All-trans Chains Research Articles

Vibrational polarizability of polyacetylene chains

Within the double harmonic oscillator approximation, ab initio vibrational contributions to the static electric dipole polarizability have been computed for the all-trans polyacetylene chains homologous series. Atomic basis set and electron correlation effects have been studied on ethylene and trans-butadiene as well as the use of semiempirical Hamiltonians. By using the 6-31G* atomic basis set within the Hartree–Fock and the second order Mo/ller–Plesset procedures as well as by using semiempirical Austin model 1 Hamiltonians, the evolution with chain length of the vibrational polarizability per structural unit has been investigated and compared to the electronic contribution. Although smaller than the electronic contributions (αvibration≊10% αelectronic), the longitudinal component to the polarizability presents a similar exaltation as chain length grows, but a slower saturation to an asymptotic value per unit cell. Inclusion of electron correlation via the second order Mo/ller–Plesset technique turns out to reduce the longitudinal component calculated at the Hartree–Fock level, but to increase the transversal and perpendicular components. Whereas it reproduces correctly the evolution with chain length of the vibrational polarizability tensor components, the Austin model 1 technique underestimates the longitudinal term and overestimates the perpendicular term. The major contribution to the vibrational polarizability results from large charge fluxes associated with asymmetric stretching motions of the carbon backbone and with the torsion motions presenting very low vibrational frequencies.

Self-Assembly of n-Alkanethiolate Monolayers on Silver Nanostructures: Determination of the Apparent Thickness of the Monolayer by Scanning Tunneling Microscopy

Abstract : The STM is employed to monitor the effect of adsorption of an n-alkanethiolate monolayer, from an aqueous solution of the thiol, on the apparent topography of nanoscopic silver adsorption sites. Silver nano-disk structures were electrochemically deposited on graphite surfaces using the STM. The topography of these adsorption sites was then determined in-situ by STM imaging prior to the exposure of the nano-structure to an aqueous solution of an n- alkane thiol. The apparent thickness of the self-assembled monolayer (SAM), estimated from the difference in the nano-structure height measured before and after adsorption of the monolayer, increased linearly with the alkyl chain length for five n-alkane thiols (i.e., CnH(2n+1)SH) having even numbered chain lengths from n=10 to 18. For SAMs of tetradecane thiol, hexadecane thiol, and octadecane thiol, the average height increments equaled the expected all-trans chain length of these molecules indicating that little penetration of the STM tip into the surface of the monolayer occurs during the STM imaging experiment. STM, N-alkane thiols, Biological, Lithography, Passivation.

Head–tail competition and modulated structures in planar surfactant (Langmuir–Blodgett) films

We have observed two distinct types of spatially modulated structures (on nanometer length scales) on the surface of Langmuir–Blodgett films of fatty acid salts using atomic force microscopy. Both involve periodic height modulation of the crystalline molecular lattice. The first type, seen in films containing Ba, Ca, and Mg, is commensurate with the molecular lattice and can be described as a regular series of packing defects that are consistent with the close-packing requirements of the alkyl tail groups. The other type, seen in films containing Cd and Mn, is not always commensurate and is less perfectly correlated than the first type. We suggest a correspondence between these two types of modulations and the two predicted by a new toy model which incorporates the competition between the in-plane density preferred by the headgroups in conjunction with the cation and the close-packing requirements of all-trans crystalline alkyl chains.

An Intrinsic Relationship between Molecular Structure in Self-Assembled n-Alkylsiloxane Monolayers and Deposition Temperature

We have studied the effect of preparation temperature, in the range 5-65 OC, on the structures of n-octadecylsiloxane monolayers prepared by self-assembly from dilute solution of n-octadecyltrichlorosilane onto the surface of freshly hydrated, oxidized silicon substrates. Structural features of the films were characterized using a combination of liquid drop contact angle measurements, null ellipsometry, and infrared transmission spectroscopy. The contact angle data confirm a previously reported observation of a critical temperature, Tc - 28 f 5 OC, below which the surface energy is constant at a near-limiting value of a pure CH3 surface and above which the surface energy monotonically increases with increasing temperature. Coverages and chain organization, as measured by ellipsometry and vibrational spectroscopic features (peak positions and integrated intensities of methylene C-H stretching modes), respectively, show changes in the same temperature region as the wetting behavior. We conclude that when prepared below T,, the films exhibit a heterogeneous structure with closely spaced islands of densely packed, nearly all-trans alkyl chains arranged nearly vertical to the surface. In contrast, when prepared above T,, the films exhibit monotonically diminishing coverage with increasing preparation temperature and the alkyl chains increasingly assume higher contents of conformational disorder. Further, the infrared data indicate that these higher temperature films are heterogeneous with coexisting domains of high and low chain conformational ordering. All the data, taken together, are in good conformity with a film formation mechanism which involves, prior to siloxy group cross-linking, the intervention of intermediate structural phases of mobile alkylsiloxy species adsorbed on a water layer adjacent to the solid substrate surface. In support of this mechanism, a strong parallel is apparent between Tc and the triple point temperature at which gas (G), liquid-expanded (LE), and liquid-condensed (LC) phases coexist for chain Langmuir monolayers at the air/bulk water interface. Below Tc the self-assembled film structure is similar to that of the nearly pure LC Langmuir phase while above Tc the film structure is similar to that of coexisting LE and LC phases. Deviations of the self-assembled film structures for the analogous equilibrium Langmuir phase structures occur at higher preparation temperatures and are rationalized in terms of both the known occurrence of nonequilibrium phases in Langmuir films above the triple point temperature and the relative acceleration of the Si-O-Si cross-linking reaction in the self-assembled film to form structures with frozen-in defects.

Dynamical analysis of linear polymers using mode-specific trajectories

Recently, a new method was presented for calculating vibrational dispersion curves for linear polymers from the spectral analysis of molecular dynamics trajectories with random initial conditions. An alternative approach is to choose initial conditions for trajectories such that only one collective mode corresponding to a specific vibrational frequency and phase relationship is preferentially excited. As a result, for the first time all the standard techniques of nonlinear dynamics (Lissajous figures, surfaces of section, etc.) may be applied to the collective coordinates of a macromolecule. After demonstrating that approximate initial conditions will preferentially excite specific collective modes, improved dispersion curves for a 100 unit all-trans polyethylene chain are compared with the results of a normal coordinate analysis. The similarity of the phase space of collective modes and local modes is then shown through plots of Lissajous figures and surfaces of section for trajectories in which multiple...

Identification and characterization of kink motifs in 1-palmitoyl-2-oleoyl- phosphatidylcholines: a molecular mechanics study

As a cis carbon-carbon double bond (delta) is introduced into the middle of an isolated all-trans hydrocarbon chain, it can be shown by molecular graphics that this delta-bond makes a bend of 130 degrees in the chain axis, thus producing a boomerang-like conformation. Such a bent structure, indeed, has been detected experimentally for oleic acid by x-ray crystallography (Abrahamson and Ryderstedt-Nahringbaur, 1962). Membrane diacyl phospholipids are largely mixed-chain lipids containing a saturated sn-1 acyl chain and an unsaturated sn-2 acyl chain. 1-Palmitoyl-2-oleoyl-phosphatidylcholine (POPC), the most abundant phospholipid in animal cell membranes, is a typical example in which the sn-2 acyl chain is the acyl chain of an oleic acid. However, this sn-2 acyl chain of POPC is unlikely to adopt a boomerang-like configuration in the gel-state lipid bilayer due to the steric hindrance imposed by neighboring chains. Instead, it has been suggested that the oleate chain in POPC is kinked in the shape of a crankshaft in the gel-state bilayer (Huang, 1977; Lagaly et al., 1977), because POPC with such a kinked sn-2 acyl chain, which is denoted here as the secondary structural element or motif, can pack efficiently against other neighboring phospholipids. In this communication, 16 different types of secondary structural elements or motifs are derived for POPC at T < Tm based on a single protocol guided by two-dimensional steric contour maps and computer-based molecular graphics. After subjecting these derived molecular species to energy minimization using the molecular mechanics method, the number of the secondary structural motifs is reduced to 13 as a result of conformational degeneracy. The structure and steric energy of each of the energy-minimized lipid rotomers are presented in this communication. Furthermore, these rotomers packed in small clusters are also simulated to mimic the lipid bilayer structure of 1-palmitoyl-2-oleoyl-phosphatidylcholines at T < Tm.

UV photoemission study of amorphous n-C 36H 74 films and their annealing process

Amorphous films of hexatriacontane n-C 36H 74 were prepared by vacuum evaporation on low-temperature substrates (≈ 80 K), and their electronic structure including the change at annealing was studied by UV photoemission spectroscopy. The spectra of as deposited films were similar to those of molten state, but indicate a smaller degree of disorder. Upon annealing, the spectra changed drastically, reflecting the change of unoccupied states, with sharp change at ≈ 268 K corresponding to crystallization. The change was discussed with reference to reported structural studies by vibrational spectroscopies. The results show that the appearance of fine structures in unoccupied states requires not only extended (all-trans) chains but also regular intermolecular arrangements.

Structure of vitaminylated lipids in aqueous dispersion: X-ray diffraction and phosphorus-31 NMR studies of N-biotinylphosphatidylethanolamines

The structures of the phases formed in excess buffer (at pH 7.4) by a homologous series of saturated diacylphosphatidylethanolamines in which the headgroup is N-derivatized with biotin have been investigated for chain lengths of C(12:0) to C(20:0), using both 31P nuclear magnetic resonance (NMR) spectroscopy and small-angle X-ray diffraction. In 1 M NaCl, all lipids display 31P NMR spectra characteristic of a lamellar gel phase at low temperature. In the fluid phase, the lipids of C(12:0) and C(14:0) chain lengths display isotropic 31P NMR spectra, corresponding to aggregated phases with high surface curvature, whereas those with C(18:0) and C(20:0) chain lengths display sharp axial powder patterns characteristic of a lamellar (L alpha) phase. The lipid of intermediate C(16:0) chain length displays a more complex temperature dependence of the 31P NMR spectra in the fluid phase. The spectra convert from an axial powder pattern of unusually low chemical shift anisotropy to one characteristic of a fluid lamellar (L alpha) phase with increasing temperature. The small-angle X-ray diffraction patterns of the lipids in 1 M NaCl have lamellar repeat spacings in the gel phase which increase linearly with chain length and are consistently lower than those in the fluid phase [for chain lengths of C(16:0) to C(20:0)]. In addition, the gradient in long spacing with chain length in the gel phase is approximately half that expected for a gel phase with untilted, all-trans chains, indicating that the lipid chains are interdigitated in the gel phase (L beta i).(ABSTRACT TRUNCATED AT 250 WORDS)

Comparative study of phototactic and photophobic receptor chromophore properties in Chlamydomonas reinhardtii

The motile, unicellular, eukaryotic alga Chlamydomonas reinhardtii exhibits two distinct behavioral reactions to light stimuli, phototaxis and the photophobic response. Both are mediated by retinal-containing receptors. This paper focuses on a direct comparison of the two photoresponses and the chromophore requirements for their photoreceptor(s). Using computerized motion analysis assays for phototaxis and photophobic responses by the same populations of cells, we measured the ability of various isomers and analogues of retinal to reconstitute photobehavior in the pigment-deficient mutant FN68. The results indicate that photophobic and phototaxis responses each require chromophores with an all-trans polyene chain configuration, planar ionone ring/polyene chain conformation, and the ability to isomerize around the retinal C13-C14 double bond. One difference between the two behaviors is that the photophobic response becomes highly desensitized after light stimuli to which the phototaxis response does not become desensitized, indicating the existence of at least one distinct step in the photophobic response pathway. A second difference is that the retinal regeneration of the photophobic response but not of phototaxis is inhibited by a 5-membered ring 13-trans-locked analogue. While showing close similarity in the chromophore structural requirements of the two behaviors, the results indicate that differences exist between the two responses at the level of their photoreceptor proteins and/or in their transduction processes.

Polymerization-induced epitaxy. Poly(vinylidene chloride) on graphite by free radical polymerization

An ultrathin, epitaxial film of poly(vinylidene chloride) (PVDC) was grown on the basal plane of graphite by free radical polymerization. Direct observation by scanning tunneling microscopy revealed the epitaxial structure of the PVDC film in atomic detail. A pair of chains, each chain in the glide form, constitutes a relevant repeating unit approximately 12 A in width. All chlorine atoms are located on the surface in a harmonic periodicity with the graphite hexagonal lattice. In addition to the previously studied epitaxy of ring-opened polymers with the all-trans chain conformation, this study demonstrates the generality of polymerization-induced epitaxy to include free radical polymerization with the nonplanar zigzag structure.

Deuterium NMR study of intermolecular interactions in lamellar phases containing palmitoyllysophosphatidylcholine

50 wt % HzO). 'H NMR spectra were obtained for the low-temperature and liquid-crystalline (L,) states of each of these mixtures. In the low-temperature state, the fit three systems yielded ZH NMR spectra characteristic of all-trans chains undergoing axial diffusion, with the methyl groups rotating about their C3 axes. The molecular order, as judged by the presenoe of spectral discontinuities and moment analysis, was found to be almost identical in the low-tempratwe phases. A different behavior was observed for the ch~lesterol/PaLPC-d~~ (1:l) sample in that the maximum splitting was close to the all-trans rotating value, with a profile of quadrupolar splittings due to inmased disorder near the chain ends. The fit three systems underwent orderdisorder phase transitions near the same midpoint temperature (range of T, values 40-48 C), whereas the ch~lesterol/PaLPC-d~~ (1:l) sample did not display a transition over the temperature range studied. In the L, phase, where order profdm were determined as a function of acyl chain segmglt position, the segmental ordering differed significantly among the samples. The differences were interpreted using a simple diamond lattice model for the acyl chain configurational statistics, as a means of comparing the effective lengths, (L), projected along the bilayer normal and estimated chain cross-sectional areas, (A), of PaLPC-d31 in the various mixtures. The derived values of (L) and (A) can be understood qualitatively in terms of average packing parameters related to the balance of forces in the headgroup and acyl chain regions, or alternatively the curvature free energy of the membrane lipid-water interface. In lamellar phases of pure P~LPC-C~~~ the curvature stnap is potentially large, and interdigitation of the acyl chains of the appoaed monolayers may occur. However, in mixtures of PaLPC-d31 with 1,2-dipalmitoyl- sn-Bly~~3-phosp~ ~~e (DPPC), the curvature elaatic stress is apparently relieved by an increase in the cross-sectional acyl chain area, (A), Le. corresponding to an increase in configurational fdom. The data were also compared to the results of statistical theories to yield additional knowledge of the intermolecular forces. These studies indicate how the segmental ordering reflects intermolecular interactions within a given lamellar phase. Avmge properties of the entire system such as average cross-sectional arm accessible to each acyl chain relative to the headgroup area can be modulated by these interactions. Such intermolecular interactions may be related to the prcaence of lipid diversity in biological membranes.

13C NMR relaxation study on molecular motion of n-alkane chains in the rotator phase

The 13C spin-lattice relaxation times ( T 1 s) of n-C 32H 66 were measured in the crystalline state, rotator phase and melting state, in order to clarify the molecular motion of the rotator phase. From these results it was found that in the rotator phase every methylene carbon has almost the same value of T 1. This indicates that all-trans zigzag chains in the rotator phase rotate rapidly about their long axes.

Langmuir-Blodgett films of amylose acetate/dye mixtures. 2. Langmuir-Blodgett multilayers of mixtures of amylose acetate and a chiral p-nitroazobis[benzene] dye

The structure of multilayers of a mixture of amylose acetate and a chiral nonlinear optical dye, a monoester of palmitic acid and 4-nitro-4'-[(3R)-hydroxypyrrolidino]-1,1'-azobis[benzene] (KMES16) has been studied. The monolayers of the mixed systems, consisting of domains of the dye in a matrix of amylose acetate, were transferred by the Langmuir-Blodgett technique onto solid substrates in the Z-type transfer mode. The structure of the multilayers was investigated by Fourier transform infrared spectroscopy, UV spectroscopy, and small-angle X-ray diffraction. The aliphatic chain of the dye molecule exhibits a remarkable orientation as revealed by infrared spectroscopy. These all-trans CH2 chains are tightly packed, and they have a specific orientation around the chain director. The dye fragment of the molecule appeared to be oriented at about 30-degrees with the surface normal, whereas the molecules are packed antiparallel in the lamellar crystals. From UV spectroscopy it was deduced that these crystals can be considered as H aggregates. After heating the multilayers and cooling, the IR spectra reveal a more well-defined structure with lamellar crystals, which also behave like H aggregates.

Orientation of specifically 13C=O labeled phosphatidylcholine multilayers from polarized attenuated total reflection FT-IR spectroscopy

Oriented multilayers of 1-myristoyl-2(1-13C)-myristoyl-sn-glycero-3-phosphatidylcholine (2[1-13C]DMPC) and 1-palmitoyl-2(1-13C)-palmitoyl-sn-glycero-3-phosphatidylcholine (2[1-13C]DPPC) were investigated by use of attenuated total reflection infrared spectroscopy with polarized light. Experiments were performed with the aim to determine the orientation of the two ester groups in these phospholipids in the solid state and in the hydrated state at temperatures below and above the respective gel to liquid-crystalline phase transitions. Substitution of the naturally occurring 12C carbonyl carbon atom by 13C in the ester group of the sn-2 chain of DMPC and DPPC shifts the infrared absorption of the carbonyl double bond stretching vibration to lower frequency. This results in two well-resolved ester C=O bands which can be assigned unequivocally to the sn-1 and sn-2 chains as they are separated by more than 40 cm-1. The two ester CO-O single bond stretching vibrations of the molecular fragments-CH2CO-OC-are also affected and the corresponding infrared absorption band shifts by 20 cm-1 on 13C-labeling of the carbonyl carbon atom. From the dichroic ratios of the individual ester bands in 2(1-13C)DMPC and 2(1-13C)DPPC we were able to demonstrate that the sn-1 and sn-2 ester C=O groups are similarly oriented with respect to the bilayer plane, with an angle greater than or equal to 60 degrees relative to the bilayer normal. The two CO-O single bonds on the other hand have very different orientations. The CH2CO-OC fragment of the sn-1 chain is oriented along the direction of the all-trans methylene chain, whereas the same molecular segment of the sn-2 carbon chain is directed toward the bilayer plane. This orientation of the ester groups is retained in the liquid-crystalline phase. The tilt angle of the hydrocarbon all-trans chains, relative to the membrane normal, is 25 degrees in the solid state of DMPC and DPPC multibilayers. In the hydrated gel state this angle varies between 26 degrees and 30 degrees, depending on temperature. Neither the orientation of the phosphate group, nor that of the choline group varies significantly in the different physical states of these phospholipids.

Characterization of Ultrathin Organic Membranes by Vibrational Spectroscopy

We first deal with a new method for quantitative evaluation of the molecular orientation in thin Langmuir-Blodgett (LB) films by Fourier transform infrared (FT-IR) transmission and reflection-absorption (RA) spectroscopy. The method was applied to the study of the 7-monolayer LB film of cadmium stearate. The orientation angle of the hydrocarbon chain axis around the surface normal was found to be 7°, being in good agreement with the average of the previous data obtained by other investigators. Then, we applied the same method to the study of temperature dependence of the molecular orientation in alternate LB films consisting of a phenylpyrazine-containing long-chain fatty acid and deuterated stearic acid, and in the corresponding alternate LB films of their barium salts. At the same time, pyroelectricity of these films was measured on heating the sample, and the results are discussed in connection with the molecular structure and orientation. It was concluded that the pyroelectricity is ascribed to changes of spontaneous polarization due to a structure modification of the polar groups of the constituent molecules with the highly oriented all-trans hydrocarbon chains.

Structures of two crystal forms of chiral smectogenic 4′-hexyloxy-4-biphenylylp-[(S)-2-methyIbuty 1] benzoate

Abstract Three crystal forms were found for the title compound. The relationship of the polymorphs was elucidated by DSC and powder X-ray diffraction methods. Two crystal structures, stable at room temperature, have been determined by single crystal X-ray analysis. Crystal data: 4′-hexyloxy-4-biphenylyl p-[(S)-2-methylbutyljbenzoate Mr = 444·6, C30H36O3, 1, triclinia P1, T=298K, a= 11·550(2), b = 22·940 (3), c= 11–810(3) A, α= 104–08(2), β= 112 87(2), γ = 99–49(2)°, V= 2676(1) A3, d x =1·110gcm−3, μ = 4·74cm−1, F(000) = 960; 2, monoclinic, P21, T=298K, a= 23·304(2), b = 5·6080(5), c = 20·451(4) A, β = 98–39(1)°, V=2644·1(6) A3, Z=4, d x =1.117gcm−3, μ=4·80cm−1, F(000) = 960. Each crystal is composed of a smectic-like layer structure with a large molecular tilt angle (45° and 60°, respectively). The molecules in 1 have largely twisted paraffin chains and the twisted biphenyl moieties, while those in 2 have all-trans zigzag paraffin chains and coplanar biphenyl moieties. Packing modes of the core moieties a...

Energetics of strain-induced conformational transitions in polymethylene chains

Deformation potentials have been calculated for highly extended polymethylene chains containing simple torsional defects. The calculations were performed by using molecular mechanics techniques. The deformation potentials show abrupt discontinuities, which have been identified as gauche-trans transitions of chains containing strained defects into chains in the fully extended zigzag form. The reverse trans- gauche transition was observed during compression of all-trans chains. The observed discontinuity in the conformational transition is a direct consequence of the input of mechanical energy into the torsional angles and also into the bond lengths and bond angles in the chain. The transition point imposes a limit on the amount of energy stored in chains containing defects; the energy is fully recovered at the transition. It is suggested that abrupt conformational transitions may occur upon drawing crystalline and glassy polymers as a mechanism of avoiding large translational movements of atoms under the conditions of strong constraints from neighboring chains. The Hookean behavior of single chains containing a conformational defect was tested and the effect of this defect on the chain modulus was estimated.

Deformation energetics of chain defects of polyethylene

The deformation energetics of static polyethylene chain defects were determined by means of molecular mechanics and energy minimization. The eight defects considered in our study were dispira- tion and dislocation (both interstitial- and vacancy-like), disclination, chain twist boundary (90' and MOO), and partial dislocation boundary. For these defects, energy minimized structures were calculated under action of tensile forces. It was found that one group of defects had moduli and deformation energetics identical with those of an all-trans chain, whereas the other group of defects had substantially lower mod- uli and a different deformation behavior. From the analysis of the distribution of deformation energy over the several degrees of freedom and by comparison to an all-trans chain, it could be concluded that defects inside a crystalline matrix are not weak links in polyethylene fibers. Weak links were concluded to be chains having higher moduli than the surrounding matrix (for example, taut tie molecules and especially entanglements in amorphous domains).

Theoretical study of the dependence of the valence electronic levels on the tacticity and conformation of acrylonitrile model oligomers

With the aim of searching for signatures of conformation and tacticity in electrodeposited polyacrylonitrile valence XPS spectra, exploratory ab initio STO-3G calculations have been performed on four model structures of H—[CH2—CH(CN)]6—H: isotactic and syndiotactic all-trans planar chains and isotactic and syndiotactic (TG)3 helical chains. Contrary to what was assumed in earlier work it is found that the (TG)3 conformation is not a suitable model helix for polyacrylonitrile. Signatures of conformation and tacticity are noted in the ab initio simulated valence XPS spectra; their characteristic features (position on the energy scale, shape and intensity) are within the limits of experimental resolution.

Fundamental studies of microscopic wetting on organic surfaces. 1. Formation and structural characterization of a self-consistent series of polyfunctional organic monolayers

Monolayers of a series of terminally substituted alkyl thiols, X(CH 2 ) 15 SH (X=CH 3 , CH 2 OH, CO 2 H, CO 2 CH 3 , and CONH 2 ), have been prepared by adsorption from solution onto evaporated gold substrates. The structures habe been characterized by infrared (IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), ellipsometry, and temperature-programmed desorption (TPD). The IR data shows the monolayer films to be densely packed, crystalline-like structures with all-trans conformation alkyl chains exhibiting average tilt angles of the chain axis in a range of 28-40° from the surface normal and an approximate 55° twist of the chain axis away from a configuration with the CCC plane perpendicular to the surface plane