Population Of Gauche Conformers Research Articles

Conformation heterogeneity of alkylammonium surfactants self-assembled on montmorillonite: Effect of head-group structure and temperature

The understanding of the organic cations arrangement on the surface of clay mineral is an important step toward optimizing the functionality of organoclays for industrial applications. In this study the effect of alkyl chain length, head-group structure (N(CH3)3, vsNH3), and temperature on the conformation of the cationic surfactants in a organo-montmorillonite (O-Mt) interlayers was systematically studied using XRD, near-IR and 13C NMR spectroscopy. Decreasing amount of the disordered gauche conformers, replaced by the ordered all-trans conformers, was observed with increasing alkyl chain length. A higher population of gauche conformers for cations with NH3 than for N(CH3)3 head-group resulted from a different mode of head-group binding to basal oxygen atoms. On increasing the temperature up to 205 °C the alkyl chains adopted a more disordered, liquid-like arrangement. In contrast, the surfactants in O-Mt cooled to −196 °C adjusted more ordered conformation, characteristic of a crystalline-like state.

Identification of alcohol conformers by Raman spectra in the C-H stretching region.

The spontaneous polarized Raman spectra of normal and deuterated alcohols (C2-C5) have been recorded in the C-H stretching region. In the isotropic Raman spectra, a doublet of -CαH stretching vibration is found for all alcohols at below 2900 cm(-1) and above 2950 cm(-1). By comparing the experimental and calculated spectra of various deuterated alcohols, the doublets are attributed to the -CαH stretching vibration of different conformers. For ethanol, the band observed at 2970 cm(-1) is assigned as the stretching vibration of -CαH in the Cα-O-H plane of the gauche-conformer, while the band at 2895 cm(-1) is contributed from both the -CαH2 symmetrical stretching vibration of the trans-conformer and the -CαH stretching vibration out of the Cα-O-H plane of the gauche-conformer. The population of gauche-conformer is estimated to be 54% in liquid ethanol. For the larger alcohols, the same assignments for the doublet are obtained, and the populations of gauche-conformers with plane carbon skeleton are found to be slightly larger than that of ethanol, which is consistent with results from molecular dynamics simulations.

The gauche effect: seeking evidence by a survey of crystal structures.

I previously blogged about anomeric effects involving π electrons as donors, and my post on the conformation of 1,2-difluorethane turned out one of the most popular. Here I thought I would present the results of searching the Cambridge crystal database for examples of the gauche effect. The basic search is defined below Here, we define a four-atom torsion (TOR1), the two central carbon atoms having two groups R which can be only H or C. These two carbons are also defined as acyclic. The restrictions of the search as defined above also include R-factor < 0.05, not disordered and no errors. These combine to reduce the number of hits significantly (although not dissimilar distributions are obtained for less restricted searches). Each search takes only a few seconds, and one can rattle through many permutations very quickly. So here come the results. First, QA=4M=F. All but one of the examples has a torsion in the region of 60°, the classic gauche effect! F-C-C-F Next, QA=O, 4M=F. Rather more hits, and the effect is almost as clear-cut. I should point out that the apparent “exceptions” to the gauche conformation may arise from structural restrictions, and each really would have to be inspected individually for the reasons (which I do not attempt here). OCCF With QA=4M=O, one has many more instances. The effect is pretty convincing (it may be that hydrogen bonding may also control the conformation). O-C-C-O Now for QA=4M=Cl. The distribution is slanted more to the anti conformation, but there are still quite a few gauche. Cl-CC-Cl With QA=4M=S, the conformations are now almost all anti; the gauche effect is no more! S-C-C-S And for QA=4M=Br, it has also almost vanished (there is only one instance for I, and that too is antiperiplanar). Br-C-C-Br I now return to an earlier post in which I speculated that a cyano group might participate in the anomeric effect. Well here it is in the gauche effect; QA=CN, 4M = any of N,O,F,Cl,S. Quite a few gauche orientations for this pseudo-halogen! Neg-C-C-CN Another group that can act as a powerful acceptor of electrons from a donor is QA=N(Me)3+.. With 4M= N, O, F, Cl, here the population of gauche conformers is large. QA=CF3 is a similar group. Neg-C-C-NMe3 Neg-C-C-CF3 One can envisage other combinations. Thus QA= C=C, 4M = any of N, O, F, Cl. An alkene seems one of the more powerful gauche effect participants! alkene-C-C-Neg And alkynes, perhaps slightly less so. Alkyne-C-C-Neg What about metals (QA = any metal, 4M = any of N, O, F, Cl, S). Well, not particularly biased either way, but clearly one in which the identity of the metal may matter. Metal-C-C-electronegative I should end with inverting the model. If QA is electropositive (any group to the left of carbon, or below it in the periodic table) and 4M is electronegative, than they align almost exclusively anti-periplanar and not gauche. But notice how relatively few examples there are. Synthetic chemists, please make more such molecules! Electropositive-C-C-Electronegative If you thought the gauche effect was restricted to just a few molecules, think again!

Neutron Spectroscopy as a Probe of Macromolecular Structure and Dynamics under Extreme Spatial Confinement

We illustrate the use of high-resolution neutron spectroscopy to explore the extreme spatial confinement of soft matter in nanostructured materials. Two well-defined limits are considered, involving either intercalation or interfacial adsorption of the ubiquitous polymer poly(ethylene oxide) in graphite-oxide-based hosts. Vibrational modes associated with the confined macromolecular phase undergo dramatic changes over a broad range of energy transfers, from those associated with intermolecular modes in the Terahertz frequency range (1 THz = 33 cm−1), to those characteristic of strong chemical bonds above 2000 cm−1. We also consider the effects of polymer chain size and chemical composition of the host material. Variation of the degree of oxidation and exfoliation of graphite oxide leads to two distinct cases, namely: (i) subnanometer two-dimensional confinement; and (ii) surface immobilization. Case (i) is characterised by significant changes to conformational and collective vibrational modes of the polymer as a consequence of a preferentially planar trans-trans-trans chain conformation, whereas case (ii) leads to a substantial increase in the population of gauche conformers. Macroscopically, case (i) translates into the complete suppression of crystallization and glassy behaviour. In contrast, case (ii) exhibits well-defined glass and melting transitions associated with the confined phase, yet at significantly lower temperatures than those of the bulk.

Two-dimensional correlation infrared spectroscopy studies on the thermal-induced mesophase of 4-nitrobenzohydrazide derivative

Two-dimensional (2D) correlation infrared (IR) spectroscopy has been applied to explore the effect of hydrogen bondings (HBs) on the structure of mesophase in the dissymmetrical 4-nitrobenzohydrazide derivative, N-(4-cetyloxybenzoyl)-N′-(4′-nitrobenzoyl) hydrazine (C16-NO2). The strength and species of HBs as well as the heat-induced structural variations in mesophase have been investigated. It has been found from 2D correlation IR spectroscopy that the sequential order of changes in the different functionalities in the course of liquid crystalline formation is that, firstly, the alkyl chain changes from the significant population of the trans conformation to the significant population of gauche conformation; then, the intermolecular HB between CO and NH groups is weakened, some even being broken, and consequently, the intermolecular distance is enlarged; finally, the skeleton of phenyl ring has enough space to change their conformation to weaken the π–π stacking interaction. In addition, besides a few free and some medium bonded NH and CO groups, strongly bonded NH and CO groups still predominantly exist in the mesophase.

Insight into the molecular recognition of spermine by DNA quadruplexes from an NMR study of the association of spermine with the thrombin-binding aptamer

The preferred residence sites and the conformation of DNA-bound polyamines are central to understanding the regulatory roles of polyamines. To this end, we have used a series of selective (13)C-edited and selective total correlation spectroscopy-edited one-dimensional (1D) nuclear Overhauser effect spectroscopy NMR experiments to determine a number of intramolecular (1)H nuclear Overhauser effect (NOE) connectivities in (13)C-labelled spermine bound to the thrombin-binding aptamer. The results provide evidence that the aptamer-bound spermine adopts a conformation that optimizes electrostatic and hydrogen bond contacts with the aptamer backbone. The distance between the nitrogen atoms of the central aminobutyl is reduced by an increase in the population of gauche conformers at the C6-C7 bonds, which results in either a curved or S-shaped spermine conformation. Molecular modelling contributes insight toward the mode of spermine binding of these spermine structures within the narrow grooves of DNA quadruplexes. In each case, the N5 ammonium group makes hydrogen bonds with two nearby phosphates across the narrow groove. Our results have implications for the understanding of chromatin structure and the rational design of quadruplex-binding drugs.

Crystallinity and orientation development upon hot multistage drawing of PET multifilament yarn

In this research, poly(ethylene terephthalate) (PET) multifilament yarn was drawn on an industrial drawing machine at hot multistage. By varying draw ratio, a number of drawn fibers with different internal structures were obtained. Total draw ratio was changed from 4.68 to 6.24. Crystallinity and molecular orientation of the drawn samples were investigated using differential scanning calorimetry, birefringence, infrared spectroscopy, and X-ray diffraction. The results show that the high population of gauche conformer in as-spun fiber decreased rapidly with fiber orientation. The absence of crystallization peak and clear T g in the drawn samples has been explained by orientation development as well as crystalline–amorphous interactions. Microstructural changes in the drawn PET fibers have been discussed in terms of the applied heat and mechanical deformation upon hot multistage drawing.

Macromolecular Structure and Vibrational Dynamics of Confined Poly(ethylene oxide): From Subnanometer 2D-Intercalation into Graphite Oxide to Surface Adsorption onto Graphene Sheets.

In this work, high-resolution inelastic neutron scattering (INS) has been used to provide novel insights into the properties of confined poly(ethylene oxide) (PEO) chains. Two limits have been explored in detail, namely, single-layer 2D-polymer intercalation into graphite oxide (GO) and surface polymer adsorption onto thermally reduced and exfoliated graphite oxide, that is, graphene (G) sheets. Careful control over the degree of GO oxidation and exfoliation reveals three distinct cases of spatial confinement: (i) subnanometer 2D-confinement; (ii) frustrated absorption; and (iii) surface immobilization. Case (i) results in drastic changes to PEO conformational (800-1000 cm-1) and collective (200-600 cm-1) vibrational modes as a consequence of a preferentially planar zigzag (trans-trans-trans) chain conformation in the confined polymer phase. These changes give rise to peculiar thermodynamic behavior, whereby confined PEO chains are unable to either crystallize or display a calorimetric glass transition. In case (ii), GO is thermally reduced resulting in a disordered pseudo-graphitic structure. As a result, we observe minimal PEO absorption owing to a dramatic reduction in the abundance of hydrophilic groups inside the distorted graphitic galleries. In case (iii), the INS data unequivocally show that PEO chains adsorb firmly onto the G sheets, with a substantial increase in the population of gauche conformers. Well-defined glass and melting transitions associated with the confined polymer phase are recovered in case (iii), albeit at significantly lower temperatures than those of the bulk.

Solvent Dependence on Conformational Transition, Dipole Moment, and Molecular Geometry of 1,2-Dichloroethane: Insight from Car−Parrinello Molecular Dynamics Calculations

We have investigated the molecular geometry and dipole moment distribution for the major conformational states of 1,2-dichloroethane (DCE) in three different solvents under ambient conditions using the Car-Parrinello mixed quantum mechanics/molecular mechanics method. The solvents studied were water, DCE, and chloroform. Within the time scale investigated, we find a conformational equilibrium existing between the gauche and trans forms of DCE in all three solvents. In the chloroform solvent, the conformational transition occurs more frequently than in water solvent and in liquid DCE (i.e., DCE solute in DCE solvent). The population of gauche conformer is more in the case of water solvent, while the trans conformer dominates in chloroform solvent. We report a bimodal nature of the dipole moment distribution for DCE in all three solute-solvents studied, where the peaks are attributed to the trans and gauche conformational states. The dipole moments of both of the conformational states increase with increasing polarity of the solvent. Also, with an increase in solvent polarity, an increase in the C-Cl bond length and magnitude of atomic charges in DCE has been observed. The increase in atomic charges of DCE is almost twice when the solvent is changed from chloroform to water.

Density functional study of gamma-aminopropyltriethoxysilane

Density functional theory calculations using Becke's three-parameter exchange functional in combination with the Lee-Young-Parr correlation functional (B3-LYP) and standard 6-311 + G(d,p) basis set were carried out to study the conformational stability and vibrational spectra of gamma-aminopropyltriethoxysilane. Calculations reveal the existence of two stable conformers trans and gauche. The calculated energy for the gauche conformation was found to be 608 cm−1 above the minimum energy of the trans conformation. Temperature dependence of Raman spectra of liquid APTES and DFT calculation enabled us to identify the vibrational bands characteristic for both conformers. It has been shown that there is an increase in the population of gauche conformer with increasing temperature.

Experimental characterisation and further molecular modelling of the conformational and elastic behaviour of poly(ethylene terephthalate) network chains

The Monte-Carlo (MC) method developed to model the elastomeric stress–strain behaviour of polyethylene (PE), poly(dimethyl siloxane) (PDMS) and poly(ethylene terephthalate) (PET) networks and the stress-optical behaviour of PE networks is now developed to investigate further the stress–strain behaviour of PET networks. Accurate infrared (IR) spectrometry measurements have been used to determine the populations of gauche conformers in the glycol residues of PET chains in melts. The proportion of gauche states was found to be 76%, consistent with the rotational energy difference of −4.16 kJ mol−1 between trans and gauche states used previously. The greater conformational flexibility of the PET chain compared with the PE chain leads to lower network moduli and smaller deviations from Gaussian and affine network behaviour. Previous results are briefly reviewed and new comparisons of the elastic behaviour of PET and PE chains are made using normalised plots. Subsequent publications will apply the present results to interpreting the measured stress–strain and the stress-optical properties of entangled PET melts.

Experimental characterisation and further molecular modelling of the conformational and elastic behaviour of poly(ethylene terephthalate) network chains

The Monte-Carlo (MC) method developed to model the elastomeric stress–strain behaviour of polyethylene (PE), poly(dimethyl siloxane) (PDMS) and poly(ethylene terephthalate) (PET) networks and the stress-optical behaviour of PE networks is now developed to investigate further the stress–strain behaviour of PET networks. Accurate infrared (IR) spectrometry measurements have been used to determine the populations of gauche conformers in the glycol residues of PET chains in melts. The proportion of gauche states was found to be 76%, consistent with the rotational energy difference of −4.16 kJ mol −1 between trans and gauche states used previously. The greater conformational flexibility of the PET chain compared with the PE chain leads to lower network moduli and smaller deviations from Gaussian and affine network behaviour. Previous results are briefly reviewed and new comparisons of the elastic behaviour of PET and PE chains are made using normalised plots. Subsequent publications will apply the present results to interpreting the measured stress–strain and the stress-optical properties of entangled PET melts.

Glass Transition Temperature and Conformational Changes of Poly(methyl methacrylate) Thin Films Determined by a Two-Dimensional Map Representation of Temperature-Dependent Reflection−Absorption FTIR Spectra

Temperature-dependent reflection-absorption Fourier transform infrared spectra of poly(methyl methacrylate) (PMMA) thin films were measured. From these spectra, two-dimensional (2D) maps of the first derivative of the absorbance with respect to temperature over the space of wavenumber and temperature were constructed. These maps were used to determine the glass transition temperature and to investigate the subtle temperature dependence of the population of trans and gauche conformers in three PMMA thin films with different stereoregularities. The glass transition temperatures determined from the 2D maps for isotactic, syndiotactic, and atactic PMMA thin films were approximately 61, 111, and 106 °C, respectively. Calculations of the fraction of gauche conformation from the conformational energy showed an abrupt increase in the population of the gauche conformer above the glass transition temperature. The temperature dependence of the fraction of gauche conformation was well reflected in our 2D maps. Furthermore, it was found that molecular reorganization of PMMA occurs even below the glass transition temperature.

Conformation of Methylene Chains in an Intercalated Surfactant Bilayer

Infrared and Raman spectroscopy have been used to establish the conformation and orientation of the methylene “tail” of cetyl trimethylammonium ions intercalated in an inorganic layered host, $CdPS_{3}$. Intercalation, effected by a two-step ion-exchange process leading to the formation of $Cd_{0.83}$$PS_{3}$ $(CTA)_{0.34}$, occurs with a lattice dilation of 26.5 \AA with the surfactant ions within the galleries adopting a bilayer structure. The frequencies of the conformationally sensitive methylene stretching modes in the infrared and Raman spectra indicate that a majority of the bonds in the methylene chain are in a trans conformation. The methylene chains are tilted with respect to the inorganic layer. The tilt angle as determined from orientation-dependent infrared spectra is \sim $35^0$. Although the population of gauche conformers is low, it has been possible to identify specific conformational sequences containing a gauche bond, in the interior and termini of the intercalated methylene chains, by their characteristic frequencies in the infrared spectrum. These high-energy conformers, except for the ones at the chain end, disappear on cooling, leaving on average all 15 methylene units of the intercalated cetyl trimethylammonium ion in trans conformational registry at 40 K. The terminal gauche defects are significant in preventing interdigitation of the low-density intercalated surfactant bilayer.

Pressure and Temperature Effects on Conformational and Hydrational Properties of Lamellar and Bicontinuous Cubic Phases of the Fully Hydrated Monoacylglyceride MonoelaidinA Fourier Transform-Infrared Spectroscopy Study Using the Diamond Anvil Technique

We report on the effects of pressure and temperature on the phase behavior and structural properties of aqueous dispersions of monoelaidin (ME) using Fourier transform−infrared spectroscopy (FT-IR) in combination with the diamond anvil technique. The IR spectral parameters, such as frequencies, intensities, band shapes, and band splittings, were used to detect structural and dynamic changes upon change of pressure and temperature. Analysis of these spectral parameters yields information on conformer population, reorientational fluctuations, interchain interaction, hydrogen bonding, and phase transformations. The monoacyglyceride ME was chosen for investigation because it exhibits various mesomorphic liquid−crystalline phases of different dimensionality, including lamellar, a cubic-primitive (QIID), and a body-centered cubic phase (QIIP). The latter two are inverse bicontinuous cubic phases. We have established the excess water p,T-phase diagram of ME over the 1−23-kbar range at ∼15−95 °C. In the high-pressure region, enhanced interchain interaction leads to a correlation field splitting of the CH2 bending and rocking modes, which is expected when entering the lamellar crystalline Lc phase that has the smallest partial molar volume. As revealed by the phase diagram, the energetic degeneracy of the cubic phases is broken. With increasing temperature or decreasing pressure, the cubic phases QIIP and QIID are formed. Interpretation of the CH2 stretching and wagging modes for evaluation of conformational states in the fluidlike disordered (Lα, QIIP, and QIID) phases reveals different populations of gauche conformers and kinks in these fluidlike phases. From the analysis of the carbonyl stretching mode vibrations we have been also able to detect small but marked differences in the level of hydration of different bicontinuous cubic phases. Compared with the QIID phase of ME, the lipid chains of the body-centered cubic phase QIIP seem to contain a slightly higher population of gauche sequences and a slightly lower level of hydration of the carbonyl group. The results are compared with recent energetic models for intercubic phase transitions.

Structure and Chain Dynamics of Alkanethiol-Capped Gold Colloids

The structure and dynamical behavior of short and long chain alkanethiols, CH3(CH2)7SH and CH3(CH)17SH, and of a hydroxyalkanethiol, HO(CH2)16SH, adsorbed onto gold nanoparticles were studied by variable temperature solid-state 13C NMR spectroscopy. In both the solution and solid state, the resonances of the first three carbons next to the sulfur headgroup disappear upon binding to the gold, indicating a strong interaction with the surface. A 13C-enriched sample, CH3(CH2)12*CH2SH/gold, displays a broad resonance centered at 42 ppm for the carbon next to the sulfur headgroup. Whereas the solid-state 13C shifts of CH3(CH2)7SH/gold are essentially the same as in solution, the methylene carbons of CH3(CH2)17SH and HO(CH2)16SH/gold shift downfield by 4.5 ppm in the solid state, indicating that the chains crystallize into an extended all-trans conformation. The high conformational order, along with reduced methylene proton line widths in the CH3(CH)17SH/gold sample, indicates that the chains are undergoing large-amplitude motions about their long axes. Molecular mobility increases toward the unbound ends which have a higher population of gauche conformers. Relaxation measurements show the coexistence of motionally restricted all-trans chains and a smaller population of liquid-like conformationally disordered chains in CH3(CH2)17SH/gold at room temperature. The two types of chains are proposed to arise from close packing of the gold colloidal spheres, resulting in interstitial spaces and regions where chains of neighboring colloids can interdigitate to produce ordered domains. Phase transitions of the thiol-capped gold nanocrystals, which are detected by differential scanning calorimetry, are shown to involve a reversible disordering of the alkyl chains.

A Study of Conformational Equilibria in Chain Molecules. I. Liquidn-Butane

Abstract We have performed molecular dynamics simulations for liquid n-butane in order to understand liquid structures in terms of both inter- and intra-molecular interactions. Each n-butane molecule consists of four sites interacting with LJ potential and only a dihedral angle is taken into account as the internal degree of freedom. The population of gauche conformations with respect to the ideal gas state is found to increase in the liquid state. To investigate how the intermolecular interaction affects the dihedral angle distribution, we also adopt the repulsive LJ potential (RLJ) model. It is found that the nearest neighbor packing of the methyl and/or methylene groups can be approximately represented by using only the repulsive interaction. From the dihedral angle distribution, however, the rate of the shift of RLJ model to gauche is larger than that of LJ model and the attractive force also plays a significant role in the conformational equilibrium.

Fourier transform infrared spectroscopic studies on model biological membranes deposited by the Langmuir-Blodgett technique

Monolayers and multilayers of (1,2-dipalmitoyl- sn-glycero-3-phosphatidic acid) (DPPA) and its calcium salt have been deposited onto silicon and metal substrates using the Langmuir-Blodgett technique. Infrared frequency shifts of the alkyl chain vibrations and their dichoric behaviour show that the lipid forms very well-oriented monolayers. As the number of layers increases the order factor (⨍) is higher and this is the case whether or not calcium is added to the subphase. The “ordered” nature of these films is confirmed by the ester group ν(CO) bands which show the presence of only a small population of gauche conformations at the ester linkage (compared with a “disordered” cast film). The presence of highly perturbed water in these lipid multilayers has been established for the first time. Such water takeup is, however, not very reproducible and it is clearly different depending on the nature of the subphase.

Study of Tails in Smectic Liquid Crystals. I. The Effect of Fluorocarbon/Hydrocarbon Ether Tails on Phenyl Ester Biphenyl Cores

Abstract The use of the mixed fluorocarbon/hydrocarbon ether sequence [1H,1H,5H-octafluoro-1-pentoxy-]ethoxy in place of aliphatic or aliphatic ether sequences significantly enhances the temperature range of the chiral smectic C (Sc*) liquid crystalline phase. Considerations derived from the literature, supported by computer modeling, suggested that stabilization of the Sc* phase results from enhancement of the population of gauche conformers. These considerations have led to liquid crystal molecules with the widest range of Sc* phase thus far reported.

Comparison of the structures and wetting properties of self-assembled monolayers of n-alkanethiols on the coinage metal surfaces, copper, silver, and gold

Long-chain alkanethiols, HS(CH2),CH3, adsorb from solution onto.the surfaces of gold, silver, and copper and form monolayers. Reflection infrared spectroscopy indicates that monolayers on silver and on copper (when carefully prepared) have the chains in well-defined molecular orientations and in crystalline-like phase states, as has been observed on gold. Monolayers on silver are structurally related to those formed by adsorption on gold, but different in details of orientation. The monolayers formed on copper are structurally more complex and show a pronounced sensitivity to the details of the sample preparation. Quantitative analysis of the IR data using numerical simulations based on an average single chain model suggests that the alkyl chains in monolayers on silver are all-trans zig-zag and canted by - 12' from the normal to the surface. The analysis also suggests a twist of the plane containing the carbon backbone of -45' from the plane defined by the tilt and surface normal vectors. For comparison, the monolayers that form on adsorption of alkanethiols on gold surfaces, as judged by their vibrational spectra, are also trans zig-zag extended but, when interpreted in the context of the same single chain model, have a cant angle of -27O and a twist of the plane of the carbon backbone of -53'. The monolayers formed on copper (when they are obtained in high quality) exhibit infrared spectra effectively indistinguishable from those on silver and thus appear to have the same structure. Films on copper are also commonly obtained that are structurally ill-defined and appear to contain significant densities of gauche conformations. These spectroscopically based interpretations are compatible with inferences from wetting and XPS measurements. The structure of the substrate-sulfur interface appears to control molecular orientations of the alkyl groups in these films. An improved structural model, incorporating a two-chain unit cell and allowing for the temperature-dependent population of gauche conformations, is presented and applied to the specific case of the structures formed on gold.