular conformation (planar and non-planar for thermochromic and photochromic compounds respectively) and the resulting different crystal packing has been considered crucial for the chromobehaviour of N-salicylideneanilines. In contrast, studies of N-salicylidenealcylamines suggested that the electron density on the imine N-atom is what is crucial to thermochromism, rather than molecular planarity, which on the other hand is detrimental to photochromism. It is natural therefore, to suppose that by influencing the electron density on the N-atom by substitution in the salicylaldehyde or/and the amine moiety of the molecule, keto or enol forms of the compounds may be observed. However, no stable keto form had been observed in the crystalline state so far among the substituted N-salicylideneamines and therefore it has not been characterised structurally. In the present study we report the first structural characterisation in the crystalline state of the cis-keto form of a number of N-salicylideneamines, which derive from methoxy substituted salicylaldehydes and aliphatic amines. Moreover, we compare it to the theoretical results derived from DFT quantum mechanical calculations in an attempt to understand the important characteristics that render the cis-keto form more stable for certain derivatives in this class of N-salicylideneamines.

Estimation of the lateral dimensions of cellulose crystallites using [formula omitted] NMR signal strengths

Differences in proton rotating-frame spin relaxation rates were exploited to edit the 13 C NMR spectra of solid lignocellulosics, separating signals assigned to cellulose crystallites from signals assigned to amorphous material. Clusters of signals at 89 and 85 ppm were assigned to C-4 in the interiors and on the surfaces of cellulose crystallites, respectively. Relative signal areas were used to estimate the weight-averaged lateral dimensions of crystallites, using a model in which crystallites have approximately square cross sections. The same 10 samples were also characterized by wide-angle X-ray scattering (WAXS). There was a strong correlation ( r 2=0.988) between the two sets of lateral dimensions, but those estimated by WAXS were typically 10% lower than those estimated by NMR. The deviations were attributed to differences in molecular conformations between interior and surface chains, causing broadening of the WAXS peaks. In the case of an eleventh sample containing well-ordered xylan, the NMR and WAXS methods were in good agreement only after exclusion of a xylan signal at 82.6 ppm from the NMR data.

Structure-fluorescence properties of some naphthoylene-benzimidazole-based Langmuir-Blodgett films

Naphthoylene benzimidazoles (NBIs) and related polymers possess promising spectral properties for photonic applications. In the present study we focus on the possibilities of a controlled variation of molecular aggregation of NBI chromophores of various chemical compositions and symmetries in Langmuir-Blodgett (LB) films. Very different π- A isotherms are found for the NBI-stearic acid (SA) complexes with different NBI isomers (cis-, trans- or a 1 2 - NBI chromophore units). The interface behavior is explained by consideration of differences in molecular conformations at the water surface under lateral pressure. This addresses also a different type of chromophore aggregation within the LB films. Spectroscopic, atomic force microscopy (AFM), and X-ray scattering methods are used thoroughly to study mono- and multilayers of NBI:SA complexes. We propose a flat-on arrangement for trans-NBI molecules and an edge-on orientation for cis- and 1 2 NBI chromophores at the water surface and then in the LB films. A strong tendency for aggregation in the solution leads to a formation of different types of dimers and n-mers (depending on the isomer used) in the LB films. The type of aggregation of NBI chromophores in molecular films affects their spectroscopic properties. J-aggregation formation is revealed from the fluorescence spectra.

Enthalpies of dilution of some polycation solutions and exchange enthalpies of polycation counterions

AbstractExperimental data of the enthalpies of dilution of aqueous polycation solutions with water and with salt solutions are presented, as well as the exchange enthalpies of polycation counterions. Measurements were performed using a titration calorimeter. The procedure of obtaining the exchange enthalpies from the calorimetric data is described. The knowledge of these exchange enthalpies reveals information about the enthalpies of formation of (polycation‐polyanion) complexes which are the basic material for the preparation of so‐called “symplex” membranes employed in pervaporation. The data obtained are also of interest for paper manufacturing industries because of the interaction energies of polyelectrolytes with multiple‐charged electrolytes, e. g. lignin sulfonate. The experimental enthalpies of dilution and exchange enthalpies determined for the different counterions are discussed and can be explained by differences in molecular conformation and by different binding of the counterions, respectively.

X-ray diffraction study of the second crystal modification of bis(2-isopropylquinoline-8-thiolato)indium chloride

An X-ray diffraction study of the second crystal modification (II) of the title compound was carried out space group P21/c, a=16.216(5), b=16.109(5), c=19.519(4) A, ⨿=99.97(3)o, Z=8. We have compared geometric parameters of two independent molecules in modification II and one independent molecule in the first crystal modification I investigated previously. The comparison revealed pronounced differences in molecular conformations and in bond angles at the indium atom, which are due to differences in the crystal field effect. At the origin of coordinates of crystal structure II, a cavity was revealed probably containing a very disordered solvate water molecule.

Studies on the intermolecular distribution of industrial pectins by means of preparative size exclusion chromatography

Three industrial high methoxyl pectins have been fractionated by size exclusion chromatography (SEC) on a preparative scale and the chemical composition, viscosity and light scattering behaviour of the fractions have been investigated. Chemical analysis revealed that the composition varies greatly from one SEC fraction to another. In all three pectin samples, the fractions of low molecular size contain most of the free neutral polysaccharides as well as some free pectin ‘hairy regions’. In addition, the lemon pectin samples contain some pectin molecules of large size which are rich in neutral sugars. Phenolic and proteinaceous compounds coelute with neutral sugar-rich fractions. However, in the apple pectin, phenolics and proteins occur predominantly in the fractions of low molecular size. Lemon pectin molecules, especially that of the lemon A sample, are prone to aggregation in the presence of calcium cations. The aggregate fraction can be disrupted by shear forces, heating or the presence of a chelating agent. The formation of such calcium-pectinate aggregates seems to be due to the presence of some molecules with low degrees of methoxylation. Light scattering measurements also suggest that even very narrow SEC fractions remain highly heterogeneous on the basis of their molecular weight, thus indicating large differences in molecular conformation.

Infrared characterization of conformational differences in the lamellar phases of [formula omitted

Fourier transform infrared spectroscopy was used to characterize the lamellar phases of 1,3- dipalmitoyl-sn- glycero-2- phosphocholine (1,3-DPPC), a positional isomer of 1,2- dipalmitoyl-sn- glycero-3- phosphocholine (1,2-DPPC). The molecule exists in three distinct phases over the temperature interval 0–70°C. In the low-temperature (L c) phase, the spectra are indicative of acyl chains packed in an orthorhombic subcell, while the carbonyl groups and phosphate ester at the head group show evidence of only partial hydration. The transition from the low-temperature (L c) phase to the intermediate-temperature (Lβ) phase at 25°C corresponds to a temperature-induced head-group hydration in which the hydration of the phosphate and carbonyl ester groups results in the reorganization of the hydrocarbon chain-packing subcell from orthorhombic to hexagonal. The transition from the intermediate (L β) to the high-temperature (L α) phase at 37°C is a gel-to-liquid-crystalline phase transition analogous to the 41.5°C transition of 1,2-DPPC. The spectra of the acyl-chain carbonyl groups show evidence of significant differences in molecular conformation at the carbonyl esters in the L c phase. In the L β and L α phases, the carbonyl band contour becomes much more symmetric. However, two components are clearly present in the spectra indicating that the sn-1 and sn-3 carbonyls experience slightly different environments. The observed differences are likely due to a preferred conformation of the phosphocholine group relative to the glycerol backbone. Indications from the infrared spectra of differences in the structure of the CO groups provide a possible explanation for the selection of the sn-1 chain of 1,3-DPPC by phospholipase A 2 on the basis of a preferred head group conformation.

Thermal Properties ofp-n-Octadecyloxybenzoic Acid (Part II)

Abstract Thermal properties of metastable and liquid crystalline properties of p-n-octadecyloxybenzoic acid were investigated by differential scanning calorimetry. The glass transition found in the metastable crystal obtained by cooling the smectic phase suggested the existence of a disordered phase. Heat capacities of thermally stable and metastable crystals of the deuterated acid also support this conclusion. From measurements of infrared absorption spectra of the original and the deuterated acids with increasing temperature, the differences in molecular conformation among phases is discussed. It is concluded that the molecules of the carboxylic acids are associated in pairs by hydrogen bonds in the thermally stable crystal, while the hydrogen bonds are partially destroyed in the metastable crystal and in the smectic phase.

High Spin and Low Spin Forms of Co(II) Carbonic Anhydrase: TEMPERATURE-DEPENDENT CHANGES IN SPIN STATE AND COORDINATION GEOMETRY

Abstract Electron spin resonance (ESR) and absorption spectral studies are described which demonstrate two types of cyanide complex of Co(II) human carbonic anhydrase B. High spin (S = 3/2) Co(II) is present at the active site of the cobalt enzyme in the presence of both 1 and 2 eq of CN- at room temperature. At liquid nitrogen temperature the 1:1 complex remains high spin, while the enzyme in the presence of 2 eq of CN- shifts to low spin (S = 1/2). ESR spectra at 111°K and 10°K and absorption spectra at 299°K and 77°K are compatible with tetrahedral coordination geometry for the 1:1 complex at all temperatures and for the enzyme in the presence of 2 eq of CN- at room temperature. Determination of the temperature dependence of the ESR and absorption spectra of the enzyme in the presence of 2 eq of CN- shows a low spin dicyanide complex to form when the sample freezes (∼273°K). The ESR spectra at liquid nitrogen temperature of the dicyanide complex formed with 12C14N-, 12C15N-, and 13C14N- show it to contain two ligands along the z-axis of the complex, a nitrogen atom from the protein and the carbon atom of a C-coordinated cyanide. A coordination complex consisting of a distorted trigonal bipyramid with five ligands to the Co(II) or an octahedral complex with six ligands would account for the ESR and absorption spectra of the low spin dicyanide complex at liquid nitrogen temperature. These changes illustrate a certain flexibility of the ligands at the active site as well as a difference in molecular conformation between the liquid and the frozen state.

X-ray structural analysis of two isomeric modifications of 1,3-diphenyl-2-(phenylazo)propene

The structures of two isomers of 1,3-diphenyl-2-(phenylazo)propene have been determined by X-ray crystallography. The trans-isomer (I) has Z= 4, a= 27·50, b= 5·62, c= 11·16 Å, β= 90° 30′, space group P21/a. The cis-isomer (II) has Z= 2, a= 12·33, b= 8·03, c= 8·45 Å, β= 92° 6′, space group P21. The structures were refined to R 0·122 [(I), 2036 reflections] and 0·113 [(II), 1732 reflections]. Slight difference in molecular conformation and crystal packing are discussed.

Form and function of protein assemblies.

Assemblies of protein molecules represent a fundamental level of biological organization. The dynamic behavior of these systems–including both the assembly process and functional rearrangements–may be accounted for by the specificity of the protein interactions, which depend on environmental conditions. Analysis of the self-assembly of virus particles has established that the design of an ordered structure can be built into the specific bonding properties of the constituent proteins. Any structure which can change its state of organization is, by definition, polymorphic. The distinctive aspect of polymorphism in protein structures, contrasted with nonliving states of matter, is that the molecular design has been selected to carry out a function and that this function is part of an integrated system. The differences in molecular conformation and arrangement in all polymorphic structures–for example, allosteric enzymes or ice crystals–depend on the intrinsic interaction properties of the molecules themselves. The structures of ice and water illustrate relations between specificity and polymorphism which are relevant to the form and function of protein assemblies. Two types of polymorphism can be distinguished: modal polymorphism, which is externally moderated, as in phase transitions between different crystals forms; and positional polymorphism, which is internally moderated, as in the different disposition of identical molecules within a single crystal lattice. Positional polymorphism, exemplified by the quasi-equivalent bonding of icosahedral virus coat proteins and the different arrangement of myosin and paramyosin at the center and polar portions of the bipolar filaments, results from specific interactions that are not compatible with a strictly equivalent packing of identical molecules. The structural rearrangements in muscle contraction and the switching between the oxy and deoxy forms of hemoglobin represent the formation of different structures in response to altered external conditions. The different structural states of many protein assemblies are characterized by conserved connections which may be regarded as providing the framework for functional rearrangements. The types of polymorphism displayed by hemoglobin, virus, and muscle proteins demonstrate the relevance of the simple view that the function of a protein is determined by the potential structures it can form.

Structure of the monoclinic form of cytidylic acid b

The crystal structure of a monoclinic modification of cytidylic acid b (cytidine-3′-phosphate) has been determined and refined by three-dimensional X-ray diffraction techniques. The space group is P2 1 with cell dimensions a = 5.987, b = 17.040, c = 6.670 A ̊ , β = 114.01° ; there are two molecules in the cell. Intensity data were collected visually. The trial structure was obtained by means of a Patterson superposition technique and was refined by the leastsquares method. The final R index for 1332 observed reflections is 0.073, and the fit is 1.5. The standard deviations in the bond distances are slightly less than 0.01 Å. Despite the large difference in density between these monoclinic crystals (1.72 g cm −3) and those of the orthorhombic form the structure of which has already been determined (1.64 g cm −3), there is no major difference in molecular conformation. The bond distances and angles in the two modifications agree closely, the largest difference being in the P—O(H) distance, which is 0.037 Å longer in the monoclinic crystals. The hydrogen-bonding scheme is different in the two modifications.