Neutron Scattering Length Density Profile Research Articles

Incorporation and localisation of alkanes in a protomembrane model by neutron diffraction

Protomembranes at the origin of life were likely composed of short-chain lipids, readily available on the early Earth. Membranes formed by such lipids are less stable and more permeable under extreme conditions, so a novel membrane architecture was suggested to validate the accuracy of this assumption. The model membrane includes the presence of a layer of alkanes in the mid-plane of the protomembrane in between the two monolayer leaflets and lying perpendicular to the lipid acyl chains. Here, we investigated such a possibility experimentally for membranes formed by the short-chain phospholipid 1,2-didecanoyl-sn-glycero-3-phophocholine, including or not the alkanes eicosane, squalane or triacontane by means of neutron membrane diffraction and contrast variation. We found strong indications for incorporation of two of the three alkanes in the membrane mid-plane through the determination of neutron scattering length density profiles with hydrogenated vs deuterated alkanes and membrane swelling at various relative humidities indicating a slightly increased bilayer thickness when the alkanes are incorporated into the bilayers. The selectivity of the incorporation points out the role of the length of the n-alkanes with respect to the capacity of the membrane to incorporate them.

Extraction of interaction parameters from specular neutron reflectivity in thin films of diblock copolymers: an "inverse problem".

Diblock copolymers have been shown to undergo microphase separation due to an interplay of repulsive interactions between dissimilar monomers, which leads to the stretching of chains and entropic loss due to the stretching. In thin films, additional effects due to confinement and monomer-surface interactions make microphase separation much more complicated than in that in bulks (i.e., without substrates). Previously, physics-based models have been used to interpret and extract various interaction parameters from the specular neutron reflectivities of annealed thin films containing diblock copolymers (J. P. Mahalik, J. W. Dugger, S. W. Sides, B. G. Sumpter, V. Lauter and R. Kumar, Interpreting neutron reflectivity profiles of diblock copolymer nanocomposite thin films using hybrid particle-field simulations, Macromolecules, 2018, 51(8), 3116; J. P. Mahalik, W. Li, A. T. Savici, S. Hahn, H. Lauter, H. Ambaye, B. G. Sumpter, V. Lauter and R. Kumar, Dispersity-driven stabilization of coexisting morphologies in asymmetric diblock copolymer thin films, Macromolecules, 2021, 54(1), 450). However, extracting Flory-Huggins χ parameters characterizing monomer-monomer, monomer-substrate, and monomer-air interactions has been labor-intensive and prone to errors, requiring the use of alternative methods for practical purposes. In this work, we have developed such an alternative method by employing a multi-layer perceptron, an autoencoder, and a variational autoencoder. These neural networks are used to extract interaction parameters not only from neutron scattering length density profiles constructed using self-consistent field theory-based simulations, but also from a noisy ad hoc model constructed previously. In particular, the variational autoencoder is shown to be the most promising tool when it comes to the reconstruction and extraction of parameters from an ad hoc neutron scattering length density profile of a thin film containing a symmetric di-block copolymer (poly(deuterated styrene-b-n-butyl methacrylate)). This work paves the way for automated analysis of specular neutron reflectivities from thin films of copolymers using machine learning tools.

Polymorphism, Nanostructures, and Barrier Properties of Ceramide-Based Lipid Films.

Ceramides belong to sphingolipids, an important group of cellular and extracellular lipids. Their physiological functions range from cell signaling to participation in the formation of barriers against water evaporation. In the skin, they are essential for the permeability barrier, together with free fatty acids and cholesterol. We examined the periodical structure and permeability of lipid films composed of ceramides (Cer; namely, N-lignoceroyl 6-hydroxysphingosine, CerNH24, and N-lignoceroyl sphingosine, CerNS24), lignoceric acid (LIG; 24:0), and cholesterol (Chol). X-ray diffraction experiments showed that the CerNH24-based samples form either a short lamellar phase (SLP, d ∼ 5.4 nm) or a medium lamellar phase (MLP, d = 10.63-10.78 nm) depending on the annealing conditions. The proposed molecular arrangement of the MLP based on extended Cer molecules also agreed with the relative neutron scattering length density profiles obtained from the neutron diffraction data. The presence of MLP increased the lipid film permeability to the lipophilic model permeant (indomethacin) relative to the CerNS24-based control samples and the samples that had the same lipid composition but formed an SLP. Thus, the arrangement of lipids in various nanostructures is responsive to external conditions during sample preparation. This polymorphic behavior directly affects the barrier properties, which could also be (patho)physiologically relevant.

Coarse-grained description of monounsaturated peroxidized phospholipid bilayers

Lipid peroxides result from a reaction between cis-unsaturated lipid chains and singlet oxygen molecules leading to the addition of a peroxide OOH side group next to the acyl-chain double bond. It is now established that HP-POPC (hydroperoxidized POPC) molecules form stable, thin, and laterally expanded bilayers. The difference in the structural organization arises from the hydrophilic character of the OOH side group that has a strong affinity with the water interface region, leading to significant reorganization of the bilayer. In this article, we describe a coarse-grained (CG) model of POPC and DOPC lipid peroxides within the framework of the Martini CG force-field (v2.2), derived from experimental data. We then discuss extensively the predicted structure and the influence of hydration and show how shifting the position of the unsaturated bonds along the chain changes the structure. Finally, we provide electron and neutron scattering length density profiles of the simulated bilayers.

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition.

Molecular dynamics simulations of mixtures of the ceramide nonhydroxy-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained force field for cholesterol was developed using the multistate iterative Boltzmann inversion (MS-IBI) method. The coarse-grained cholesterol force field is compatible with previously developed coarse-grained force fields for ceramide NS, free fatty acids, and water and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the single bilayer in water structures typically studied using molecular simulation. Cholesterol fluidizes the membrane by promoting packing defects, and an increase in cholesterol content is found to reduce the bilayer thickness due to an increase in interdigitation of the C24 lipid tails, consistent with experimental observations. Using a reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. This work highlights the importance of simulating multilayer structures, as compared to the more commonly studied bilayer systems, to enable more appropriate comparisons with multilayer experimental membranes. These results also provide validation of the efficacy of the MS-IBI derived coarse-grained force fields and the framework for multiscale simulation.

An introduction to neutron reflectometry

Specular neutron reflectivity is a neutron diffraction technique that provides information about the structure of surfaces or thin films. It enables the measurement of the neutron scattering length density profile perpendicular to the plane of a surface or an interface, and thereby gives access to the profile of the chemical composition of the film. The wave-particle duality allows to describe neutrons as waves; at an interface between two media of different refractive indexes, neutrons are partially reflected and refracted by the interface. Interferences can occur between waves reflected at the top and at the bottom of a thin film at an interface, which gives rise to interference fringes in the reflectivity profile directly related to its thickness. The characteristic sizes that can be probed range from 5Å to 2000 Å. Neutron-matter interaction directly occurs between neutron and the atom nuclei, which enable to tune the contrast by isotopic substitution. This makes it particularly interesting in the fields of soft matter and biophysics. This course is composed of two parts describing respectively its principle and the experimental aspects of the method (instruments, samples). Examples of applications of neutron reflectometry in the biological domain are presented by Y. Gerelli in the book section “Applications of neutron reflectometry in biology”.

Molecular Structure of the Long Periodicity Phase in the Stratum Corneum.

All-atom models of the long periodicity phase (LPP) in the stratum corneum (SC) are studied using bilayer-slab-bilayer (sandwich) structures and multi-microsecond simulations. Linoleate promotes melting of the interior slab, which contains ceramide (Cer) in the posturing chain conformation, a structurally distinct conformation from full chain extension. The mechanism of Cer transitioning into full extension is characterized by initial anchoring of the head-proximal carbons and occurs over tens of nanoseconds. Free fatty acids translocate through the interior over hundreds of nanoseconds, while Cer and cholesterol take around a microsecond or longer to translocate. Electron density and neutron scattering length density profiles from simulation agree with experiment, and the high disorder of linoleate in CerEOS supports experiments with infrared spectroscopy and nuclear magnetic resonance. Lateral organization demonstrates dependence on lipid composition and bilayer thickness. To further validate the LPP model, umbrella sampling was used to calculate ethanol permeability in comparison with experiment (log(P) values obtained from modeling the SC's multiple LPP layers are -7.6 and -6.6 cm/s, and that from experiment on cadaver skin is -6.65 cm/s). A "leapfrog" mechanism for ethanol permeation is proposed which is associated with its role as a topical enhancer. These models, the first experimentally verified atomistic sandwich models of the LPP, will aid in the design and optimization of transdermal drug delivery.

Neutron reflectivity for soft matter

Specular neutron reflectivity is a technique enabling the measurement of coherent neutron scattering length density profile perpendicular to the plane of a surface or interface, and thereby the profile of chemical composition. The characteristic sizes that are probed range from around 5Å up 5000 Å. It is a scattering technique that averages information over the entire surface and it is therefore not possible to obtain information on correlations in the plane of the interface. The specific properties of neutrons (possibility of tuning the contrast by isotopic substitution, negligible absorption, low energy of the incident neutrons) makes it particularly interesting in the fields of soft matter and biophysics. This course is composed of three parts describing respectively its principle, the experimental aspects (diffractometers, samples), and some scientific examples of neutron reflectometry focusing on the use of contrast variation to probe polymeric systems.

Synthesis of Perdeuterated 1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine ([D82 ]POPC) and Characterisation of Its Lipid Bilayer Membrane Structure by Neutron Reflectometry.

1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), an unsaturated acyl chain containing lipid, is often the predominant lipid in eukaryotic cell membranes in which it is crucial for the fluidity of membranes under physiological conditions. Commercially available, partially deuterated [D31 ]1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine ([D31 ]POPC) does not provide sufficient isotopic contrast for detailed structural studies of multicomponent membranes through neutron techniques. Herein, a relatively straightforward and generic chemical deuteration method is discussed for the asymmetric synthesis of perdeuterated [D31 ]1-palmitoyl-[D33 ]2-oleoyl-sn-[D5 ]glycero-[D13 ]3-phosphocholine ([D82 ]POPC) that also allows selective deuteration of any of its constituent groups. Neutron reflectivity of a [D82 ]POPC-supported bilayer was used to experimentally determine the neutron scattering length density profile of the lipid. The acyl chains of [D82 ]POPC are closely contrast-matched to heavy water, whereas the very high scattering length density of the deuterated glycerophosphocholine head groups provides good contrast to membrane-binding agents in both deuterated and non-deuterated solvent environments.

Volume profile of α-chymotrypsin during adsorption and enzymatic reaction on a poly(acrylic acid) brush.

Poly(acrylic acid) (PAA) brushes are known to provide a native-like environment for proteins. In this study, we explore this biocompatibility under high pressure conditions. Using α-chymotrypsin (α-CT) as a model enzyme, we report on the pressure dependencies of the enzymatic activity and the neutron scattering length density profile, when this enzyme is adsorbed on a PAA brush. From high pressure total internal reflection fluorescence spectroscopy, an increasing enzymatic activity has been observed up to 1000 bar, but a rather pressure independent enzymatic activity at higher pressures up to 2000 bar. This finding suggests a non-constant activation volume of α-CT on the PAA brush that is negative below 1000 bar. Thus, the compact nature of the transition state of α-CT is largely preserved upon adsorption. We have also performed high pressure neutron reflectivity experiments to determine the spatial distribution of α-CT inside the PAA brush. Apparently, the enzyme is strongly binding to the PAA chains with 2.3 mg m(-2) of adsorbed enzyme that is reduced to about 1.7 mg m(-2) at 1000-2000 bar. This change of adsorbed mass is consistent with a positive volume change of adsorption, which is probably reflecting electrostriction upon protein-PAA interaction. Thus, the performed high pressure experiments provide new insights into the volume profile of α-CT during adsorption and enzymatic activity on the PAA brush. They also demonstrate that the biocompatible properties of a PAA brush can even be enhanced by pressure.

Temperature responsive behavior of polymer brush/polyelectrolyte multilayer composites

The complex interaction of polyelectrolyte multilayers (PEMs) physisorbed onto end-grafted polymer brushes with focus on the temperature-responsive behavior of the system is addressed in this work. The investigated brush/multilayer composite consists of a poly(styrene sulfonate)/poly(diallyldimethylammonium chloride) (PSS/PDADMAC) multilayer deposited onto the poly(N-isopropylacrylamide-b-dimethylaminoethyl methacrylate) P(NIPAM-b-DMAEMA) brush. Ellipsometry and neutron reflectometry were used to monitor the brush collapse with the thickness decrease as a function of temperature and the change in the monomer distribution perpendicular to the substrate at temperatures below, across and above the phase transition, respectively. It was found that the adsorption of PEMs onto polymer brushes had a hydrophobization effect on PDMAEMA, inducing the shift of its phase transition to lower temperatures, but without suppressing its temperature-responsiveness. Moreover, the diffusion of the free polyelectrolyte chains inside the charged brush was proved by comparing the neutron scattering length density profile of pure and the corresponding PEM-capped brushes, eased by the enhanced contrast between hydrogenated brushes and deuterated PSS chains. The results presented herein demonstrate the possibility of combining a temperature-responsive brush with polyelectrolyte multilayers without quenching the responsive behavior, even though significant interpolyelectrolyte interactions are present. This is of importance for the design of multicompartment coatings, where the brush can be used as a reservoir for the controlled release of substances and the multilayer on the top as a membrane to control the diffusion in/out by applying different stimuli.

Localization of Cholesterol and Fatty Acid in a Model Lipid Membrane: A Neutron Diffraction Approach

The intercellular lipid matrix of the skin’s stratum corneum serves to protect the body against desiccation and simultaneously limits the passage of drugs and other xenobiotics into the body. The matrix is made up of ceramides, free fatty acids, and cholesterol, which are organized as two coexisting crystalline lamellar phases. In studies reported here, we sought to use the technique of neutron diffraction, together with the device of isotopic (H/D) substitution, to determine the molecular architecture of the lamellar phase having a repeat distance of 53.9 ± 0.3 Å. Using hydrogenous samples as well as samples incorporating perdeuterated (C24:0) fatty acids and selectively deuterated cholesterol, the diffraction data obtained were used to construct neutron scattering length density profiles. By this means, the locations within the unit cell were determined for the cholesterol and fatty acids. The cholesterol headgroup was found to lie slightly inward from the unit cell boundary and the tail of the molecule located 6.2 ± 0.2 Å from the unit cell center. The fatty acid headgroups were located at the unit cell boundary with their acyl chains straddling the unit cell center. Based on these results, a molecular model is proposed for the arrangement of the lipids within the unit cell.

Membrane Organization of Vitamin E is Sensitive to Lipid Unsaturation

Vitamin E (α-tocopherol) has long been known as the major antioxidant in biological membranes. However, there remain many structurally related questions. Details of the molecular organization of α-tocopherol in membranes, for instance, lack the precision to address whether the vitamin has preferential affinity for unsaturated lipids in support of its role as an antioxidant. To observe how α-tocopherol interacts with unsaturated phospholipids, we determine, from one-dimensional neutron scattering length density profiles, the depth of deuterated analogs in phosphatidylcholine (PC) bilayers. The profiles obtained with α-[5-2H3]tocopherol and α-[9′-2H2]tocopherol in 1,2-dioloeylphosphatidylcholine (18:1-18:1PC) bilayers place the centers of mass of the labels 13 and 0 A, respectively, from the bilayer center. They are consistent with the vitamin molecule sitting upright in the bilayer so that the hydroxyl group on the chromanol is near the aqueous interface and a highly disordered sidechain extends towards the middle of the membrane. The profile obtained for α-[5-2H3]tocopherol in 1-palmitoyl-2-oleeylphosphatidylcholine (16:0-18:1PC) reveals that, in contrast, the center of mass of the label sits 10 A higher than in 18:1-18:1PC. A remarkable sensitivity upon membrane unsaturation for the depth of penetration of vitamin E is implied, and we are currently using solid state 2H NMR and MD simulations to provide a detailed view of dynamical organization.

Basic Nanostructure of Stratum Corneum Lipid Matrices Based on Ceramides [EOS] and [AP]: A Neutron Diffraction Study

The goal of this study was to investigate the nanostructure of SC lipid model membranes comprising the most relevant SC lipids such as the unique-structured ω-acylceramide [EOS] in a near natural ratio with neutron diffraction. In models proposed recently the presence of ceramide [EOS] and FFA are necessary for the formation of one of the two existent crystalline lamellar phases of the SC lipids, the long-periodicity phase as well as for the normal barrier function of the SC. The focus of this study was placed on the influence of the FFA BA on the membrane structure and its localization within the membrane based on the ceramides [EOS] and [AP]. The internal nanostructure of such membranes was obtained by Fourier synthesis from the experimental diffraction patterns. The resulting neutron scattering length density profiles showed that the exceptionally long ceramide [EOS] is arranged in a short-periodicity phase created by ceramide [AP] by spanning through the whole bilayer and extending even further into the adjacent bilayer. Specifically deuterated BA allowed us to determine the exact position of this FFA inside this SC lipid model membrane. Furthermore, hydration experiments showed that the presented SC mimic system shows an extremely small intermembrane hydration of ∼1 Å, consequently the headgroups of the neighboring leaflets are positioned close to each other.

Effect of Cations on the Structure of Bilayers Formed by Lipopolysaccharides Isolated from Pseudomonas aeruginosa PAO1

The asymmetric outer membrane of Gram-negative bacteria contains lipopolysaccharides (LPSs) which contribute significantly to the bacterium's surface properties and play a crucial role in regulating membrane permeability. We report on neutron diffraction studies performed on aligned, self-assembled bilayers of Na-, Ca-, and Mg-salt forms of LPS isolated from Pseudomonas aeruginosa PAO1. From the one-dimensional neutron scattering length density profiles we find that water penetrates Ca2+-LPS bilayers to a lesser extent than either Na+- or Mg2+-LPS bilayers. This differential water penetration could have implications as to how small molecules permeate the outer membrane of Gram-negative bacteria and, possibly, how nonlamellar phases are formed.

Arrangement of ceramide [EOS] in a stratum corneum lipid model matrix: new aspects revealed by neutron diffraction studies

The lipid matrix in stratum corneum (SC) plays a key role in the barrier function of the mammalian skin. The major lipids are ceramides (CER), cholesterol (CHOL) and free fatty acids (FFA). Especially the unique-structured omega-acylceramide CER[EOS] is regarded to be essential for skin barrier properties by inducing the formation of a long-periodicity phase of 130 angstroms (LPP). In the present study, the arrangement of CER[EOS], either mixed with CER[AP] and CHOL or with CER[AP], CHOL and palmitic acid (PA), inside a SC lipid model membrane has been studied for the first time by neutron diffraction. For a mixed CER[EOS]/CER[AP]/CHOL membrane in a partly dehydrated state, the internal membrane nanostructure, i.e. the neutron scattering length density profile in the direction normal to the surface, was obtained by Fourier synthesis from the experimental diffraction patterns. The membrane repeat distance is equal to that of the formerly used SC lipid model system composed of CER[AP]/CHOL/PA/ChS. By comparing both the neutron scattering length density profiles, a possible arrangement of synthetic long-chain CER[EOS] molecules inside a SC lipid model matrix is suggested. The analysis of the internal membrane nanostructure implies that one CER[EOS] molecule penetrates from one membrane layer into an adjacent layer. A 130 angstroms periodicity phase could not be observed under experimental conditions, either in CER/CHOL mixtures or in CER/CHOL/FFA mixture. CER[EOS] can be arranged inside a phase with a repeat unit of 45.2 angstroms which is predominately formed by short-chain CER[AP] with distinct polarity.

Localisation of partially deuterated cholesterol in quaternary SC lipid model membranes: a neutron diffraction study

This letter presents our first results in using the benefit of selective deuteration in neutron diffraction studies on stratum corneum (SC) lipid model systems. The SC represents the outermost layer of the mammalian skin and exhibits the main skin barrier. It is essential for studying drug penetration through the SC to know the internal structure and hydration behaviour on the molecular level. The SC intercellular matrix is mainly formed by ceramides (CER), cholesterol (CHOL) and long-chain free fatty acids (FFA). Among them, CHOL is the most abundant individual lipid, but a detailed knowledge about its localisation in the SC lipid matrix is still lacking. The structure of the quaternary SC lipid model membranes composed of either CER[AP]/CHOL-D6/palmitic acid (PA)/cholesterol sulphate (ChS) or CER[AP]/CHOL-D7/PA/ChS is characterized by neutron diffraction. Neutron diffraction patterns from the oriented samples are collected at the V1 diffractometer of the Hahn-Meitner-Institute, Berlin, measured at 32 degrees C, 60% humidity and at different D2O contents. The neutron scattering length density profile in the direction normal to the surface is restored by Fourier synthesis from the experimental diffraction patterns. The analysis of scattering length density profile is a suitable tool for investigating the internal structure of the SC lipid model membranes. The major finding is the experimental proof of the CHOL localisation in SC model membrane by deuterium labelling at prominent positions in the CHOL molecules.

Fatty acid interdigitation in stratum corneum model membranes: a neutron diffraction study

The influence of the chain length of the free fatty acid (FFA) in a stratum corneum (SC) lipid model membrane composed of N-(alpha-hydroxyoctadecanoyl)-phytosphingosine (CER [AP]), cholesterol (Ch), FFA and cholesterol sulphate (ChS) was investigated by neutron diffraction. The internal nanostructure of the SC lipid membrane in addition to the water distribution function was determined via calculation of the neutron scattering length density profile (Fourier profile). The Fourier profiles of the studied SC model membranes revealed that such membranes have a repeat distance approximately equal to the membrane thickness. Increasing the chain length of the FFA in the CER[AP] based model membrane did not cause an alteration of the internal nanostructure but led to a decrease in the membrane repeat distance from 45.6 angstroms (palmitic acid, C16:0) to 43.7 angstroms (cerotic acid, C26:0) due to a partial interdigitation of the FFA chains. Ceramide [AP] forces the long chain fatty acids to incorporate into the unchanged spacing of the bilayer, thereby obligating the FFA protrude partly through opposing leaflet. Furthermore, the longer chained free fatty acids tend to form a new separate so-called "fatty acid rich phase". Therefore, the elongation of the chain length of the FFA decreases the solubility of the FFA in the SC model membrane based on CER[AP].

Determination of graft density of substrate-supported polymer films

Determining the graft density of polymers adsorbed on a substrate from neutron scattering-length density profile can be challenging. A scheme based on integrating a select region of the profile is proposed and applied to results obtained from a recent neutron reflectometry experiment that investigated the physical properties of polyethylene oxide (PEO) chemisorbed onto a gold-coated Si substrate. Reflectivity measurements were performed with the PEO exposed to a H 2O/D 2O mixture contrast matched to the underlying gold. The graft density obtained by the integration technique is 60% higher than the value determined using scaling relations.

Neutron reflectivity studies on the DNA adsorption on lipid monolayers at the air–liquid interface

In situ neutron reflectivity was used to study the DC-Chol and TC-Chol monolayers at the air–liquid interface in the presence and absence of DNA in the subphase. It was found that the DC-Chol is more effective in adsorbing the DNA than the TC-Chol. It was also found that a compact DNA layer formed beneath the DC-Chol monolayer with a DNA gap spacing around 20 Å and a less compact DNA layer adsorbed to the TC-Chol monolayer with a DNA spacing around 60 Å, as estimated from the determined neutron scattering length density. From the determined neutron scattering length density profiles, the adsorbed DNA somewhat penetrates into the head group region of the charged lipids.