Constituent Molecules Research Articles

Impact of Storage Conditions on the Quality of Raw Camel Milk.

The preservation and transportation of raw camel milk are essential for the maintenance of its molecular biological activity. Prolonged storage periods and improper storage temperatures can diminish both the nutritional value and biological functionality of its constituent molecules. This study examines the effects of storage conditions on commercially sourced Bactrian camel milk from Delingha City, Qinghai Province, China. Results indicate that the levels of protein, amino acids, fats, and fatty acids in camel milk stored in a 4°C milk tanker truck decrease progressively over a period of 0 to 7 days. Microbial analysis indicates a shift in microbial composition over time, characterized by a notable rise in Psychrobacter and a marked decline in Kocuria. These alterations in microbial populations result in the degradation of various components. Drawing on previous research, this study underscores the unsuitability of transporting camel milk over long distances in 4°C milk tankers to preserve the quality and nutritional integrity of the product.

Effect of alkyl chain length on the dielectric and electro-optical properties of graphene quantum dots doped cyanobiphenyl based nematic liquid crystals composites

The effects of alkyl chain length and doping of biocompatible/eco-friendly graphene quantum dots (GQDs) at 0.5 wt% on the dielectric and electro-optical properties of cyanobiphenyl (nCB, n = 5, 7) nematic liquid crystals (NLCs) are investigated using optical polarising microscope, electro-optical and dielectric spectroscopic techniques. Our results revealed that GQDs modulated the dielectric and electro-optical properties of nCB. Optical textural studies confirmed the uniform dispersion of GQDs in both NLCs (5CB and 7CB). The threshold voltage evaluated from voltage-dependent optical transmission was found to decrease by 16 % and 6 % in GQDs-5CB and GQDs-7CB composites compared to pure NLCs, respectively. The increment in birefringence by 2 % and 1.3 % and order parameter by 4 % and 0.6 % in GQDs composites with 5CB and 7CB, respectively was observed. Both transverse and longitudinal components of the dielectric permittivity (εˈ⊥ and εˈ∥) showed positive increments of 12 % and 5.4 % in GQDs-5CB composite as compared to pure 5CB. However, the increment was found to be 8.9 % and 4.1 % in GQDs-7CB composite. The GQDs-7CB composite exhibited fewer noticeable changes due to the stronger interaction between the molecules, as compared to GQDs-5CB composite. Our results showed that dispersion of GQDs and the number of carbon atoms ‘n’ in the alkyl chain of CB’s constituent molecules affects their properties, such as display parameters and mesophase stability of 5CB and 7CB homologues. Such GQDs-NLCs composites would be certainly useful in the tunable electrical and electro-optical devices.

Covalent Bonds versus van der Waals Forces: A Picture in Thermal Conduction of Organic Materials.

We present a direct comparison of the heat transport properties between the state in which the constituent molecules are assembled by intermolecular forces and the one in which they are covalently bonded, in a molecular system with identical constituent elements and masses, as well as a nearly identical structure and density. This comparison leading to an essential understanding of thermal conduction in organic materials is made possible by the unique compound found by Wudl et al., which exhibits a single-crystal-to-single-crystal topochemical polymerization with a yield of >99%, in combination with microtemperature wave analysis (μTWA), which allows accurate measurements of the thermal diffusivity of small single crystals. At room temperature, the thermal conductivity of monomer and polymer single crystals is not significantly different. For both crystals, the thermal conductivity increases monotonically with decreasing temperature. However, below the Debye temperature, the thermal conductivity of the polymer single crystal increases exponentially, giving much larger values than those of the monomer single crystal. Based on physical quantities related to the behavior of phonons, derived from the specific heat analysis, we discuss the differences in heat transport properties in the two states and provide guidelines for achieving high thermal conductivity in organic materials.

Electrochemical Reduction of Nitrogen to Ammonia Using Zinc Telluride.

Electrosynthesis of ammonia (NH3), an important constituent molecule of various commercial fertilizers, is a promising and sustainable alternative strategy compared with the century-old Haber-Bosch process. Herein, zinc telluride (ZnTe) is demonstrated as an efficient electrocatalyst for reducing nitrogen (N2) under ambient conditions to NH3. In this simple chemical strategy, Zn preferentially binds N2 over hydrogen (H2), and Te, by virtue of its superior electronic properties, enhances the electrocatalytic activity of ZnTe. The analysis of the X-ray diffraction data using the Bravais-Friedel-Donnay-Harker (BFDH) theory predicted a crystal geometry with the active electrocatalytic sites predominantly confined to the (111) planes of ZnTe. The preferential binding of nitrogen (N2; adsorption energy = -0.043 eV) over hydrogen (H2, adsorption energy = -0.028 eV) to Zn on the (111) plane of ZnTe is further confirmed by density functional theory. The ZnTe catalyst is observed to be stable in the acidic medium and delivers a very high yield of NH3 (19.85 μg/h-1 mgcat -1) and a Faradaic efficiency of 6.24% at -0.6 V (versus RHE). Additional verification experiments do not reveal the formation of side products (such as NH2-NH2) during N2 reduction by ZnTe. Further, density functional theory calculations strongly predict that the electrocatalytic reduction of N2 to NH3 by ZnTe preferentially occurs via the alternate pathway.

Proton Conduction in Chiral Molecular Assemblies of Azolium-Camphorsulfonate Salts.

Chiral molecular assemblies have attracted considerable attention because of their interesting physical properties, such as spin-selective electron transport. Cation-anion salts of three azolium cations, imidazolium (HIm+), triazolium (HTrz+), and thiazolium (HThz+), in combination with a chiral camphorsulfonate (1S-CS-) and their racemic compounds (rac-CS-) were prepared and compared in terms of phase transitions, crystal structures, dynamics of constituent molecules, dielectric responses, and proton conductivities. The cation-anion crystals containing HIm+ showed no significant difference in proton conductivity between the homochiral and racemic crystals, whereas the HTrz+-containing crystals showed higher proton conductivity and lower activation energy in the homochiral form than in the racemic form. A two-dimensional hydrogen-bonding network consisting of HTrz+ and -SO3- groups and similar in-plane rotational motion was observed in both crystals; however, the HTrz+ cation in the homochiral crystal exhibited the rotational motion modulated with translational motion, whereas the HTrz+ cation in the racemic crystal exhibited almost steady in-plane rotational motion. The different motional degrees of freedom were confirmed by crystal structure analyses and temperature- and frequency-dependent dielectric constants. In contrast, steady in-plane rotational motion with the thermally activated fluctuating motion of CS- was observed both in homochiral and racemic crystals containing HIm+, which averaged the motional space of protons resulting in similar dielectric responses and proton conductivities. The control of motional degrees of freedom in homochiral crystals affects the proton conductivity and is useful for the design of molecular proton conductors.

Spontaneous symmetry breaking in polar fluids

Spontaneous symmetry breaking and emergent polar order are each of fundamental importance to a range of scientific disciplines, as well as generating rich phase behaviour in liquid crystals (LCs). Here, we show the union of these phenomena to lead to two previously undiscovered polar liquid states of matter. Both phases have a lamellar structure with an inherent polar ordering of their constituent molecules. The first of these phases is characterised by polar order and a local tilted structure; the tilt direction processes about a helix orthogonal to the layer normal, the period of which is such that we observe selective reflection of light. The second new phase type is anti-ferroelectric, with the constituent molecules aligning orthogonally to the layer normal. This has led us to term the phases the SmCPH\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{{{\\rm{Sm}}}}}}{{{{{{\\rm{C}}}}}}}_{{{{{{\\rm{P}}}}}}}^{{{{{{\\rm{H}}}}}}}$$\\end{document} and SmAAF phases, respectively. Further to this, we obtain room temperature ferroelectric nematic (NF) and SmCPH\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{{{{\\rm{Sm}}}}}}{{{{{{\\rm{C}}}}}}}_{{{{{{\\rm{P}}}}}}}^{{{{{{\\rm{H}}}}}}}$$\\end{document} phases via binary mixture formulation of the novel materials described here with a standard NF compound (DIO), with the resultant materials having melting points (and/or glass transitions) which are significantly below ambient temperature. The new soft matter phase types discovered herein can be considered as electrical analogues of topological structures of magnetic spins in hard matter.

IN ATMOSPHERIC COLLOID DISPERSE ENVIRONMENT THE DISCOVERY OF COAGULATION

In the present paper in the atmospheric coagulation has been revealed. The physico-chemical analysis of the atmospheric aerosol formation by analytical means and using a phase diagram is presented. The bordershe of the atmospheric colloid-disperse medium are put forward. Atmospheric coagulation is determined by kinetic and potential energies of the constituent molecules and ions, which are characterized the degrees of freedom of ion movement and parameters of changing in the position of ions with different isotopes. As a result of coagulation, the energy balance of the atmospheric membrane was presendet by the energy of the phase transition and by the work done. In the frames of revealing the atmospheric coagulation, the problem of climate mitigation is solved.

Landau theory of barocaloric plastic crystals

We present a minimal Landau theory of plastic-to-crystal phase transitions in which the key components are a multipole-moment order parameter that describes the orientational ordering of the constituent molecules, coupling between such order parameter and elastic strains, and thermal expansion. We illustrate the theory with the simplest non-trivial model in which the orientational ordering is described by a quadrupole moment, and use such model to calculate barocaloric effects in plastic crystals that are driven by hydrostatic pressure. The model captures characteristic features of plastic-to-crystal phase transitions, namely large changes in volume and entropy at the transition, as well as the linear dependence of the transition temperature with pressure. We identify temperature regions in the barocaloric response associated with the individual plastic and crystal phases, and those involving the phase transition. Our model is in overall agreement with previous experiments in powdered samples of fullerite C60, and predicts peak isothermal entropy changes of ∼90JK−1kg−1 and peak adiabatic temperature changes of ∼35K under 0.60 GPa at 265 K in fullerite single crystals.

A Transdermal Prion-Bionics Supermolecule as a RAB3A Antagonist for Enhancing Facial Youthfulness.

The mechanism research of skin wrinkles, conducted on volunteers underwent high-intensity desk work and mice subjected to partial sleep deprivation, revealed a significant reduction in dermal thickness associated with the presence of wrinkles. This can be attributed to the activation of facial nerves in a state of hysteria due to an abnormally elevated interaction between SNAP25 and RAB3A proteins involved in the synaptic vesicle cycle (SVC). Facilitated by AI-assisted structural design, a refined peptide called RSIpep is developed to modulate this interaction and normalize SVC. Drawing inspiration from prions, which possess the ability to protect themselves against proteolysis and invade neighboring nerve cells through macropinocytosis, RSIpep is engineered to demonstrate a GSH-responsive reversible self-assembly into a prion-like supermolecule (RSIprion). RSIprion showcases protease resistance, micropinocytosis-dependent cellular internalization, and low adhesion with constituent molecules in the cuticle, thereby endowing it with the transdermic absorption and subsequent biofunction in redressing the frenzied SVC. As a facial mud mask, it effectively reduces periorbital and perinasal wrinkles in the human face. Collectively, RSIprion not only presents a clinical potential as an anti-wrinkle prion-like supermolecule, but also exemplifies a reproducible instance of bionic strategy-guided drug development that bestows transdermal ability upon the pharmaceutical molecule.

Hydrogen bonds and elastic anisotropy of nitrile molecular crystals: an investigation from first-principles

ABSTRACT Atomistic calculations based on semi-classical dispersion-corrected density functional theory were performed to investigate bonding and elastic properties of low temperature polymorphs of three nitrile molecular crystals. For that purpose, the DFT-PBE-D3ijk method, which account for both pair and three-body interactions, was applied. The analysis of Hirshfeld surfaces demonstrated that the (C-N…H) hydrogen bonds are the strongest and the dominant ones in the three nitrile molecular crystals. The latter were found to share a common structural feature, consisting of an antiparallel orientation of the terminal nitrile groups at their constituent molecules. Our prediction of the elastic properties demonstrated that malonitrile has the highest Young modulus and succinonitrile has the lower one. The three nitrile crystals are expected to have similar resistance to volume variation while succinonitrle is predicted to exhibit the lowest resistance to shape change. Otherwise, succinonitrile was found to be ductile while malononitrile and acetonitrile were shown to be brittle. Elasticity anisotropy analysis demonstrated that the directions of maximum Young’s modulus are always nearly parallel to the direction of alignment of strong (C-H…N) hydrogen bonds in the three nitrile crystals. The present analyses are relevant for understanding the structure and the properties of more complex high temperature phases.

Ferroelectric Smectic Liquid Crystals

Since the discovery of the first ferroelectric liquid crystal (FLC) in the chiral smectic C (SmC*) phase, ferroelectricity in liquid crystals has attracted much attention due to not only the fundamental interest but also the applications. This review focuses on the evolution of the design concept for ferroelectric smectic liquid crystals. It progresses from considering macroscopic phase symmetry to designing intermolecular interactions. For the purpose of understanding the molecular organization in smectic phases, we propose a dynamic model of constituent molecules in the smectic A (SmA) and SmC* phases based on 13C NMR studies. Then, we follow the structure–property relationship in ferroelectric SmC* liquid crystals for FLC displays. We reconsider de Vries-like materials that can provide defect-free alignment. We pay attention to the electro-optical switching in the chiral de Vries smectic A phase. Finally, we show several liquid crystals exhibiting polar smectic A phases and discuss how the polar order occurs in the highest symmetric smectic A phase.

Exploring the essence of celery seeds (Apium graveolens L.): Innovations in microwave-assisted hydrodistillation for essential oil extraction using in vitro, in vivo and in silico studies

This study presents the composition analysis of essential oils extracted from celery seeds (Apium graveolens L.) collected from Morocco. Essential oil of A. graveolens (AG-EO), were obtained through microwave-assisted hydro-distillation, and its composition was characterized using gas chromatography/mass spectrometry (GC/MS). antimicrobial properties were assessed utilizing disc diffusion and microdilution assay methods, while antioxidant activities were evaluated through spectrophotometric techniques. Additionally, in vivo anti-inflammatory effects were investigated. The molecular docking technique, a computational approach utilized to predict the binding of small molecules to specific proteins, was employed to elucidate the antioxidative and antibacterial characteristics of the constituent molecules. The physicochemical and pharmacokinetic features of absorption, distribution, metabolism, excretion, and toxicity (ADME-Tox) tests were anticipated to provide insights into the drug likeness, pharmacokinetic characteristics, and expected safety profiles upon ingestion and the potential pharmacological activity of the identified compounds. Fifteen constituent compounds representing 99.99% of AG-EO were identified and quantified by the use of GC/MS. The main constituent, comprising 64.58% of AG-EO was limonene. AG-EO demonstrated a significant DPPH free radical scavenging activity, showing estimated scavenging rates of 8.49±0.00 µg/mL, and 5.09±0.04 µg/mL for ABTS+. AG-EO exhibited reducing Power (RP) and total antioxidant activity (TAC) of 3.42±0.01 µg/mL and 245.93±0.04 mg AAE/mL, respectively. AG-EO exhibited significant antimicrobial activity against all tested microorganisms. Additionally, the anti-inflammatory activity demonstrated the remarkable efficacy of AG-EO. Taken together, the essential oil derived from celery seeds holds promise for large-scale utilization as an environmentally friendly preservative within the food and agriculture industries, effectively countering fungal growth and aflatoxin contamination in stored commodities. Additionally, it exhibits potential as a suitable candidate for the development of pharmaceutical drugs.

Study of Thermophysical Properties of Binary Mixtures of 1,4-Butanediol + Cresols at Different Temperatures

Density (ρ) and ultrasonic velocity (u) of liquid binary mixtures of 1,4-butanediol (1,4-BD), o-cresol (OC), m-cresol (MC) and p-cresol (PC) have been measured at four distinct temperatures (303.15 K, 308.15 K, 313.15 K and 318.15 K) as a function of composition. Using data, significant thermodynamic and thermophysical parameters viz., internal pressure-IP (πi), free volume-FV (Vf), enthalpy-EH (H), entropy-ET (Ts) and their excess counterparts have been evaluated. The excess parameter functions EFV (VfE), EEH (HE), EFE (GE) and EET (TsE) were observed to be primarily negative, while πiE is positive indicating that the constituent molecules in these mixtures have discernible interactions with one another.

Chemical profiling of volatile compounds of the essential oil of grey-leaved rockrose (Cistus albidus L.) and its antioxidant, anti-inflammatory, antibacterial, antifungal, and anticancer activity in vitro and in silico.

Cistus albidus: L., also known as Grey-leaved rockrose and locally addressed as šṭab or tûzzâla lbîḍa, is a plant species with a well-established reputation for its health-promoting properties and traditional use for the treatment of various diseases. This research delves into exploring the essential oil extracted from the aerial components of Cistus albidus (referred to as CAEO), aiming to comprehend its properties concerning antioxidation, anti-inflammation, antimicrobial efficacy, and cytotoxicity. Firstly, a comprehensive analysis of CAEO's chemical composition was performed through Gas Chromatography-Mass Spectrometry (GC-MS). Subsequently, four complementary assays were conducted to assess its antioxidant potential, including DPPH scavenging, β-carotene bleaching, ABTS scavenging, and total antioxidant capacity assays. The investigation delved into the anti-inflammatory properties via the 5-lipoxygenase assay and the antimicrobial effects of CAEO against various bacterial and fungal strains. Additionally, the research investigated the cytotoxic effects of CAEO on two human breast cancer subtypes, namely, MCF-7 and MDA-MB-231. Chemical analysis revealed camphene as the major compound, comprising 39.21% of the composition, followed by α-pinene (19.01%), bornyl acetate (18.32%), tricyclene (6.86%), and melonal (5.44%). Notably, CAEO exhibited robust antioxidant activity, as demonstrated by the low IC50 values in DPPH (153.92 ± 4.30μg/mL) and β-carotene (95.25 ± 3.75μg/mL) assays, indicating its ability to counteract oxidative damage. The ABTS assay and the total antioxidant capacity assay also confirmed the potent antioxidant potential with IC50 values of 120.51 ± 3.33TEμmol/mL and 458.25 ± 3.67µg AAE/mg, respectively. In terms of anti-inflammatory activity, CAEO displayed a substantial lipoxygenase inhibition at 0.5mg/mL. Its antimicrobial properties were broad-spectrum, although some resistance was observed in the case of Escherichia coli and Staphylococcus aureus. CAEO exhibited significant dose-dependent inhibitory effects on tumor cell lines in vitro. Additionally, computational analyses were carried out to appraise the physicochemical characteristics, drug-likeness, and pharmacokinetic properties of CAEO's constituent molecules, while the toxicity was assessed using the Protox II web server.

Characterizing amyloid protein conformation with a multi-resonant metasurface based biosensor in the infrared window.

Misfolding of amyloid protein will cause neurodegeneration and trigger conformational disease. The lack of an effective detection approach is a brake on unveiling the mechanism of protein misfolding. We theoretically proposed a novel metasurface-based biosensor for characterizing the protein's conformation. The coupling complementary split ring resonator (cSRR) was engineered to manipulate incident waves in the near-infrared (NIR) and mid-infrared (MIR) windows at the same sensing surface. The cSRRs had the advantages of intensifying the electric field and sharpening the resonance profile, resulting in a highly qualified biosensing performance. In the NIR window, the biolayer's refractive index and thickness change were detected by the dual-wavelength, which resolved into an optogeometrical parameter of the amyloid biolayer. In the MIR window, the resonant wave specifically triggered the rotation-vibration transition of amyloid protein molecules with different conformations, which was shown as the unique Amide I and II bands in the fingerprint spectrum. Thus, our proposed biosensor presented sensitive detection of biolayer and specific identification of constituent molecules. It is helpful to interpret the protein's misfolding behavior on the molecular level by associating the biolayer's structure and the constituent molecule's conformational change.

Thermodynamic properties of P-methyl acetophenone with cyclohexylamine, cyclohexanol, and cyclohexane at various temperatures (strong and weak interactions)

ABSTRACT The density, viscosity and sound velocity of the binary liquid mixtures of P-methyl acetophenone with cyclohexylamine, cyclohexanol, and cyclohexane are measured over the complete composition range at temperatures of 303.15–313.15 K and at atmospheric pressure of 0.1 M. Excess molar volume, excess isentropic compressibility and viscosity deviation are calculated from the experimental measurements. The sign and magnitude of the derived parameters reveal the nature and type of interactions between the constituent molecules in the binary mixtures. Thermodynamic properties for this work reveal association interactions between dissimilar molecules in the binary systems P-methyl acetophenone + cyclohexylamine and P-methyl acetophenone + cyclohexanol systems, whereas dispersion forces cause the opposite trend in the other binary system P-methyl acetophenone + cyclohexane.

A state-of-the-art theoretical method for estimating ultrasonic velocity in ionic liquid mixtures: An extension of McAllister's interaction model

McAllister’s Interaction Model has been extended to predict ultrasonic velocities in eight binary mixtures of ionic liquids and water at temperatures T = 288.15 K, 298.15 K, and 308.15 K.The ionic liquids chosen for the current study are [BMim][TfO], [BMpyr][TfO], [BMpy][TfO], [BMim][dca], [HMim][dca], [BMpyr][dca], [Mpy][MSO4], and [EEpy][ESO4]. The interactions considered in present cases have been investigated for a range of variations from three-body interactions to nine-body interactions. The experimental values of ultrasonic velocities for all the mixturesat temperatures T = 288.15 K, 298.15 K, and 308.15 Kare compared with the computed values. The differences between the experimental and theoretically predicted velocities are determined in terms of absolute percentage deviation. It is worth mentioning that McAllister’s Model of interactions has been extended, for consideration, from three-body interactions to nine-body interactions among constituent molecules of binary mixtures and applied for the prediction of ultrasonic velocities in binary mixtures of water and ionic liquids for the first time. The extended Huckel theory (EHT) is used to calculate the charge distributions in eight ionic liquids and water molecules to understand the active sites available for interactions on each constituting molecule of the binary mixtures under investigation. The results we obtained complemented our decision to extend McAllister’s interactions model (MAIM) to higher orders (four-body to nine-body interactions). The results obtained (using extended MAIM) report an excellent agreement with experimental velocity values for nine-body interactions for all the systems under study. It is also pointed out that McAllister’s assumption that the free energies of activation are the additive quantity for viscosity investigation in organic liquid mixtures is also valid in the case of ultrasonic velocity studies for ionic liquids and water mixtures. Considering McAllister’s conjecture that rather than a planar system of interactions among solvent-solute molecules, a three-dimensional approach to intermolecular interactions can be more appropriate, authors have confirmed the validity of McAlliter’s conjecture by successfully investigating three-dimensional multi-body (in the present case: 9-body) interactions in the binary mixtures of ionic liquids and water.

Effect of an Electric Field on the Structure and Stability of Atmospheric Clusters.

We study the influence of an applied electric field on the structure and stability of some common bimolecular clusters that are found in the atmosphere. These clusters play an important role in new particle formation (NPF). For low values of the electric field (i.e., |E| ≤ 0.01 V Å-1), we demonstrate that the field response of the clusters can be predicted from simply calculating the dipole moment of the cluster and the dipole moments of the constituent molecules and that the influence on the association energy of the cluster is minimal (i.e., <0.5 kcal mol-1). For higher field strengths |E| > 0.2 V Å-1, there can be more dramatic effects on both structure and energetics, as the induced dipole, charge transfer, and geometric distortion play a larger role. Although such large fields are not very relevant in the atmosphere, they do exist in some situations of experimental interest, such as near interfaces and in intense laser fields.

Cryo-EM structure and B-factor refinement with ensemble representation

Cryo-EM experiments produce images of macromolecular assemblies that are combined to produce three-dimensional density maps. Typically, atomic models of the constituent molecules are fitted into these maps, followed by a density-guided refinement. We introduce TEMPy-ReFF, a method for atomic structure refinement in cryo-EM density maps. Our method represents atomic positions as components of a Gaussian mixture model, utilising their variances as B-factors, which are used to derive an ensemble description. Extensively tested on a substantial dataset of 229 cryo-EM maps from EMDB ranging in resolution from 2.1-4.9 Å with corresponding PDB and CERES atomic models, our results demonstrate that TEMPy-ReFF ensembles provide a superior representation of cryo-EM maps. On a single-model basis, it performs similarly to the CERES re-refinement protocol, although there are cases where it provides a better fit to the map. Furthermore, our method enables the creation of composite maps free of boundary artefacts. TEMPy-ReFF is useful for better interpretation of flexible structures, such as those involving RNA, DNA or ligands.

Energy landscape of perylenediimide chromophoric aggregates.

Understanding the self-assembly of conjugated organic materials at the molecular level is crucial in their potential applications as active components in electronic and optoelectronic devices. The type of aggregation significantly influences the intriguing electronic and optical characteristics differing from their constituent molecules. Perylenediimides (PDIs), electron-deficient molecules exhibiting remarkable n-type semiconducting properties, are among the most explored organic fluorescent materials due to their high fluorescence efficiency, photostability, and optoelectronic properties. PDI derivatives are reported to form well-tailored supramolecular architectures: cofacial with minor slip (H-aggregates), staggered with major slip (J-aggregates), magic angle stacking (M-aggregates), rotated (X-aggregates), rotated orthogonal ((+)-aggregates), etc. H*-aggregates are defined here as an ideal case of H-aggregate with an eclipsed configuration. Although numerous reports regarding the formation and optical properties of various PDI aggregates are known, the key driving force within the PDI units guiding the self-assembly to form distinct aggregate systems remains elusive. To unravel the molecular-level mechanisms behind the self-assembly of PDI units by probing the intermolecular interactions, symmetry-adapted perturbation theory-based energy decomposition, potential energy surface scans, and non-covalent interaction index analyses were employed on PDI dimer models. Quantum theory of atoms in molecules and frontier molecular orbital analyses were implemented on the dimer models to comprehend the effect of heteroatoms and orbital interactions in stabilising the X-aggregates over the other PDI aggregate systems. Competition between the attractive and repulsive non-covalent interactions dictates a stability order of X > H > J > M > (+) > H* for the PDI aggregate system, while in the parent perylene system, the stability order was found to be X > (+) > H > M > J > H*.