Effect Of Molecular Orientation Research Articles

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.

Effect of molecular alignment and orientation on elliptically polarized high-order harmonic generation

Effect of molecular alignment and orientation on elliptically polarized high-order harmonic generation

Exploring long-range fluorine–carbon J-coupling for conformational analysis of deoxyfluorinated disaccharides: A combined computational and NMR study

In this study, we investigated the potential of long-range fluorine–carbon J-coupling for determining the structures of deoxyfluorinated disaccharides. Three disaccharides, previously synthesized as potential galectin inhibitors, exhibited through-space fluorine–carbon J-couplings. In our independent conformational analysis of these disaccharide derivatives, we employed a combination of density functional theory (DFT) calculations and nuclear magnetic resonance (NMR) experiments. By comparing the calculated nuclear shieldings with the experimental carbon chemical shifts, we were able to identify the most probable conformers for each compound. A model comprising fluoromethane and methane molecules was used to study the relationship between molecular arrangements and intermolecular through-space J-coupling. Our study demonstrates the important effect of internuclear distance and molecular orientation on the magnitude of fluorine–carbon coupling. The experimental values for the fluorine–carbon through-space couplings (TSCs) of the disaccharides corresponded with values calculated for the most probable conformers identified by the conformational analysis. These results unlock the broader application of fluorine–carbon TSCs as powerful tools for conformational analysis of flexible molecules, offering valuable insights for future structural investigations.

Molecular dynamics insights into gas-water interfacial tension: Optimizing hydrogen storage in subsurface conditions

This study presents a comprehensive analysis of interfacial tension (IFT) between pore water and hydrogen-cushion gas mixtures in subsurface porous media, a key variable in the distribution of gas mixtures for hydrogen storage. Employing molecular dynamics simulations, we developed two IFT models at 20 MPa and 373 K: one for an H2–CO2–H2O system and another for an H2–CH4–H2O system. The models reveal that increasing cushion gas concentration reduces gas-water IFT. Notably, for H2–CO2–H2O mixtures, the IFT substantially decreases with CO2 concentration up to 40%, after which the reduction rate diminishes. In H2–CH4–H2O mixtures, the IFT decreases linearly with CH4 concentration. The study attributes these variations to local density distributions and molecular orientation effects. Specifically, CO2 adsorption at the interface up to 40% concentration significantly lowers IFT, while CH4 adsorption proportionally decreases IFT. The influence of CO2 on water molecule orientation at the interface, in contrast to the non-effect of CH4, is also critical in enhancing IFT reduction. Our results also highlight the reduction of H2 self-diffusion at the interface caused by CO2 and CH4, an essential factor in optimizing subsurface hydrogen storage operations.

Theory construction and computation for polymer film melt stretching by modified Leonov model

Polymer film melt stretching exhibits a unique stress–strain behavior, featuring a stress plateau followed by a sudden increase with increasing the strain. This phenomenon poses a challenge to conventional melt-extension theories and methods. To address this, we derive a simplified flow theory according to the symmetric characteristics of thin melt-stretching, and propose a modified multi-mode Leonov model (m-Leonov) that accounts for molecular orientation effects, a crucial factor in accurately simulating the process. In order to improve the computational efficiency, an iterative algorithm was developed to decouple the interdependence between governing and constitutive equations. The computational results reveal that the viscoelastic nature of the film contributes to a delay in the transformation of stretching forces, leading to the observed stress plateau. Significantly, our m-Leonov model successfully predicts both the plateau and the subsequent abrupt increase in stress, across various temperatures and stretching rates. These simulations closely agree with experimental data, underlining the robustness of our approach. Our findings would enhance the understanding of rheological complexities in film stretching, offering potential applications in various materials and polymer processing.

3D Prestress Bioprinting of Directed Tissues.

Many mammalian tissues adopt a specific cellular arrangement under stress stimulus that enables their unique function. However, conventional 3D encapsulation often fails to recapitulate the complexities of these arrangements, thus motivating the need for advanced cellular arrangement approaches. Here, an original 3D prestress bioprinting approach of directed tissues under the synergistic effect of static sustained tensile stress and molecular chain orientation, with an aid of slow crosslinking in bioink, is developed. The semi-crosslinking state of the designed bioink exhibits excellent elasticity for applying stress on the cells during the sewing-like process. After bioprinting, the bioink gradually forms complete crosslinking and keeps the applied stress force to induce cell-orientated growth. More importantly, multiple cell types can be arranged directionally by this approach, while the internal stress of the hydrogel filament is also adjustable. In addition, compared with conventional bioprinted skin, the 3D prestress bioprinted skin results in a better wound healing effect due to promoting the angiogenesis of granulation tissue. This study provides a prospective strategy to engineer skeletal muscles, as well as tendons, ligaments, vascular networks, or combinations thereof in the future.

Effects of Molecular Orientation and Relative Phase of Combined Fields on Generation of Isolated Attosecond Pulses Using CO Molecules

Effects of Molecular Orientation and Relative Phase of Combined Fields on Generation of Isolated Attosecond Pulses Using CO Molecules

Effects of molecular size and orientation on the interfacial properties and wetting behavior of water/n-alkane systems: a molecular-dynamics study.

Molecular dynamics simulations (MD) are performed to study the interfacial structure/tension and wetting behavior of water/n-alkane systems (water/nC5 to water/nC16 where nCx = CxH(2x + 2)). In particular, we study complete-to-partial wetting transitions by changing the n-alkane chain length (NC) at a constant temperature, T = 295 K. Simulations are carried out with a united-atom TraPPE model for n-alkanes and the TIP4P-2005 model of water. Simulation results are in excellent agreement with the initial spreading coefficients and contact angles calculated using experimental values of the surface and interfacial tensions. In addition, it has been determined that water/(nC5-nC7) and water/(nC8-nC16), respectively, exhibit complete and partial initial wetting modes. Simulations show that the interfacial structures of water/(nC5-nC7) are different from water/(nC8-nC16) systems. In the latter, water preferentially orients near the interface to increase the number of hydrogen bonds and the charge and mass densities. Moreover, the orientation of n-alkane molecules at water/(nC8-nC16) interfaces has a long-range persistence, resulting in layered structures that increase with NC. In addition, simulation results of the orientational order parameter Sz show alignment behavior of the n-alkane molecules with respect to the interfaces. Simulations predict that the central segments of n-alkane are strongly packed in the interfaces while the end segments (methyl groups) form smaller peaks in the outer edge of the layer. This observation confirms the "horseshoe" or "C-shaped" structure of n-alkane molecules in the water/n-alkane interfaces. At constant temperature, the interface widths of both water and the n-alkanes decrease with increasing n-alkane molecular length. These results suggest that increasing the n-alkane chain length affects the water/n-alkane interfacial properties in a manner similar to that of cooling.

Molecular simulation of the rheological properties and shear thinning principles of supramolecular drilling fluids at different burial depths.

In order to investigate the rheological properties and shear thinning principles of supramolecular drilling fluids, the salt-responsive supramolecular ionomer polymers with different components were designed and the change in shear viscosity of supramolecular polymer drilling fluid system with shear rate was studied using the molecular dynamics simulation method. The result indicated that the ionic supramolecular polymer drilling fluid system exhibits better self-assembly performance than the nonionic acrylamide drilling fluid system. Moreover, the drilling fluid system exhibits the best rheological properties and self-assembly performance when the feeding ratios of the three monomers in the two polymers are m : n : o = 5 : 90 : 5 and m : n : o = 30 : 40 : 30, respectively. The shear viscosity recovery rate of the #3 ionic supramolecular polymer drilling fluid system at different burial depths (1-5 km) is >87%, where the shear viscosity is mainly determined at ambient pressure. The shear thinning phenomenon of the supramolecular polymer drilling fluid system occurs because of the combined effect of the polymer molecular orientation and entanglement structure. When the shear rate is above a critical value, the polymer molecules are oriented along the flow field direction, decreasing the shear viscosity. However, when the shear rate is very high, the entanglement structure of the molecules is opened and the mesh structure of the fluids is disrupted, decreasing the shear viscosity of the drilling fluid.

Effect of molecular axis orientation of 3.6 MeV Si2+ projectiles on the ion-induced secondary electron emission from a carbon foil

We study ion-induced secondary electron emission from solid surfaces. This work focuses on the dependence of the energy distribution of secondary electrons on the orientation of Si-dimers impinging on thin carbon foils. The orientation was determined by the foil-induced Coulomb explosion method. Furthermore, the electron energy was measured with a retarding field analyzer. The correlation between the electron energy distribution and the cluster orientation was obtained through simultaneous measurements. A comparison of the electron energy distribution for parallel and perpendicular orientations indicated that the electron yields at an energy below 20 eV are lower for parallel orientation. This reduction can be explained by the orientation dependence of the energy loss of Si2+ in carbon. It was suggested that the orientation effect is due to the distant collision between the cluster and the target atom, in which low-energy electrons are produced.

Thermal actuation shape memory of ultra-high-molecular-weight polyethylene (UHMWPE) with molecular orientation

• Preparation of shape memory UHMWPE/HDPE samples with molecular orientation. • Cyclic tensile shape memory property of UHMWPE/HDPE samples. • Movement and evolution of chain segments in shape-changing process. Conventional compression-molding method cannot illustrate the effect of molecular orientation on shape memory property. Herein, high-density polyethylene (HDPE) is incorporated into ultra-high-molecular-weight polyethylene (UHMWPE) to prepare samples with molecular orientation by the single screw extrusion and traction machine. Interestingly, the shape recovery rate (R r ) of samples with the same tensile direction as molecular orientation decreases from 66.13% to 60.71% with the traction rate, while the R r of samples with tensile direction perpendicular to molecular orientation exhibits an opposite tendency in cyclic tensile shape memory tests. Meanwhile, the shape fixation rate of these two samples does not change significantly. In addition, the possible mechanism of thermal actuation shape memory of samples with molecular orientation is interpreted.

Effect of molecular orientation on predissociation of NaI molecules

Based on the time-depend quantum wave packet method, a scheme is proposed to investigate the effect of the molecular orientation on the predissociation of NaI molecules. The molecular orientation in the ground state is steered by THz half-cycle pulse. Then the oriented molecule is excited by femtosecond pump pulse. Molecular orientation has a significant effect on the angular distribution of wave packets. The excited wave packet is distributed in a more narrow region with the increase of molecular orientation degree. The angular distribution of dissociated products is essentially consistent with the angular distribution of excited wave packet. The dissociation probability is proportional to the excitation probability of pump pulse, which is related to the molecular orientations. Compared with the result of predissociation without molecular orientation, the maximal dissociation probability can increase by 6.5% in our work. The electric field intensity of the pump pulse also has a significant influence on dissociation probability.

Effect of Molecular Position and Orientation on Adsorbate-Induced Shifts of Plasmon Resonances

Effect of Molecular Position and Orientation on Adsorbate-Induced Shifts of Plasmon Resonances

The Effect of Molecular Orientation in Disperse Red-1 Film on Its Refractive Index

The refractive index of materials is an important physical quantity in the design of various photonic devices. For thin-film based devices, the fabrication method should be compatible with existing processes in microelectronic fabrication and allow for controlling the refractive index. In this research, the material used is a polar Disperse Red 1 (DR1) molecule. The film fabrication was carried out using the physical vapor deposition method which had been equipped with an electric poling installation. The poling of the electric field during the deposition process was applied perpendicular to the substrate. The thickness measurement and the refractive index of the films were carried out using a reflectometer where the light was incident perpendicular to the substrate. The refractive index was determined by the multiple beam interference method. As a result, it was found that the application of an electric field causes a change in the orientation of the molecules, which were initially parallel to the substrate to become perpendicular. Increasing the field strength further reduces the number of molecules parallel to the substrate. This correlates with a decrease in the refractive index of the film.

Hierarchical self-assembled structure and frictional response of phthalocyanine molecules

Solid evidence is needed to demonstrate the effect of molecular orientation and structure on the frictional property of boundary lubricants. In this work, the frictional properties of phthalocyanine self-assembled monolayers (SAMs) with face-on (aromatic cores parallel to the substrate) and edge-on (aromatic cores stand on the substrate) orientations have been compared and the in situ structural variation of edge-on SAMs under frictional shear has been revealed by atomic force microscope (AFM). Face-on oriented SAMs show lower adhesion, lower friction, and stronger wear resistance, compared with edge-on oriented SAMs. Hierarchical structures of edge-on oriented SAMs have been revealed by frictional topography, which are consisted of nanoscale columns, micron-scale stripes, and centimeter-scale monolayer. The column structure deforms under increasing load force, leading to a stepwise friction force curve and a transition among three friction states (ordered friction, collapsed friction, and worn friction). The structural deformation depends on both the order degree and anisotropic stiffness of columns. Columns in phthalocyanine SAMs show a larger stiffness when shearing against molecular plane than shearing along the molecular plane. The presented study on the interfacial structure and frictional mechanism promisingly supports the designing of novel boundary lubricants and their application in engineering.

Viscosity, surface tension, and density of binary mixtures of the liquid organic hydrogen carrier diphenylmethane with benzophenone

The liquid organic hydrogen carrier (LOHC) diphenylmethane may react to benzophenone in the presence of air, especially at elevated temperatures. Therefore, information about the influence of benzophenone added to diphenylmethane on process-relevant thermophysical properties is required. In the present contribution, the liquid viscosity, surface tension, and liquid density of binary mixtures of diphenylmethane with benzophenone are determined between (283 and 573) K using complementary experimental methods. Investigations on the surface tension by the pendant-drop method and surface light scattering indicate molecular orientation effects of benzophenone at the vapor-liquid interface. With increasing benzophenone content, an increase in density, surface tension, and especially viscosity is found. For the latter property, a distinct change in the temperature dependence is observed at the transition from the liquid to the supercooled liquid state. Furthermore, water dissolved in benzophenone causes changes within 15% and 3% relative to the viscosity and surface tension of benzophenone, respectively. • Surface light scattering and conventional methods applied between 283 and 573 K. • Surface tension measurements indicate surface orientation effects of benzophenone. • Larger density, surface tension, and viscosity with increasing benzophenone content. • Big change in temperature dependence of viscosity from liquid to supercooled liquid. • Dissolved water has minor impact on viscosity and surface tension of benzophenone.

Incident Energy Dependence of the Molecular Orientation Effect of MeV \(\text{C}_{2}^{ + }\) Projectiles in Secondary-Ion Emission Processes

Incident Energy Dependence of the Molecular Orientation Effect of MeV \(\text{C}_{2}^{ + }\) Projectiles in Secondary-Ion Emission Processes

Dissociative ionization of the H2 molecule under a strong elliptically polarized laser field: carrier-envelope phase and orientation effect.

A coupled electron-nuclear dynamical study is performed to investigate the sub-cycle dissociation and ionization of the H2 molecule in a strong 750 nm 4.5 fs elliptically polarized laser pulse. A quasi-classical method is employed in which additional momentum-dependent potentials are added to the molecular Hamiltonian to account for the non-classical effects. The effect of molecular orientation with respect to the laser polarization plane on the probabilities of different dynamical channels and proton energy spectra has been examined. We demonstrate the 2D-control of proton anisotropy by manipulating the carrier-envelope phase of the pulse. We demonstrate that the quasi-classical method can capture the carrier-envelope phase effects in the dissociative ionization of the H2 molecule. Our results indicate that the classical models provide an efficient approach to study the mechanistic insights of strong-field molecular dynamics.

The effects of molecular weight and orientation on the membrane permeation and partitioning of polycyclic aromatic hydrocarbons: a computational study.

Membrane permeation and the partitioning of polycyclic aromatic hydrocarbons (PAHs) are crucial aspects affecting their carcinogenicity and mutagenicity. However, a clear understanding of these processes is still rare due to the difficulty of determining the details experimentally. Here, the interactions between PAHs and lipid bilayers were studied by molecular simulations, mainly to check the influence of molecular weight and orientation. The liposome-water partition coefficient (KLW), transmembrane time (τ), and permeability coefficient (P) of the PAHs were calculated by integrating free energy profiles from umbrella sampling. For selected PAHs, the membrane adsorption is a spontaneous process. The preferred location is near the CC bond and the orientation is related to the molecular structure. The P values of all the PAHs are basically the same order of magnitude, which means that the molecular weight contributes little to the process. As for KLW and τ, they show obvious increases with different molecular weights. Unconstrained simulations showed that a flat orientation on the membrane surface would prevent PAHs from being transported through the membrane. Highly hydrophobic driving forces are not always good for the absorption of PAHs, especially the formation of aggregates. In addition, the orientations and energetic barriers of PAHs near the midplane of the lipid bilayer explain the different transitions of high- and low-weight PAHs. This work provides molecular level details relating to the interactions of PAHs with lipid membranes, with significance for understanding the health effects of PAHs.

Attosecond Delays of High-Harmonic Emissions from Hydrogen Isotopes Measured by XUV Interferometer

High-harmonic spectroscopy can access structural and dynamical information on molecular systems encoded in the amplitude and phase of high-harmonic generation (HHG) signals. However, measurement of the harmonic phase is a daunting task. Here, we present a precise measurement of HHG phase difference between two isotopes of molecular hydrogen using the advanced extreme-ultraviolet (XUV) Gouy phase interferometer. The measured phase difference is about 200 mrad, corresponding to ~3 attoseconds ( 1 as = 10 − 18 s ) time delay which is nearly independent of harmonic order. The measurements agree very well with numerical calculations of a four-dimensional time-dependent Schödinger equation. Numerical simulations also reveal the effects of molecular orientation and intramolecular two-center interference on the measured phase difference. This technique opens a new avenue for measuring the phase of harmonic emission for different atoms and molecules. Together with isomeric or isotopic comparisons, it also enables the observation of subtle effects of molecular structures and nuclear motion on electron dynamics in strong laser fields.