Intermolecular Spacing Research Articles

Lattice Mismatch Drives Spatial Modulation of Corannulene Tilt on Ag(111)

We investigated the adsorption of corannulene (C20H10) on the Ag(111) surface by experimental and simulated scanning tunneling microscopy (STM), X-ray photoemission (XPS), and near-edge X-ray absorption fine structure (NEXAFS). Structural optimizations of the adsorbed molecules were performed by density functional theory (DFT) and the core excited spectra evaluated within the transition-potential approach. Corannulene is physisorbed in a bowl-up orientation displaying a very high mobility (diffusing) and dynamics (tilting and spinning) at room temperature. At the monolayer saturation coverage, molecules order into a close-compact phase with an average intermolecular spacing of ∼10.5 ± 0.3 A. The lattice mismatch drives a long wavelength structural modulation of the molecular rows, which, however, could not be identified with a specific superlattice periodicity. DFT calculations indicate that the structural and spectroscopic properties are intermediate between those predicted for the limiting cases of an o...

Robust singlet fission in pentacene thin films with tuned charge transfer interactions

Singlet fission, the spin-allowed photophysical process converting an excited singlet state into two triplet states, has attracted significant attention for device applications. Research so far has focused mainly on the understanding of singlet fission in pure materials, yet blends offer the promise of a controlled tuning of intermolecular interactions, impacting singlet fission efficiencies. Here we report a study of singlet fission in mixtures of pentacene with weakly interacting spacer molecules. Comparison of experimentally determined stationary optical properties and theoretical calculations indicates a reduction of charge-transfer interactions between pentacene molecules with increasing spacer molecule fraction. Theory predicts that the reduced interactions slow down singlet fission in these blends, but surprisingly we find that singlet fission occurs on a timescale comparable to that in pure crystalline pentacene. We explain the observed robustness of singlet fission in such mixed films by a mechanism of exciton diffusion to hot spots with closer intermolecular spacings.

Nanomechanics and modelling of hydrogen stored carbon nanotubes under compression for PEM fuel cell applications

Compressive strength of single walled carbon nanotubes (SWCNTs) filled with hydrogen molecules is analysed in this work utilising molecular dynamics simulation. Understanding mechanical characteristics of SWCNTs with hydrogen interactions are urgently important for providing solid groundwork to design robust and effective on-board hydrogen storage systems for proton exchange membrane fuel cell (PEMFC). This study analyses impact of SWNCTs’ geometry, weight percentage of hydrogen storage, temperature variation and vacancy defects. It is obtained that effect of hydrogen storage increases compressive resistance of SWCNTs. Furthermore, temperature increase and presence of defects negatively impacts compressive strength of SWCNTs. The compressive resistance of hydrogen stored SWCNTs were also found to depend on inter-molecular spacing of hydrogen molecules. It is expected that this work could provide important fundamentals in understanding mechanical behaviour of hydrogen stored SWNCTs subjected to compression that could assist in the development of effective on-board hydrogen storage systems for fuel cells.

In-situ activity of α-amylase in the presence of controlled-frequency moderate electric fields

Studies on the effects of electric fields on enzymatic activity have typically focused on post-treatment residual activity. However, information on their effects on in-situ activity is scant. The objective of this study was to investigate the effect of controlled-frequency Moderate Electric Fields (MEF) on α-amylase activity. Relative α-amylase activities were measured in-situ in the presence of an electric field (1 V/cm, 1 Hz-1MHz) at 60 °C, with a zero electric field at the same temperature serving as a control treatment. Results show a significant nonthermal effect of electric field frequency on α-amylase activity, with up to 41% enhancement of the activity in the 1–60 Hz frequency window. At higher frequencies, activity was either unaffected, or slightly inhibited by the presence of the electric field. Molecular dynamics simulation results show that in the 1–60 Hz frequency window, the translational electrophoretic enzyme displacement approaches the intermolecular spacing of water. Interestingly, enzyme rotational motion transitions from oscillatory behavior to full rotation below 60 Hz. Application of higher frequencies restricts the electrophoretic displacement of the enzyme due to rapid reversal of the direction of the electric field.

Acellular dermal matrix collagen responds to strain by intermolecular spacing contraction with fibril extension and rearrangement.

Acellular dermal matrix (ADM) materials are used as scaffold materials in reconstructive surgery. The internal structural response of these materials in load-bearing clinical applications is not well understood. Bovine ADM is characterized by small-angle X-ray scattering while subjected to strain. Changes in collagen fibril orientation (O), degree of orientation as an orientation index (OI) (measured both edge-on and flat-on to the ADM), extension (from d-spacing changes) and changes to intermolecular spacing are measured as a result of the strain and stress in conjunction with mechanical measurements. As is already well established in similar systems, when strained, collagen fibrils in ADM can accommodate the strain by reorienting by up to 50° (as an average of all the fibrils). This reorientation corresponds to the OI increasing from 0.3 to 0.7. Here it is shown that concurrently, the intermolecular spacing between tropocollagen decreases by 10% from 15.8 to 14.3Å, with the fibril diameter decreasing from 400 to 375Å, and the individual fibrils extending by an average of 3.1% (D-spacing from 63.9 to 65.9nm). ADM materials can withstand large strain and high stress due to the combined mechanisms of collagen reorientation, individual fibril extension, sliding and changes in the molecular packing density.

Collagen Fibril Intermolecular Spacing Changes with 2-Propanol: A Mechanism for Tissue Stiffness.

Materials composed primarily of collagen are important as surgical scaffolds and other medical devices and require flexibility. However, the factors that control the suppleness and flexibility of these materials are not well understood. Acellular dermal matrix materials in aqueous mixtures of 2-propanol were studied. Synchrotron-based small-angle X-ray scattering was used to characterize the collagen structure and structural arrangement. Stiffness was measured by bend tests. Bend modulus increased logarithmically with 2-propanol concentration from 0.5 kPa in water to 103 kPa in pure 2-propanol. The intermolecular spacing between tropocollagen molecules decreased from 15.3 to 11.4 Å with increasing 2-propanol concentration while fibril diameter decreased from 57.2 to 37.2 nm. D-spacing initially increased from 63.6 to 64.2 nm at 50% 2-propanol then decreased to 60.3 nm in pure 2-propanol. The decrease in intermolecular spacing and fibril diameter are due to removal of water and the collapse of the hydrogen bond structure between tropocollagen molecules causing closer packing of the molecules within a fibril. We speculate this tighter molecular packing may restrict the sliding of collagen within fibrils, and similar disruption of the extended hydration layer between fibrils may lead to restriction of sliding between fibrils. This mechanism for tissue stiffness may be more general.

The structural response of the cornea to changes in stromal hydration.

The primary aim of this study was to quantify the relationship between corneal structure and hydration in humans and pigs. X-ray scattering data were collected from human and porcine corneas equilibrated with polyethylene glycol (PEG) to varying levels of hydration, to obtain measurements of collagen fibril diameter, interfibrillar spacing (IFS) and intermolecular spacing. Both species showed a strong positive linear correlation between hydration and IFS2 and a nonlinear, bi-phasic relationship between hydration and fibril diameter, whereby fibril diameter increased up to approximately physiological hydration, H = 3.0, with little change thereafter. Above H = 3.0, porcine corneas exhibited a larger fibril diameter than human corneas (p < 0.001). Intermolecular spacing also varied with hydration in a bi-phasic manner but reached a maximum value at a lower hydration (H = 1.5) than fibril diameter. Human corneas displayed a higher intermolecular spacing than porcine corneas at all hydrations (p < 0.0001). Human and porcine corneas required a similar PEG concentration to reach physiological hydration, suggesting that the total fixed charge that gives rise to the swelling pressure is the same. The difference in their structural responses to hydration can be explained by variations in molecular cross-linking and intra/interfibrillar water partitioning.

Monitoring and manipulating single molecule rotors on the Bi(111) surface by the scanning tunneling microscopy

MnPc rotors were started and stopped by controlling the intermolecular spacing with the STM tip.

Quantifying the Heterogeneous Dynamics of a Simulated Dipalmitoylphosphatidylcholine (DPPC) Membrane.

Heterogeneity of dynamics plays a vital role in membrane function, but the methods for quantifying this heterogeneity are still being developed. Here we examine membrane dynamical heterogeneity via molecular simulations of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid bilayer using the MARTINI force field. We draw upon well-established analysis methods developed in the study of glass-forming fluids and find significant changes in lipid dynamics between the fluid (Lα), and gel (Lβ) phases. In particular, we distinguish two mobility groups in the more ordered Lβ phase: (i) lipids that are transiently trapped by their neighbors and (ii) lipids with displacements on the scale of the intermolecular spacing. These distinct mobility groups spatially segregate, forming dynamic clusters that have characteristic time (1-2 μs) and length (1-10 nm) scales comparable to those of proteins and other biomolecules. We suggest that these dynamic clusters could couple to biomolecules within the membrane and thus may play a role in many membrane functions. In the equilibrium membrane, lipid molecules dynamically exchange between the mobility groups, and the resulting clusters are not associated with a thermodynamic phase separation. Dynamical clusters having similar characteristics arise in many other condensed phase materials, placing membranes in a broad class of materials with strong intermolecular interactions.

Investigation of ethanol infiltration into demineralized dentin collagen fibrils using molecular dynamics simulations

The purpose of this study is to investigate the interaction of neat ethanol with bound and non-bound water in completely demineralized dentin that is fully hydrated, using molecular dynamics (MD) simulation method. The key to creating ideal resin-dentin bonds is the removal of residual free water layers and its replacement by ethanol solvent in which resin monomers are soluble, using the ethanol wet-bonding technique. The test null hypotheses were that ethanol cannot remove any collagen-bound water, and that ethanol cannot infiltrate into the spacing between collagen triple helix due to narrow interlayer spacing. Collagen fibrillar structures of overlap and gap regions were constructed by aligning the collagen triple helix of infinite length in hexagonal packing. Three layers of the water molecules were specified as the layers of 0.15–0.22nm, 0.22–0.43nm and 0.43–0.63nm from collagen atoms by investigating the water distribution surrounding collagen molecules. Our simulation results show that ethanol molecules infiltrated into the intermolecular spacing in the gap region, which increased due to the lateral shrinkage of the collagen structures in contact with ethanol solution, while there was no ethanol infiltration observed in the overlap region. Infiltrated ethanol molecules in the gap region removed residual water molecules via modifying mostly the third water layer (50% decrease), which would be considered as a loosely-bound water layer. The first and second hydration layers, which would be considered as tightly bound water layers, were not removed by the ethanol molecules, thus maintaining the helical structures of the collagen molecules.

Coarse-grained simulations of poly(propylene imine) dendrimers in solution.

The behavior of poly(propylene imine) (PPI) dendrimers in concentrated solutions has been investigated using molecular dynamics simulations containing up to a thousand PPI dendrimers of generation 4 or 5 in explicit water. To deal with large system sizes and time scales required to study the solutions over a wide range of dendrimer concentrations, a previously published coarse-grained model was applied. Simulation results on the radius of gyration, structure factor, intermolecular spacing, dendrimer interpenetration, and water penetration are compared with available experimental data, providing a clear concentration dependent molecular picture of PPI dendrimers. It is shown that with increasing concentration the dendrimer volume diminishes accompanied by a reduction of internalized water, ultimately resulting in solvent filled cavities between stacked dendrimers. Concurrently dendrimer interpenetration increases only slightly, leaving each dendrimer a separate entity also at high concentrations. Moreover, we compare apparent structure factors, as calculated in experimental studies relying on the decoupling approximation and the constant atomic form factor assumption, with directly computed structure factors. We demonstrate that these already diverge at rather low concentrations, not because of small changes in form factor, but rather because the decoupling approximation fails as monomer positions of separate dendrimers become correlated at concentrations well below the overlap concentration.

Real-time measurements to characterize dynamics of emulsion interface during simulated intestinal digestion

Efficient delivery of bioactives remains a critical challenge due to their limited bioavailability and solubility. While many encapsulation systems are designed to modulate the digestion and release of bioactives within the human gastrointestinal tract, there is limited understanding of how engineered structures influence the delivery of bioactives. The objective of this study was to develop a real-time quantitative method to measure structural changes in emulsion interface during simulated intestinal digestion and to correlate these changes with the release of free fatty acids (FFAs). Fluorescence resonant energy transfer (FRET) was used for rapid in-situ measurement of the structural changes in emulsion interface during simulated intestinal digestion. By using FRET, changes in the intermolecular spacing between the two different fluorescent probes labeled emulsifier were characterized. Changes in FRET measurements were compared with the release of FFAs. The results showed that bile salts and pancreatic lipase interacted immediately with the emulsion droplets and disrupted the emulsion interface as evidenced by reduction in FRET efficacy compared to the control. Similarly, a significant amount of FFAs was released during digestion. Moreover, addition of a second layer of polymers at emulsion interface decreased the extent of interface disruption by bile salts and pancreatic lipase and impacted the amount or rate of FFA release during digestion. These results were consistent with the lower donor/acceptor ratio of the labeled probes from the FRET result. Overall, this study provides a novel approach to analyze the dynamics of emulsion interface during digestion and their relationship with the release of FFAs.

Side-Chain Influence on the Mass Density and Refractive Index of Polyfluorenes and Star-Shaped Oligofluorene Truxenes

The density of organic semiconductor films is an important quantity because it is related to intermolecular spacing which in turn determines the electronic and photophysical properties. We report thin film density and refractive index measurements of polyfluorenes and star-shaped oligofluorene truxene molecules. An ellipsometer and a procedure using a spectrophotometer were used to determine film thickness and mass of spin-coated films, respectively. We present a study of the effect of alkyl side-chain length on the volumetric mass density and refractive index of the materials studied. The density measured for poly(9,9-di-n-octylfluorene) (PF8) was 0.88 ± 0.04 g/cm3 and decreased with longer alkyl side chains. For the truxene molecule with butyl side chains (T3 butyl), we measured a density of 0.90 ± 0.04 g/cm3, which also decreased with increasing side-chain length.

Well-Balanced Carrier Mobilities in Ambipolar Transistors Based on Solution-Processable Low Band Gap Small Molecules

We synthesized a solution-processable low band gap small molecule, Si1TDPP-EE-COC6, for use as a semiconducting channel material in organic thin film transistors (OTFTs). The Si1TDPP-EE-COC6 is composed of electron-rich thiophene–dithienosilole–thiophene (Si1T) units and electron-deficient diketopyrrolopyrrole (DPP) and carbonyl units. SiTDPP-EE-COC6-based OTFTs with Au source/drain electrodes were fabricated, and their electrical properties were systematically investigated with increasing thermal annealing temperature. The hole and electron mobilities of as-spun Si1TDPP-EE-COC6 were 3.3 × 10–4 and 1.7 × 10–4 cm2 V–1 s–1, respectively. The carrier mobilities increased significantly upon thermal annealing at 150 °C, yielding a hole mobility of 0.003 cm2 V–1 s–1 and an electron mobility of 0.002 cm2 V–1 s–1. The performance enhancement upon thermal annealing was strongly associated with the formation of a layered edge-on structure and a reduction in the π–π intermolecular spacing. Importantly, the use of at...

Modelling the temperature dependence of the threshold voltage of bis(1,4-dithiolbenzene) molecular assembly system

We present a new analytical model for the threshold voltage Vth of the molecular assembly system (MAS) made of bis(1,4-dithiolbenzene) in a parallel arrangement. The relationship between Vth and the temperature T associated with the intermolecular coupling effect is investigated under various geometrical MAS structures. The results show a linear relationship between Vth and T with an average slope of −0.0042 V/K and Y-intercept in the interval of 2.2584–3.4236 V described by polynomial regression of order 5. Vth decreases linearly by approximately 1.2 V when the temperature changes from 50 to 325 K. At constant temperature, when the intermolecular spacing d decreases from 6.9 to 3.3 Å, strengthening π-orbital interactions further reduce the threshold voltage. This approach of modeling the temperature effects in a linear form significantly simplifies the model parameter extraction of MAS devices, which is an important and useful guideline for the design of future nanoscale devices.

Thermal hysteresis in a spin-crossover Fe(III) quinolylsalicylaldimine complex, Fe(III)(5-Br-qsal)2Ni(dmit)2·solv: solvent effects.

The Fe(III) complexes Fe(5-Br-qsal)2Ni(dmit)2·solv with solv = CH2Cl2 (1) and (CH3)2CO (2) were synthesized, and their structural and magnetic properties were studied. While magnetization and Mössbauer spectroscopy data of 1 showed a gradual spin transition, compound 2 evidenced an abrupt transition with a thermal hysteresis of 13 K close to room temperature (T1/2 ↓ ∼273 K and T1/2 ↑ ∼286 K). A similar packing arrangement of segregated layers of cations and anions was found for 1 and 2. In both low-spin, LS, structures there are a large number of short intra- and interchain contacts. This number is lower in the high-spin, HS, phases, particularly in the case of 1. The significant loss of strong π-π interactions in the cationic chains and short contacts in the anionic chains in the HS structure of 1 leads to alternating strong and weak bonds between cations along the cationic chains and the formation of unconnected dimers along the anionic chains. This is consistent with a significant weakening of the extended interactions in 1. On the other hand, in the HS phase of 2 the 3D dimensionality of the short contacts observed in the LS phases is preserved. The effect of distinct solvent molecules on the intermolecular spacings explains the different spin crossover behaviors of the title compounds.

Packing directed beneficial role of 3-D rigid alicyclic arms on the templated molecular aggregation problem

Tuning of solid state emission by controlling intermolecular interactions and spacing.

A structural and physical study of sol-gel methacrylate-silica hybrids: intermolecular spacing dictates the mechanical properties.

Sol-gel hybrids are inorganic/organic co-networks with nanoscale interactions between the components leading to unique synergistic mechanical properties, which can be tailored, via a selection of the organic moiety. Methacrylate based polymers present several benefits for class II hybrids (which exhibit formal covalent bonding between the networks) as they introduce great versatility and can be designed with a variety of chemical side-groups, structures and morphologies. In this study, the effect of high cross-linking density polymers on the structure-property relationships of hybrids generated using poly(3-trimethoxysilylpropyl methacrylate) (pTMSPMA) and tetraethyl orthosilicate (TEOS) was investigated. The complexity and fine scale of the co-network interactions requires the development of new analytical methods to understand how network evolution dictates the wide-ranging mechanical properties. Within this work we developed data manipulation techniques of acoustic-AFM and solid state NMR output that provide new approaches to understand the influence of the network structure on the macroscopic elasticity. The concentration of pTMSPMA in the silica sol affected the gelation time, ranging from 2 h for a hybrid made with 75 wt% inorganic with pTMSPMA at 2.5 kDa, to 1 minute for pTMSPMA with molecular weight of 30 kDa without any TEOS. A new mechanism of gelation was proposed based on the different morphologies derived by AC-AFM observations. We established that the volumetric density of bridging oxygen bonds is an important parameter in structure/property relationships in SiO2 hybrids and developed a method for determining it from solid state NMR data. The variation in the elasticity of pTMSPMA/SiO2 hybrids originated from pTMSPMA acting as a molecular spacer, thus decreasing the volumetric density of bridging oxygen bonds as the inorganic to organic ratio decreased.

Charge Neutralization of the Central Lysine Cluster in Prion Protein (PrP) Promotes PrPSc-like Folding of Recombinant PrP Amyloids

The structure of the infectious form of prion protein, PrP(Sc), remains unclear. Most pure recombinant prion protein (PrP) amyloids generated in vitro are not infectious and lack the extent of the protease-resistant core and solvent exclusion of infectious PrP(Sc), especially within residues ∼90-160. Polyanionic cofactors can enhance infectivity and PrP(Sc)-like characteristics of such fibrils, but the mechanism of this enhancement is unknown. In considering structural models of PrP(Sc) multimers, we identified an obstacle to tight packing that might be overcome with polyanionic cofactors, namely, electrostatic repulsion between four closely spaced cationic lysines within a central lysine cluster of residues 101-110. For example, in our parallel in-register intermolecular β-sheet model of PrP(Sc), not only would these lysines be clustered within the 101-110 region of the primary sequence, but they would have intermolecular spacings of only ∼4.8 Å between stacked β-strands. We have now performed molecular dynamics simulations predicting that neutralization of the charges on these lysine residues would allow more stable parallel in-register packing in this region. We also show empirically that substitution of these clustered lysine residues with alanines or asparagines results in recombinant PrP amyloid fibrils with extended proteinase-K resistant β-sheet cores and infrared spectra that are more reminiscent of bona fide PrP(Sc). These findings indicate that charge neutralization at the central lysine cluster is critical for the folding and tight packing of N-proximal residues within PrP amyloid fibrils. This charge neutralization may be a key aspect of the mechanism by which anionic cofactors promote PrP(Sc) formation.

Investigation of Ferroelectric Polymer Langmuir Film Properties

ABSTRACTThin films of Polyvinylidene Fluoride (PVDF) copolymers have been incorporated within ferroelectric field effect transistors, all organic thin film transistor devices (OTFTs), piezoelectric actuators, and recently proposed as the ferroelectric layer in a promising multiferroic tunnel junction configuration [1]. The properties of most of these devices would benefit from reduced thickness and better thickness control of the ferroelectric layer during device processing.A proven means for fabricating ultrathin films of the PVDF copolymer is the Langmuir-Blodgett (LB) technique. This technique involves dissolving the polymer in a volatile solvent which is then dispersed dropwise onto a purified water subphase, leaving an ultrathin layer of the copolymer on the water surface. The ability to control the thickness on the molecular level is the most prominent feature of this technique.In some early studies [2], the minimum thickness of these films was found to be about 5 Angstroms, or roughly the same thickness as the intermolecular spacing of the all-trans β phase for the ferroelectric polymers. Later studies have led to the fabrication of films composed of thicker transfer steps: ∼ 1.8 nm per deposition [3]. The discrepancy is likely explained by the nature of the VDF molecule: it is not an amphiphile.In this study, we further investigate the properties of Langmuir films of ferroelectric copolymers and discuss the observation of an apparent monolayer phase transition based on abrupt changes observed in the compressibility of the films. The main goal of this project is to discover the extent to which the device properties (like transfer step thickness) of PVDF films can be modified through processing conditions.