Molecular Orientation Research Articles

Bayesian electron density determination from sparse and noisy single-molecule X-ray scattering images.

Single molecule x-ray scattering experiments using free-electron lasers hold the potential to resolve biomolecular structures and structural ensembles. However, molecular electron density determination has so far not been achieved because of low photon counts, high noise levels, and low hit rates. Most approaches therefore focus on large specimen like entire viruses, which scatter sufficiently many photons to allow orientation determination of each image. Small specimens like proteins, however, scatter too few photons for the molecular orientations to be determined. Here, we present a rigorous Bayesian approach to overcome these limitations, additionally taking into account intensity fluctuations, beam polarization, irregular detector shapes, incoherent scattering, and background scattering. We demonstrate using synthetic scattering images that electron density determination of small proteins is possible in this extreme high noise Poisson regime. Tests on published virus data achieved the detector-limited resolution of 9 nm, using only 0.01% of the available photons per image.

Configurational Isomerization‐Induced Orientation Switching: Non‐Fused Ring Dipodal Phosphonic Acids as Hole‐Extraction Layers for Efficient Organic Solar Cells

AbstractPhosphonic acid (PA) self‐assembled molecules have recently emerged as efficient hole‐extraction layers (HELs) for organic solar cells (OSCs). However, the structural effects of PAs on their self‐assembly behaviors on indium tin oxide (ITO) and thus photovoltaic performance remain obscure. Herein, we present a novel class of PAs, namely “non‐fused ring dipodal phosphonic acids” (NFR‐DPAs), featuring simple and malleable non‐fused ring backbones and dipodal phosphonic acid anchoring groups. The efficacy of configurational isomerism in modulating the photoelectronic properties and switching molecular orientation of PAs atop electrodes results in distinct substrate surface energy and electronic characteristics. The NFR‐DPA with linear (C2h symmetry) and brominated backbone exhibits favorable face‐on orientation and enhanced work function modification capability compared to its angular (C2v symmetry) and non‐brominated counterparts. This makes it versatile HELs in mitigating interfacial resistance for energy barrier‐free hole collection, and affording optimal active layer morphology, which results in an impressive efficiency of 19.11 % with a low voltage loss of 0.52 V for binary OSC devices and an excellent efficiency of 19.66 % for ternary OSC devices. This study presents a new dimension to design PA‐based HELs for high‐performance OSCs.

Extracting the Heterogeneous 3D Structure of Molecular Films Using Higher Dimensional SFG Microscopy.

Ultrathin molecular films are widespread in both natural and industrial settings, where details of the molecular structure such as density, out-of-plane tilt angles, and in-plane directionality determine their physicochemical properties. Many of these films possess important molecular-to-macroscopic heterogeneity in these structural parameters, which have traditionally been difficult to characterize. Here, we show how extending sum-frequency generation (SFG) microscopy measurements to higher dimensionality by azimuthal-scanning can extract the spatial variation in the three-dimensional molecular structure at an interface. We extend the commonly applied theoretical assumptions used to analyze SFG signals to the study of systems possessing in-plane anisotropy. This theoretical framework is then applied to a phase-separated mixed lipid monolayer to investigate the variation in molecular density and 3D orientation across the chirally packed lipid domains. The results show little variation in out-of-plane structure but a distinct micron-scale region at the domain boundaries with a reduction in both density and in-plane ordering.

Insights into the phase behavior at interfaces using vibrational sum frequency generation spectroscopy.

Phase separation is ubiquitous at the interface between two distinct phases. Physical transformation during phase separation often plays a crucial role in many important mechanisms, such as lipid phase separation, which is fundamental for transport through biological membranes. Phase separation can be complex, involving changes in the physical state and the reorganization of molecular structures, influencing the behavior and function of materials and biological systems. Surface-sensitive vibrational sum frequency generation (VSFG) spectroscopy provides a powerful tool for investigating these interfacial processes. As a non-linear optical technique, VSFG spectroscopy is sensitive to changes in molecular orientation and interactions at interfaces, making it an ideal method for studying phase separation processes. Here, we review the molecular interaction mechanisms underlying phase separation. We also explore the application of VSFG spectroscopy in studying phase separation processes at different interfaces. In particular, we focus on oil-water interfaces, which are relevant in environmental and industrial contexts; polymer and lipid surfaces, important for materials science and biological membranes; and intrinsically disordered protein systems, which play key roles in cellular function and disease.

Theoretical predictions of CO2, H2 and H2O adsorption mechanisms on M2C-MXene: Selectivity and potential application insights

M2C-MXenes, owing to their abundant adsorption sites, exhibit significant potential in CO2 capture, utilization, and storage (CCUS) and hydrogen energy applications, contributing to hydrogen utilization and global carbon reduction, and thus solving intractable energy and environmental problems. However, the extensive variety of M2C compounds poses challenges to the systematic evaluation of their applications in these fields. The exploration of the adsorption properties of M2Cs is a key fundamental aspect of these studies, and therefore, this study employs calculations across 456 adsorption systems to elucidate the adsorption mechanisms of 19 M2C compounds for small molecules (CO2, H2 and H2O). The results indicate that these M2C materials possess structural stability and metallic characteristics, with periodic variations in the d-band center aligning with trends in CO2 adsorption energy. Notably, molecular orientation impacts adsorption energy more significantly than adsorption sites, particularly for CO2, while M2C compounds primarily exhibit physical adsorption towards H2. Specifically, Sc2C preferentially adsorbs CO2 in atmospheric conditions, and shows chemical adsorption towards H2O, but exhibits negligible adsorption for H2; conversely, Cr2C demonstrates higher adsorption potential for H2. Both materials exhibit favorable thermodynamic stability, suggesting Sc2C is suitable for CCUS applications, while Cr2C holds promising prospects for hydrogen storage.

Chlorophyll Films for Radiation Dosimetry: A Feasibility Study

Abstract Novel Chlorophyll-PVA composite films have been prepared and tested for the dosimetry of therapeutic radiation. The radiation response has been quantified using UV-Vis spectroscopy. FTIR and XRD spectroscopies have been used to characterize the physical properties and irradiation response of the films. The films have shown response towards the therapeutic x-rays beams of 6 MV nominal energy in the tested dose range of 0.25 Gy to 32 Gy in discrete dose levels occurring in the geometric progression series of 2. The dosimeter has been found to exhibit sensitivity at a low dose of 0.25 Gy. The dose response curve of the dosimeter exhibits an exponential relationship of the absorbance and absorbed dose. A region of saturated absorbance has been observed beyond 4 Gy. The peak intensities of the FTIR spectra have been found to decrease with increasing doses as compared to the unirradiated samples, because of the changes in the bond polarities and molecular geometries. The XRD spectra indicates a change in the molecular orientation resulting in a decrease in peak intensity with increasing dose. This study indicates the feasibility of chl-PVA films in the dosimetry of therapeutic radiation. This film dosimeter can be processed locally with minimum resources and standardized against a known standard before clinical use. The chlorophyll molecules need careful handling owing to their sensitivity to light and temperature.

Microscopic view on the polarization-resolved S-SHG intensity of the vapor/liquid interface of pure water.

Second harmonic generation (SHG) is a nonlinear optical phenomenon where two photons at the frequency ω combine to form a single photon at the second-harmonic frequency 2ω. Since that second-order process is very weak in bulk isotropic media, optical SHG responses of interfaces provide a powerful and versatile technique to probe the molecular structure and dynamics of liquid interfaces. Both local dipole contributions and non-local quadrupole contributions can be interesting to investigate different properties of the interface, such as the molecular orientation or the charge density. However, a major difficulty is to comprehend the link between the S-SHG intensity and molecular details. This article reports a numerical approach to model the polarization-resolved SHG intensities of a model vapor/liquid interface of pure water. The influence of the interfacial local environment on the hyperpolarizability is taken into account using quantum mechanical/molecular mechanics calculations. The numerical predictions are in very good agreement with experiments. We detail the hypotheses made during the modeling steps and discuss the impact of various factors on the modeled SHG intensities, including the description of the exciting field in the interfacial layer, the effect of neighboring molecules on the second-harmonic polarization, and the presence of an additional static electric field at the interface.

Silk fibroin-based bioelectronic devices for high-sensitivity, stable, and prolonged in vivo recording

Silk fibroin, recognized for its biocompatibility and modifiable properties, has significant potential in bioelectronics. Traditional silk bioelectronic devices, however, face rapid functional losses in aqueous or in vivo environments due to high water absorption of silk fibroin, which leads to expansion, structural damage, and conductive failure. In this study, we developed a novel approach by creating oriented crystallization (OC) silk fibroin through physical modification of the silk protein. This advancement enabled the fabrication of electronic interfaces for chronic biopotential recording. A pre-stretching treatment of the silk membrane allowed for tunable molecular orientation and crystallization, markedly enhancing its aqueous stability, biocompatibility, and electronic shielding capabilities. The OC devices demonstrated robust performance in sensitive detection and motion tracking of cutaneous electrical signals, long-term (over seven days) electromyographic signal acquisition in live mice with high signal-to-noise ratio (SNR >20), and accurate detection of high-frequency oscillations (HFO) in epileptic models (200–500 Hz). This work not only improves the structural and functional integrity of silk fibroin but also extends its application in durable bioelectronics and interfaces suited for long-term physiological environments.

Formation of positionally ordered but orientationally disordered molecular organization on surface

Positionally ordered but orientationally disordered molecular structures are commonly found in materials like liquid crystals and molecular glasses. Understanding these structures and their phase transitions helps in designing materials with a wide range of applications. Herein, we report the formation of positionally ordered but orientationally disordered structures via adsorption and organization of 2,4,6-tri([1,1'-biphenyl]-2-yl)-1,3,5-triazine (TBTA) molecules on different coin metal surfaces. It is found that deposition of TBTA molecules on Au(111), Ag(111), and Cu(111) surfaces leads to similar hexagonal lattices, differing in molecular orientation. The molecules have two orientations on Au(111) and Ag(111) surfaces, giving birth to positionally ordered but orientationally disordered molecular structures. The regularity of the structures on Ag(111) is slightly better than that on Au(111). On Cu(111) surface, however, all molecules exhibit the same orientation, resulting in a long-range ordered hexagonal assembly. The density functional theory calculations demonstrate that the matching between the substrate lattice and the hexagonal lattice of molecular structure is responsible for the different molecular organizations.

Analytical Evaluation of Ground State Gradients in Quantum Electrodynamics Coupled Cluster Theory.

Analytical gradients of potential energy surfaces play a central role in quantum chemistry, allowing for molecular geometry optimizations and molecular dynamics simulations. In strong coupling conditions, potential energy surfaces can account for strong interactions between matter and the quantized electromagnetic field. In this paper, we derive expressions for the ground state analytical gradients in quantum electrodynamics coupled cluster theory. We also present a Cholesky-based implementation for the coupled cluster singles and doubles model. We report timings to show the performance of the implementation and present optimized geometries to highlight cavity-induced molecular orientation effects in strong coupling conditions.

Climbing Plant‐Inspired Multi‐Responsive Biomimetic Actuator with Transitioning Complex Surfaces

AbstractBionic robots have great potential in healthcare, rescue, and surveillance. However, most soft actuators can only realize one or two deformation modes, which largely limit the application in complex environments. This study develops electric/Infrared (IR) light/magnetic multi‐field coupling soft actuators by combining liquid crystal elastomers (LCE), liquid metal (LM) and magnetic Ecoflex (Mecoflex). Originated from the synergistic effect of the differed thermal expansion and the liquid crystal phase transition, the actuator can realize outstanding large deformations (bending angle > 300°) at ultra‐low voltages (1.0 V). In addition, by designing the molecular orientation in the LCE layer and programming the magnetization in the Mecoflex layer, the bending or helical bending deformations can be controlled under electric/magnetic and IR light/magnetic coupling actuation. Based on the complex deformation capability, bionic climbing plants and two kinds of quadrupedal robots are developed. With the structural design of the quadrupedal robots, they can flexibly switch deformations to pass through complex environments by controlling the externally applied coupling fields, which demonstrates their broad potential in practical applications.

Structure, orientation, and dynamics of per- and polyfluoroalkyl substance (PFAS) surfactants at the air-water interface: Molecular-level insights

HypothesisUnderstanding the intricate molecular-level details of toxic per- and polyfluoroalkyl substances (PFAS) partitioning to the air–water interface holds paramount importance in evaluating their fate and transport, as well as for finding safer alternatives for various applications, including aqueous film forming foams. The behavior of these substances at interfaces strongly depends on molecular architecture, chemistry, and concentration, which define molecular packing, self-assembly, interfacial diffusion, and the surface tension. SimulationsModeling of three PFAS surfactants, namely, longer-tail (perfluorooctanoate (PFOA)) and shorter-tail (perfluorobutanoate (PFBA) and 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy) propanoate (GenX)) has been conducted using atomistic molecular dynamics simulations. A systematic comparison between these representative PFAS of different sizes and structure reveals factors influencing their association behavior, mechanism of surface tension reduction, and interfacial mobility as a function of surface coverage. FindingsShorter-chain PFAS surfactants (GenX or PFBA) require lower surface coverage compared to longer chain (PFOA) PFAS to achieve the same decrease in surface tension. However, a higher concentration of GenX and PFBA is necessary in the bulk aqueous solution to achieve the same surface coverage as PFOA, due to their higher solubility in water. The PFAS molecular orientation and mobility at the interface are found to be vastly influenced by the length and architecture of the hydrophobic fluorocarbon tail. A significant ordering of the water dipole moment near the anionic headgroup is apparent at high surface concentration. A direct correlation is established between the PFAS interfacial properties and PFAS-PFAS, PFAS-counterion, and PFAS-water interactions.

Quercetin: Potential antidiabetic effects through enzyme inhibition and starch digestibility

AbstractDiabetes mellitus involves high blood sugar levels due to insufficient insulin action. Furthermore, enzymes such as α‐amylase and α‐glucosidase break down carbohydrates into glucose, leading to postprandial hyperglycemia. Flavonoids, particularly quercetin, inhibit these enzymes, slowing carbohydrate digestion and reducing glucose absorption. Quercetin has significant hypoglycemic effects with inhibitory concentration (IC50) values comparable to acarbose, a standard inhibitor, suggesting its potential as a natural alternative for diabetes management. In silico models, including molecular docking, molecular dynamics (MD) simulations, and quantitative structure‐activity relationship (QSAR) approaches, help researchers understand the molecular interactions of therapeutic agents. These techniques identify potential inhibitors, determine enzyme‐inhibitor structures, and calculate binding energies, correlating findings with in vitro or in vivo data. Molecular docking predicts molecular orientations, MD simulations offer insights into enzyme–inhibitor dynamics, and QSAR models predict inhibitory potential based on structural properties. Studies have shown that quercetin effectively inhibits α‐glucosidase and α‐amylase by forming hydrogen bonds with specific amino acid residues. Quercetin interacts with starches and reduces their digestibility, increases the formation of resistant starch, lowers the glycemic index, and inhibits digestive enzymes. Studies show that the effects of quercetin on starch digestion vary with concentration and type of starch, and its incorporation into foods such as bakery products, pasta, etc. can significantly decrease starch hydrolysis. The incorporation of quercetin into starch matrices may aid in the development of functional foods aimed at improving glycemic control.

A Novel Upside-Down Thermal Annealing Method Toward High-Quality Active Layers Enables Organic Solar Cells with Efficiency Approaching 20.

The emerging non-fullerene acceptors with low voltage losses have pushed the power conversion efficiency of organic solar cells (OSCs) to ≈20% with auxiliary morphology optimization. Thermal annealing (TA), as the most widely adopted post-treatment method, has been playing an essential role in realizing the potential of various material systems. However, the procedure of TA, i.e., the way that TA is performed, is almost identical among thousands of OSC papers since ≈30 years ago other than changes in temperature and annealing time. Herein, a reverse thermal annealing (RTA) technique is developed, which can enhance the dielectric constant of active layer film, thereby producing a smaller Coulomb capture radius (14.93 nm), meanwhile, forming a moderate nano-scale phase aggregation and a more favorable face-on molecular stacking orientation. Thus, this method can reduce the decline in open circuit voltage of the conventional TA method by achieving decreased radiative (0.334 eV) and non-radiative (0.215 eV) recombination loss. The power conversion efficiency of the RTA PM6:L8-BO-X device increases to 19.91% (certified 19.42%) compared to the TA device (18.98%). It is shown that this method exhibits a superb universality in 4 other material systems, revealing its dramatic potential to be employed in a wide range of OSCs.

Uniaxial Molecular Alignment in Thin Films Composed of Discrete NDI‐T2 Oligomers Investigated by Variable‐Angle Spectroscopic and Imaging Ellipsometry

The understanding of the optical characteristics and the influence of thermally induced crystallization is vital to evaluate newly synthesized organic semiconductors for their potential applications. Variable‐angle spectroscopic ellipsometry (VASE) is employed to determine the complex dielectric function of two recently developed discrete oligomers based on naphthalene diimide (NDI) and bithiophene (T2), applying an anisotropic optical model. It is shown that the as‐cast films are optically near‐isotropic, while the annealed films exhibit pronounced anisotropies with respect to the orientation of the π−π* transition. Differences between the two distinct molecules are observed and discussed. The degree of optical anisotropy is quantified using the average molecular orientation angle φ, associated with the orientation of the π−π* transition dipole, and the related orientation order parameter S. The molecules are shown to form crystallites of several microns in size upon annealing. Imaging ellipsometry is thus additionally employed to study their optical anisotropy on a microscopic scale, and the agreement with results from macroscopic measurements is evaluated.

A molecular dynamics simulation study of EthylChlorophyllide A molecules confined in a SiO2 nanoslit.

This paper investigates the dynamic behavior of EthylChlorophyllide A (EChlideA) molecules in a methanol solution confined within a 4nm silica nanoslit, using molecular dynamics simulations over a duration of 1ms. Three systems, containing 1, 2, and 4 solutes, were studied at 298K. The results demonstrate that EChlideA molecules predominantly adsorb onto the silica surfaces, driven by specific interactions between chlorin ring's methyl group and the hydroxyl groups of the silica. This adsorption leads to stable binding, particularly in less crowded environments, as indicated by the potential of mean force analysis. Higher molecular concentrations, such as those with four EChlideA molecules, introduce variation in binding strength due to molecular aggregation and complex interactions. The orientation analysis reveals that the chlorin ring tends to align parallel to the surface, requiring rotational adjustments during surface diffusion. In addition, solvent coordination around the Mg ion remains consistent under bulk conditions, although with some variation in higher concentrations. This study also highlights a decrease in linear diffusion and an increase in rotational relaxation times for EChlideA molecules within the confined nanoslit, reflecting the influence of molecular concentration and arrangement on their dynamics. These findings provide valuable insights into the role of surface interactions, molecular orientation, and solvent coordination in confined environments, offering implications for the design of nanoscale systems.

Enhancing the Mechanical Properties of Regenerated Cellulose through High-Temperature Pre-Gelation

This paper investigates the effects of pre-gelation on cellulose dissolved in LiCl/DMAc solutions to enhance the properties of regenerated cellulose materials. This study focuses on characterizing the crystallinity, molecular orientation, and mechanical performance of cellulose fibers and hydrogels prepared with and without pre-gelation treatment. X-ray diffraction (XRD) analysis reveals that crystallinity improvement from 55% in untreated fibers to 59% in fibers pre-gelled for 3 and 7 days, indicating a more ordered arrangement of cellulose chains post-regeneration. Additionally, XRD patterns show improved chain alignment in pre-gelled fibers, as indicated by reduced full width at half the maximum of Azimuthal scans. Mechanical testing demonstrates a 30% increase in tensile strength and a doubling of the compression modulus for pre-gelled fibers compared to untreated fibers. These findings underscore the role of pre-gelation in optimizing cellulose material properties for applications ranging from advanced textiles to biomaterials and sustainable packaging. Future research directions include further exploration of the structural and functional benefits of pre-gelation in cellulose processing and its broader implications in material science and engineering.

Nanoscale Chemical Imaging of Amyloid Fibrils in Water Using Total-Internal-Reflection Tip-Enhanced Raman Spectroscopy.

Total-internal-reflection tip-enhanced Raman spectroscopy (TIR-TERS) imaging of amyloid-β (Aβ1-42-L34T) fibrils is performed with nanoscale spatial resolution in water, using TERS tips fabricated by bipolar electrodeposition. Ideal experimental parameters are corroborated by both theoretical simulations and TIR-TERS measurements. TIR-TERS imaging reveals the predominant parallel β-sheet secondary structure of Aβ1-42-L34T fibrils as well as the nanoscale spatial distribution of tyrosine, histidine, and phenylalanine aromatic amino acids. Their proportion in TERS spectra can be qualitatively explained by the combined effect of their localization in the Aβ1-42-L34T fibril structure and their molecular orientation with respect to the excitation laser light polarization. Conclusions drawn from the TERS experiments in water corroborate and significantly enrich our previous study in ambient air, thus confirming that hydration has only a marginal impact on the structure of such amyloid fibrils. This first TIR-TERS study in liquid opens fascinating perspectives for future applications in biology.

Effect of charge inversion on the electrokinetic transport of nanoconfined multivalent ionic solutions

Understanding the effects of phenomena occurring at electrically charged interfaces, such as charge inversion (CI), is crucial for enabling electroosmosis as an efficient transport mechanism in nanodevices. Here, we employ molecular dynamics (MD) simulations to systematically analyze the effect of CI on the electrokinetic transport of multivalent ionic solutions confined in amorphous silica nanochannels. We employ mixtures of monovalent and multivalent counterions while fixing the total ionic concentration to establish correlations between observed phenomena and the amount of multivalent ionic species in the electrolyte solution. The results show that the development of CI is related to a decrease in the mobility of the fluid layers adjacent to the charged surface. In addition, we observe that interfacial overcharging disrupts the water molecular orientation in the fluid layers adjacent to the channel walls. From the non-equilibrium MD simulations of electro-osmotic flow, we disclose the influence of phenomena related to the presence of CI. In particular, flow reversal occurs in scenarios involving CI due to increased local viscosity and a higher concentration of coions within the hydrodynamically mobile and electrokinetically active region of the charged interface. We also find that the magnitude of the wall zeta (ζ) potential displays a monotonic increase with the development of CI in the system. Moreover, we explain why positioning the wall ζ potential at an imaginary (slip) plane, which separates the hydrodynamically mobile and immobile fluid, is misleading.

Investigation of the double layer structure of 1-butyl-3-methylimidazolium thiocyanate at the air-water interface using sum-frequency generation vibrational spectroscopy.

The interfacial structure and adsorption behavior of 1-butyl-3-methylimidazolium thiocyanate ionic liquids (ILs) aqueous solutions were investigated using sum-frequency generation vibrational spectroscopy (SFG-VS) and surface tension measurements. Polarization-dependent measurements revealed a dramatic increase in the SFG signal for both CH and CN stretching modes with increasing ILs concentration, reaching a maximum at a mole fraction of 0.01. This concentration dependence was accompanied by a dramatic drop in surface tension. Upon further increasing the concentration, surface tension varied slightly and reached a constant value, while the SFG signal decreased significantly. Quantitative polarization analysis showed that as the bulk concentration increased, the apparent molecular orientation of the SCN- transition dipole at the interface changed from 51° to 46°, and the tilt angle of CH3 group of the butyl chain attached to the imidazole cationic ring changed from 18° to 32°. The decrease in the SFG signal can be explained by the formation of a double layer adsorption structure at the air/water interface. It was also demonstrated that the anions were adsorbed at the interface simultaneously with the cationic group, rather than by successive adsorption as proposed in a previous study. Using the Shereshefsky model, the thermodynamic Gibbs free energy of adsorption deduced from surface tension data was compared with SFG results.