Molecular Packing Research Articles

The Dependence of Hydrophobic Interactions on the Shape of Solute Surface.

According to our recent studies on hydrophobicity, this work is aimed at understanding the dependence of hydrophobic interactions on the shape of a solute's surface. It has been observed that dissolved solutes primarily affect the structure of interfacial water, which refers to the top layer of water at the interface between the solute and water. As solutes aggregate in a solution, hydrophobic interactions become closely related to the transition of water molecules from the interfacial region to the bulk water. It is inferred that hydrophobic interactions may depend on the shape of the solute surface. To enhance the strength of hydrophobic interactions, the solutes tend to aggregate, thereby minimizing their surface area-to-volume ratio. This also suggests that hydrophobic interactions may exhibit directional characteristics. Moreover, this phenomenon can be supported by calculated potential mean forces (PMFs) using molecular dynamics (MD) simulations, where different surfaces, such as convex, flat, or concave, are associated with a sphere. Furthermore, this concept can be extended to comprehend the molecular packing parameter, commonly utilized in studying the self-assembly behavior of amphiphilic molecules in aqueous solutions.

Tuning Molecular Packing and Boosting Self-Assembling Properties via Ring Fusion Strategy in Naphthalimide-Based A-D-A Conjugated Systems.

Two fully fused acceptor-donor-acceptor (A-D-A) architecture conjugated derivatives (NPF and NCF) comprising an electron-withdrawing naphthalimide (NMI) and two different electron-donating cores, phenanthrene and carbazole, respectively, were conveniently synthesized by bismuth(III)-catalyzed selective cyclization of vinyl ethers. Compared with their corresponding single bond-linked A-D-A molecules NPS and NCS, both having a moderately twisted aromatic configuration, the ring fusion strategy leads to fully coplanar conjugated skeletons and greatly changes the electronic structures, photophysical properties, self-assembling behaviors, and molecular packing motifs. In particular, the naphthalimide/carbazole derivative NCF exhibits intriguing 2D brickwork packing and significantly enhanced self-assembling properties.

Theoretical calculations and photodegradation of methylene blue for three isostructural transition M2+ compounds expanded by 1,10-phenanthroline and SCN- under hydrothermal in situ reaction

Three isostructural transition M2+ compounds containing SCN- and 1,10-phenantroline (phen), [M(SCN)2(phen)2] (M2+ = Cd2+1, Mn2+2, Zn2+3), were synthesized under hydrothermal conditions. Noteworthily, the SCN- in the compounds were all originated from the in situ reaction of ligand. Although they were only mononuclear structure, they all further self-assemble into interesting supramolecular networks via π···π stacking of aromatic rings. The different interaction contacts of the molecule and the molecular packing strength in the compounds were investigated using Hirshfeld surface. The energy composition of these compounds was studied by energy framework. Meanwhile, the UV visible diffuse reflection of compounds 1–3 was also investigated. The photocatalytic activity toward methylene blue (MB) showed that the highest degradation efficiency reached 92.2 % for 1, 86.3 % for 2 and 93.7 % for 3 at pH = 10, respectively. The photocatalytic stability of compound 1–3 was confirmed by cyclic experiments and PXRD analysis. The possible reaction mechanism was inferred based on the Radical trapping experiments and Mott–Schottky curve. Radical trapping experiments was conducted to determine the active species involved in the catalytic reaction.

FTIR spectroscopy revealed nonplanar conformers, chain order, and packaging density in diOctadecylamine- and octadecylamine-passivated gold nanoparticles

This work reveals that diOctadecylamine (diODA) outperforms its primary amine counterpart ODA in intra- and intermolecular order, forming passivation monolayers on 5 nm small gold nanoparticles. We support this conclusion by meticulously analyzing the differences in the Fourier Transform Infrared (FTIR) spectrum of diODA and ODA molecules in their pure- and coordinated-to-gold-nanoparticle phases. Detailed diODA spectral data are scarce in the literature and are absent for diODA-passivated nanoparticles, whose merits have gone unnoticed. The analysis compares the signatures of defects and all indicators for molecular packing in the ligand. The results align with the High-Resolution Transmission Electron Microscopy (HR-TEM) based analysis. We observe unexpectedly that pure diODA molecules are not prone to form trans-gauche (TG) [CH3-CH2-gauche] end-conformation. At the same time, an intensive absorption structure at the relevant TG position around 760 cm−1 indicates its presence in pure ODA. The spectrum of pure ODA indicates higher energy of the internal kink defects in the vicinity of 1306 cm−1 than pure diODA. In the coordinated phase, both molecules reduce their initial energy. However, the observed better-pronounced red shift of the structures reveals a crystal-like chain arrangement for diODA. Consequently, the HR-TEM images reveal a spontaneous formation of 2D arrangement only for diODA passivated nanoparticles having nearly twice as large gold core separation as the one provided by ODA molecules. The present analysis can be used as a preliminary test in demanding applications where tightly packed coatings of nanoparticles with impenetrable organic passivation are essential.

High Mobility n‐Type Imide‐Based Semiconductor with Unusual Single‐Crystal Packing Structure in Solution‐Processed Thin Film

AbstractSolid‐state molecular arrangement has been recognized as the most important role in the charge transport properties of organic semiconductors. Although highly ordered molecular stacking is achieved in single crystals, maintaining single‐crystal molecular packing in solution‐processed thin films remains a significant challenge. Herein, a new type of n‐type organic semiconductors based on an asymmetric fluoranthene imide unit is reported, whose intermolecular packing and aggregation behavior in the thin film state can be effectively controlled by regulating the cyano substitution sites and alkyl chain types in the imide group. F10 with cyano groups at 4,9‐sites and branched 2‐ethylhexyl chain encouragingly shows a highly ordered single‐crystal‐like molecular packing in solution‐processed thin film after thermal annealing, and thus the resulting organic field‐effect transistors exhibit impressive charge transport performance, with the electron mobility as high as 0.116 cm2 V−1 s−1. This work opens a new avenue for developing high‐performance solution‐processed n‐type semiconductors.

Molecular Packing Topology and Interactions to Decipher Mechanical Compliances in Dicyano-Distyrylbenzene Derivatives.

Flexible optoelectronics is the need of the hour as the market moves toward wearable and conformable devices. Crystalline π-conjugated materials offer high performance as active materials compared to their amorphous counterpart, but they are typically brittle. This poses a significant challenge that needs to be overcome to unfold their potential in optoelectronic devices. Unveiling the molecular packing topology and identifying interaction descriptors that can accommodate strain offers essential guiding principles for developing conjugated materials as active components in flexible optoelectronics. The molecular packing and interaction topology of eight crystal systems of dicyano-distyrylbenzene derivatives are investigated. Face-to-face π-stacks in an inclined orientation relative to the bending surface can accommodate expansion and compression with minimal molecular motion from their equilibrium positions. This configuration exhibits good compliance towards mechanical strain, while a similar structure with a criss-cross arrangement capable of distributing applied strain equally in opposite directions enhances the flexibility. Molecular arrangements that cannot reversibly undergo expansion and compression exhibit brittleness. In the isometric CT crystals, the disproportionate strength of the interactions along the bending plane and orthogonal directions makes these materials sustain a moderate bending strain. These results provide an updated explanation for the elastic bending in semiconducting π-conjugated crystals.

Tuning Molecular Packing, Charge Transport, and Luminescence in Thiophene–Phenylene Co-Oligomer Crystals via Terminal Substituents

Tuning Molecular Packing, Charge Transport, and Luminescence in Thiophene–Phenylene Co-Oligomer Crystals via Terminal Substituents

Hydrophobic and zincophilic organic hierarchical nano-membranes with ordered molecular packing for stable zinc metal anodes

Rechargeable aqueous Zn metal batteries hold significant potentials as one of the next-generation energy-storage devices due to their low cost and high safety. However, the uncontrollable dendrite growth and low efficiency in plating/stripping of Zn anodes hinder the commercial application of aqueous Zn-ion batteries (AZIBs). Herein, inspired by hydrophobic lotus, a multifunctional organic hierarchical nano-membrane serving as an artificial protective layer is constructed through the gas-liquid interface method, using self-assembled organic nanosheets (NOS). The organic nano-membrane exhibits ordered molecular packing, accompanied by uniform distribution of zincophilic carbonyl (CO) groups on the Zn metal surface. These groups function as active sites, homogenizing Zn2+ flux and accelerating Zn2+ deposition. Simultaneously, the hydrophobic membrane isolates active water, thereby restraining side reactions, effectively suppressing corrosion and extremely inhibiting dendrite growth. Consequently, NOS@Zn anode exhibits stable cycling over 2400 h and an average coulombic efficiency (CE) of 99.69 % (600 cycles) at 1 mA cm−2. Furthermore, NOS@Zn||CNT-MnO2 full cell presents remarkable capacity retention, approximately 5 times higher than that of Zn||CNT-MnO2 after 3000 cycles at 2 A g−1. This work develops an innovative organic interface modification material paving the way for dendrite-free Zn metal anodes and advancing the practical application of large-scale Zn-based energy storage systems.

Anomalous Correlation between Thermal Conductivity and Elastic Modulus in Two-Dimensional Hybrid Metal Halide Perovskites.

Device-level implementation of soft materials for energy conversion and thermal management demands a comprehensive understanding of their thermal conductivity and elastic modulus to mitigate thermo-mechanical challenges and ensure long-term stability. Thermal conductivity and elastic modulus are usually positively correlated in soft materials, such as amorphous macromolecules, which poses a challenge to discover materials that are either soft and thermally conductive or hard and thermally insulative. Here, we show anomalous correlations of thermal conductivity and elastic modulus in two-dimensional (2D) hybrid organic-inorganic perovskites (HOIP) by engineering the molecular interactions between organic cations. By replacing conventional alkyl-alkyl and aryl-aryl type organic interactions with mixed alkyl-aryl interactions, we observe an enhancement in elastic modulus with a reduction in thermal conductivity. This anomalous dependence provides a route to engineer thermal conductivity and elastic modulus independently and a guideline to search for better thermal management materials. Further, introducing chirality into the organic cation induces a molecular packing that leads to the same thermal conductivity and elastic modulus regardless of the composition across all half-chiral 2D HOIPs. This finding provides substantial leeway for further investigations in chiral 2D HOIPs to tune optoelectronic properties without compromising thermal and mechanical stability.

NIR-II Fluorescence Sensor Based on Steric Hindrance Regulated Molecular Packing for In Vivo Epilepsy Visualization.

Fluorescence sensing is crucial to studying biological processes and diagnosing diseases, especially in the second near-infrared (NIR-II) window with reduced background signals. However, it's still a great challenge to construct "off-on" sensors when the sensing wavelength extends into the NIR-II region to obtain higher imaging contrast, mainly due to the difficult synthesis of spectral overlapped quencher. Here, we present a new fluorescence quenching strategy, which utilizes steric hindrance quencher (SHQ) to tune the molecular packing state of fluorophores and suppress the emission signal. Density functional theory (DFT) calculations further reveal that large SHQs can competitively pack with fluorophores and prevent their self-aggregation. Based on this quenching mechanism, a novel activatable "off-on" sensing method is achieved via bio-analyte responsive invalidation of SHQ, namely the Steric Hindrance Invalidation geNerated Emission (SHINE) strategy. As a proof of concept, the ClO--sensitive SHQ lead to the bright NIR-II signal release in epileptic mouse hippocampus under the skull and high photon scattering brain tissue, providing the real-time visualization of ClO- generation process in living epileptic mice.

NIR‐II Fluorescence Sensor Based on Steric Hindrance Regulated Molecular Packing for In Vivo Epilepsy Visualization

AbstractFluorescence sensing is crucial to studying biological processes and diagnosing diseases, especially in the second near‐infrared (NIR‐II) window with reduced background signals. However, it's still a great challenge to construct “off‐on” sensors when the sensing wavelength extends into the NIR‐II region to obtain higher imaging contrast, mainly due to the difficult synthesis of spectral overlapped quencher. Here, we present a new fluorescence quenching strategy, which utilizes steric hindrance quencher (SHQ) to tune the molecular packing state of fluorophores and suppress the emission signal. Density functional theory (DFT) calculations further reveal that large SHQs can competitively pack with fluorophores and prevent their self‐aggregation. Based on this quenching mechanism, a novel activatable “off‐on” sensing method is achieved via bio‐analyte responsive invalidation of SHQ, namely the Steric Hindrance Invalidation geNerated Emission (SHINE) strategy. As a proof of concept, the ClO−‐sensitive SHQ lead to the bright NIR‐II signal release in epileptic mouse hippocampus under the skull and high photon scattering brain tissue, providing the real‐time visualization of ClO− generation process in living epileptic mice.

Different lateral packing stress in acyl chains alters KcsA orientation and structure in lipid membranes

The molecular structures of the various intrinsic lipids in membranes regulate lipid-protein interactions. These different lipid structures with unique volumes produce different lipid molecular packing stresses/lateral stresses in lipid membranes. Most studies examining lipid packing effects have used phosphatidylcholine and phosphatidylethanolamine (PE), which are the main phospholipids of eukaryotic cell membranes. In contrast, Gram-negative or Gram-positive bacterial membranes are composed primarily of phosphatidylglycerol (PG) and PE, and the physical and thermodynamic properties of each acyl chain in PG at the molecular level remain unresolved. In this study, we used 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG, 16:0–18:1 PG) and 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (PAPG, 16:0–20:4 PG) to prepare lipid bilayers (liposome) with the rod-type fluorescence probe DPH. We measured the lipid packing conditions by determining the rotational freedom of DPH in POPG or PAPG bilayers. Furthermore, we investigated the effect of different monoacyl chains on a K+ channel (KcsA) structure when embedded in POPG or PAPG membranes. The results revealed that differences in the number of double bonds and carbon chain length in the monoacyl chain at sn-2 affected the physicochemical properties of the membrane and the structure and orientation of KcsA.

Spectrally Resolved Exciton Polarizability for Understanding Charge Generation in Organic Bulk Hetero-Junction Diodes.

Despite decades of research, the dominant charge generation mechanism in organic bulk heterojunction (BHJ) devices is not completely understood. While the local dielectric environments of the photoexcited molecules are important for exciton dissociation, conventional characterizations cannot separately measure the polarizability of electron-donor and electron-acceptor, respectively, in their blends, making it difficult to decipher the spectrally different charge generation efficiencies in organic BHJ devices. Here, by spectrally resolved electroabsorption spectroscopy, we report extraction of the excited state polarizability for individual donors and acceptors in a series of organic blend films. Regardless of the donor and acceptor, we discovered that larger exciton polarizability is linked to larger π-π coherence length and faster charge transfer across the heterojunction, which fundamentally explains the origin of the higher charge generation efficiency near 100% in the BHJ photodiodes. We also show that the molecular packing of the donor and acceptor influence each other, resulting in a synergetic enhancement in the exciton polarizability.

Dual Semi-Interpenetrating Networks of Water-Soluble Macromolecules and Supramolecular Polymer-like Chains: The Role of Component Interactions

Dual networks formed by entangled polymer chains and wormlike surfactant micelles have attracted increasing interest in their application as thickeners in various fields since they combine the advantages of both polymer- and surfactant-based fluids. In particular, such polymer-surfactant mixtures are of great interest as novel hydraulic fracturing fluids with enhanced properties. In this study, we demonstrated the effect of the chemical composition of an uncharged polymer poly(vinyl alcohol) (PVA) and pH on the rheological properties and structure of its mixtures with a cationic surfactant erucyl bis(hydroxyethyl)methylammonium chloride already exploited in fracturing operations. Using a combination of several complementary techniques (rheometry, cryo-transmission electron microscopy, small-angle neutron scattering, and nuclear magnetic resonance spectroscopy), we showed that a small number of residual acetate groups (2–12.7 mol%) in PVA could significantly reduce the viscosity of the mixed system. This result was attributed to the incorporation of acetate groups in the corona of the micellar aggregates, decreasing the molecular packing parameter and thereby inducing the shortening of worm-like micelles. When these groups are removed by hydrolysis at a pH higher than 7, viscosity increases by five orders of magnitude due to the growth of worm-like micelles in length. The findings of this study create pathways for the development of dual semi-interpenetrating polymer-micellar networks, which are highly desired by the petroleum industry.

A Difluoro-Methoxylated Ending-Group Asymmetric Small Molecule Acceptor Lead Efficient Binary Organic Photovoltaic Blend.

Developing a new end group for synthesizing asymmetric small molecule acceptors (SMAs) is crucial for achieving high-performance organic photovoltaics (OPVs). Herein, an asymmetric small molecule acceptor, BTP-BO-4FO, featuring a new difluoro-methoxylated end-group is reported. Compared to its symmetric counterpart L8-BO, BTP-BO-4FO exhibits an upshifted energy level, larger dipole moment, and more sequential crystallinity. By adopting two representative and widely available solvent additives (1-chloronaphthalene (CN) and 1,8-diiodooctane (DIO)), the device based on PM6:BTP-BO-4FO (CN) photovoltaic blend demonstrates a power conversion efficiency (PCE) of 18.62% with an excellent open-circuit voltage (VOC) of 0.933V, which surpasses the optimal result of L8-BO. The PCE of 18.62% realizes the best efficiencies for binary OPVs based on SMAs with asymmetric end groups. A series of investigations reveal that optimized PM6:BTP-BO-4FO film demonstrates similar molecular packing motif and fibrillar phase distribution as PM6:L8-BO (DIO) does, resulting in comparable recombination dynamics, thus, similar fill factor. Besides, it is found PM6:BTP-BO-4FO possesses more efficient charge generation, which yields better VOC-JSC balance. This study provides a new ending group that enables a cutting-edge efficiency in asymmetric SMA-based OPVs, enriching the material library and shed light on further design ideas.

Synthesis, X-ray, Hirshfeld combined with DFT, anticancer effects with molecular docking confirmation of (E)-4-cyanobenzaldehyde oxime and (Z)–N-methyl-C-4-substituted phenyl aldonitrones

(E)-4-cyanobenzaldehyde oxime 1 and (Z)–N-methyl-C-4-substituted phenyl aldonitrones 2 and 3 were synthesised and fully characterised. With the help of Hirshfeld calculations, the molecular packing of 1 is found to be controlled by short N…H contacts (28.3%) in addition to the aromatic π-π stacking where the%C…C interactions is calculated to be 9.7%. In this case, the second most abundant interaction is H…H contact (28.1%). For 2, the N…H (24.4%) and O…H (13.8%) contacts are the most important while the most abundant interaction is H…H contacts (36.0%). DFT calculations were utilised to explore the structural and electronic parameters of both compounds at their optimised geometries which were found in good agreement with the X-ray structures. The structure of 2 (6.9829 Debye) is more polar than 1 (4.5282 Debye). The compounds 1–3 reduced the growth of MCF-7 and T47D. Compound 1 which has the lowest IC50 values against the MCF-7 and T47D cell lines, is thought to be the most promising applicant as an anticancer drug. The in-silico combination of compounds 1–3 with proliferative proteins PIK3 and CDK5, autophagic proteins mTOR and beclin, antiapoptotic proteins BCL2, and apoptotic proteins caspase 3 was examined. Compound 3 binds to PIK3, CDK5, mTOR, Beclin, BCL2 and caspase 3, and displays higher free energy bindings of −5.12, −5.45, −4.923, −5.72, −4.45 and −4.73 kcal/mol, which suggested that these proteins had the strongest inhibitory or enhanced effects. The findings show that compound 3 was the most well-docked chemical with the greatest IC50. Compound 3 impacted the autophagy, apoptotic and mitotic proteins of cell growth.

Tailoring Cyano Substitutions on Quinoxaline‐based Small‐Molecule Acceptors Enabling Enhanced Molecular Packing for High‐Performance Organic Solar Cells

AbstractCyanation is a common chemical modification strategy to fine‐tune the energy levels and molecular packing of organic semiconductors, especially materials used in organic solar cells (OSCs). Generally, cyanation is used to modify the end groups of high‐performance small‐molecule acceptors (SMAs). However, the cyanation strategy has not been investigated on the central backbone of SMAs, which could introduce stronger intermolecular interaction and enhance the π–π stacking for rapid charge transport. This paper, for the first time, reports a new cyanation strategy on the central benzo‐quinoxaline core and synthesizes two novel A‐DA'D‐A type SMAs, named BQx‐CN and BQx‐2CN, with mono‐ and di‐cyanide groups, respectively. Through tailoring the number of CN groups, the BQx‐CN‐based OSC exhibits the best device performance of 18.8%, which is significantly higher than the non‐cyano BQx‐based one. The reason for the superior performance of BQx‐CN‐based devices can be attributed to the fine‐tuned energy level, stronger packing, and ideal phase segregation, which lead to superior exciton dissociation, faster charge transport, and suppressed recombination, therefore the highest fill factor (FF) and power conversion efficiencies (PCE). The research demonstrates the effectiveness of the cyanation strategy on the central core of SMAs for enhanced molecular packing and better performance of OSCs.

On the properties of water in betaine – based Deep Eutectic Solvents

Deep eutectic solvents have gained attention as environmentally friendly alternatives in various technological applications. Likewise, it is known the relevant effect of water on the physicochemical properties of Deep Eutectics, especially for hydrophilic ones. In this study, Betaine – based type III Deep Eutectic solvents (with ethylene glycol, fructose, malic acid or citric acid as Hydrogen Bond Donors) are considered and the properties and structuring of water in Deep Eutectic solutions (content lower than 20 %) were investigated considering volumetric properties, optical properties (refraction index), dynamic properties (viscosity, thermal conductivity, and electrical conductivity) as well as relevant characteristics for liquid phase nature such as polarizability and molecular packing. Viscosity measurements demonstrated a wide variation in viscosities, with water content playing a significant role, thus probing how water content largely affect dynamic properties of Deep Eutectics. Additionally, high water content led to improved thermal and electrical conductivity, particularly in mixtures containing citric acid and malic acid as Hydrogen Bond Donors. The polarizability decreased with increasing water content, and packing calculations indicated that the most voluminous molecules occupied interstitial voids. Our findings contribute to the understanding of water in Deep Eutectics solution, aiding their optimization for sustainable applications.

Synthesis of Perylene Diimide Modified by POSS and its Assembly Behavior in Solution and SBS Matrix

In this work, Perylene diimide derivatives 1,7- POSS-PDI-C12 (PPC) were synthesized using 1,7-Br-PDI- C12, 18-crown-6 ether as phase transfer agent, K2CO3 as catalyst and THF as solvent in a reaction system. Subsequently, the POSS-SH group was successfully introduced into the perylene imide bay site in high yield. The chemical structure and molecular weight of the products were characterized by 1H-NMR, 13C-NMR, MALDI-TOF MS and FT-IR. The self-assembly behavior in different solvents was studied using the research solution self-assembly method. PPC remained in a single monomolecular state due to the bulky POSS group, which introduced large steric hindrance in the molecular packing, leading to the weakening of the π–π interactions. Then, the Composite thin films containing PPC in SBS was prepared. PPC do not exhibit significant force-chromic behavior owing to the dispersion of single- molecule states. This shows that in the construction of mechanochromic materials, chromophore molecules need to have a certain degree of aggregation in the matrix, but the aggregation degree should not be too high.

Side‐chain symmetry‐breaking strategy on porphyrin donors enables high‐efficiency binary all‐small‐molecule organic solar cells

AbstractSide‐chain symmetry‐breaking strategy plays an important role in developing photovoltaic materials for high‐efficiency all‐small‐molecule organic solar cells (ASM OSCs). However, the power conversion efficiencies (PCEs) of ASM OSCs still lag behind their polymer‐based counterparts, which can be attributed to the difficulties in achieving favorable morphology. Herein, two asymmetric porphyrin‐based donors named DAPor‐DPP and DDPor‐DPP were synthesized, presenting stronger intermolecular interaction and closer molecular stacking compared to the symmetric ZnP‐TEH. The DAPor‐DPP:6TIC blend afforded a favorable morphology with nanoscale phase separation and more ordered molecular packing, thus achieving more efficient charge transportation and suppressed charge recombination. Consequently, the DAPor‐DPP:6TIC‐based device exhibited superior photovoltaic parameters, yielding a champion PCE of 16.62% higher than that of the DDPor‐DPP‐based device (14.96%). To our knowledge, 16.62% can be ranked as one of the highest PCE values among the binary ASM OSC filed. This work provides a prospective approach to address the challenge of ASM OSCs in improving film morphology and further achieving high efficiency via side‐chain symmetry‐breaking strategy, exhibiting great potential in constructing efficient ASM OSCs.