Molecular Structure Research Articles

On the Cancer

This article theoretically speculates that after replication of a pair of DNA they must be allocated to two daughter cells in a transverse division or erect division manner. Transverse division represents differentiation, while erect division represents transformation. The molecular structure determines that DNA has greater hydrophobicity than RNA. The hydrophobic modification of chromatin regulates gene activity and centromere similarity between new and old DNA. A difference in division between cancer cells and embryonic stem cells is discussed

The nonresonant sum-frequency generation response: The not-so-silent partner.

Vibrational sum-frequency generation (VSFG) has become a powerful tool for investigating the molecular structure of surfaces and interfaces. One aspect of the technique that has been overlooked is the source and nature of the nonresonant contribution to the measured signal. If not properly accounted for, interaction between the resonant and nonresonant responses can lead to misinterpretation of the resonant signals. The nonresonant response itself also carries important information about the system under study. This Perspective reviews some of the experimental and post-processing techniques that have been developed to isolate the nonresonant response. The focus of such approaches has generally been on the resonant signal, meaning more can be done to learn about the nonresonant response. Some examples of information carried by the nonresonant response are also presented, again showing that there is more to do to understand this signal. The nonresonant sum-frequency generation response is an important component of VSFG measurement, and the VSFG community needs to learn to better understand what it is telling us about our samples.

Iridium Complexes with Bidentate Pyridinylidene/N-Amidate Ligands for Transfer Hydrogenation Catalysis.

A series of iridium pentamethylcyclopentadienyl (Cp*) complexes, [Cp*Ir(κ2-RLp/m)Cl], that contain the strongly coordinating bidentate ligands RLp/m were synthesized. The donor groups of the bidentate ligands were an N-amidate and either a para-pyridinylidene remote N-heterocyclic carbene (RLp) or a meta-pyridinylidene remote N-heterocyclic carbene (RLm). For each type of bidentate ligand, a set of iridium complexes was synthesized, which differed only according to the substituents (R) on the phenyl ring associated with the amidate group. The iridium complexes were all fully characterized and molecular structures were obtained by single-crystal X-ray diffraction studies for representative examples. The complexes were found to be good precatalysts in iso-propanol for the transfer hydrogenation of benzaldehyde to give benzyl alcohol. The catalytic activity correlated with the Hammett σm/p parameters of the phenyl ring substituents, with more electron-donating substituents leading to increased catalytic activity. In all cases, the meta-pyridinylidene complexes, [Cp*Ir(κ2-RLm)Cl], performed better than the corresponding para analogues, [Cp*Ir(κ2-RLp)Cl].

Lwreg: A Lightweight System for Chemical Registration and Data Storage.

Here, we present lwreg, a lightweight, yet flexible chemical registration system supporting the capture of both two-dimensional molecular structures (topologies) and three-dimensional conformers. lwreg is open source, with a simple Python API, and is designed to be easily integrated into computational workflows. In addition to lwreg itself, we also introduce a straightforward schema for storing experimental data and metadata in the registration database. This direct connection between compound structural information and data generated using those structures creates a powerful tool for data analysis and experimental reproducibility. The software is available at and installable directly from https://github.com/rinikerlab/lightweight-registration.

N-Type Doping Effect of Anthracene-Based Cationic Dyes in Organic Electronics.

n-Type doping for improving the electrical characteristics and air stability of n-type organic semiconductors (OSCs) is important for realizing advanced future electronics. Herein, we report a selection method for an effective n-type dopant with an optimized structure and thickness based on anthracene cationic dyes with high miscibility induced by a molecular structure similar to that of OSCs. Among the doped OSCs evaluated, rhodamine B (RhoB)-doped OSC exhibits the highest density, a smallest roughness of 2.69 nm, a phase deviation of 0.85° according to atomic force microscopy measurements, and the highest electron mobility (μ), showing its high miscibility. Surface doping of RhoB affords the lowest contact resistance of 2.01 × 105 Ω cm compared to bulk and contact doping, resulting in an effective doping structure. The RhoB-doped OSC retains 81.63% of the original μ value of 6.13 × 10-2 cm2 V-1 s-1 after 15 days, whereas pristine OSC shows a lower μ of 2.33 × 10-2 cm2 V-1 s-1 and maintains only 4.41% of the original value after 15 days. Our findings demonstrate that this methodology is effective for the selection of a high-performance n-type dopant for OSCs toward the development of high-performance and air-stable n-type organic electronics.

Excited-State Intramolecular Proton Transfer toward Conical Intersections in Indigo, Epindolidione, and Indirubin.

Indigo exhibits a high degree of photostability, experimentally supported by observations such as quenching of fluorescence and an exceptionally short excited-state lifetime. Epindolidione, a structural isomer of indigo, is highly fluorescent in contrast to indigo, while indirubin, another structural isomer, exhibits weak fluorescence similar to that of indigo. To elucidate the origin of the difference in photophysical and photochemical behavior, potential energy profiles of the excited-state intramolecular proton transfer in indigo, epindolidione, and indirubin are computationally studied by quantum chemical calculations using the TDDFT and extended MS-CASPT2 (XMS-CASPT2) methods. As a result, it is found that indigo and indirubin exhibit little energy barrier for the single proton transfer (SPT) in the S1(ππ*) state from the diketo to keto-enol form and low energy of the S1/S0 conical intersection (CI) in the latter form with a planar molecular structure. Epindolidione, on the other hand, exhibits much higher barriers for SPT and access to CI. These results suggest that the excited-state SPT and subsequent nonradiative deactivation via CI are more likely to occur in indigo and indirubin than in epindolidione, which is consistent with the experimental observations described above. For indigo and epindolidione, the deactivation channels via the second SPT from the keto-enol to dienol form are also compared.

Unveiling the potential of triphenylphosphine salts in tuning organic room temperature phosphorescence.

Triphenylphosphine (TPP) salt derivatives, with their rich chemistry of core-substitution, have emerged as promising candidates for ultralong room temperature phosphorescence (RTP) materials owing to their distinct molecular structures, high quantum efficiency and exceptional phosphorescence properties. This feature article highlights the vast potential of TPP salt derivatives in tunable RTP properties by exploring some factors such as the alkyl chains, halogen anions, through-space charge transfer states, etc., and recent advancements in multi-level information encryption, high-level anticounterfeiting tags and X-ray imaging applications. We anticipate that this article will assist in directing future analyses based on the mechanisms underlying the RTP behavior of TPP derivatives and offer guidance for the rational design of high-performance RTP materials.

Sequence-encoded bioactive protein-multiblock polymer conjugates via quantitative one-pot iterative living polymerization

Protein therapeutics are essential in treating various diseases, but their inherent biological instability and short circulatory half-lives in vivo pose challenges. Herein, a quantitative one-pot iterative living polymerization technique is reported towards precision control over the molecular structure and monomer sequence of protein-polymer conjugates, aiming to maximize physicochemical properties and biological functions of proteins. Using this quantitative one-pot iterative living polymerization technique, we successfully develop a series of sequence-controlled protein-multiblock polymer conjugates, enhancing their biostability, pharmacokinetics, cellular uptake, and in vivo biodistribution. All-atom molecular dynamics simulations are performed to disclose the definite sequence-function relationship of the bioconjugates, further demonstrating their sequence-encoded cellular uptake behavior and in vivo biodistribution in mice. Overall, this work provides a robust approach for creating precision protein-polymer conjugates with defined sequences and advanced functions as a promising candidate in disease treatment.

Experimental molecular structures in the gas phase at the upper size limit: The case of Si6Tip6.

Currently, the largest (ramax = 19.9Å) and by far the most complicated (234 atoms, C1 symmetry, 696 independent geometrical parameters, and 27 261 interatomic terms) experimental molecular structure of a cage-type Si6Tip6 (Tip = 2,4,6-iPr3C6H2) isomer has been investigated in the gas phase by the electron diffraction method (Tav = 645K) supplemented with theoretical simulations. A detailed analysis of the current possibilities for experimentally investigating large molecular structures is performed. A series of density functional theory approximations and the role of dispersion interactions have been benchmarked using the obtained data. Based on the refined geometry of Si6Tip6, various quantum-chemical methods have been applied for the investigation of the electronic structure of its Si6 core. In particular, natural bond orbital, quantum theory of atoms in molecules, interacting quantum atoms, fractional occupation number weighted density, and complete active space self-consistent field (CASSCF) methods were utilized. The diradical character of the molecule has been assessed by the UHF and CASSCF approximations. The problem of bonding between the hemispheroidal silicon atoms has been investigated.

Identification of Active Molecules against Thrombocytopenia through Machine Learning.

Thrombocytopenia, which is associated with thrombopoietin (TPO) deficiency, presents very limited treatment options and can lead to life-threatening complications. Discovering new therapeutic agents against thrombocytopenia has proven to be a challenging task using traditional screening approaches. Fortunately, machine learning (ML) techniques offer a rapid avenue for exploring chemical space, thereby increasing the likelihood of uncovering new drug candidates. In this study, we focused on computational modeling for drug-induced megakaryocyte differentiation and platelet production using ML methods, aiming to gain insights into the structural characteristics of hematopoietic activity. We developed 112 different classifiers by combining eight ML algorithms with 14 molecule features. The top-performing model achieved good results on both 5-fold cross-validation (with an accuracy of 81.6% and MCC value of 0.589) and external validation (with an accuracy of 83.1% and MCC value of 0.642). Additionally, by leveraging the Shapley additive explanations method, the best model provided quantitative assessments of molecular properties and structures that significantly contributed to the predictions. Furthermore, we employed an ensemble strategy to integrate predictions from multiple models and performed in silico predictions for new molecules with potential activity against thrombocytopenia, sourced from traditional Chinese medicine and the Drug Repurposing Hub. The findings of this study could offer valuable insights into the structural characteristics and computational prediction of thrombopoiesis inducers.

Unraveling the Surface Activity of Ethanol-Water Mixtures through Experiments and Molecular Dynamics Simulations.

Ethanol's complete miscibility in water makes it a widely used solvent in various applications, such as organic compound synthesis, paint manufacture, chromatography, and cosmetics preservation. Studies suggest that ethanol's concentration at interfaces can be higher than in the bulk due to its amphiphilic nature, especially at lower concentrations, making it a surface-active agent. Accordingly, ethanol plays a crucial role in controlling the emulsion stability, foam formation, heat transfer, and coating adhesion. However, the precise concentration ranges up to which ethanol's surface activity dominates its interfacial properties, and the underlying molecular mechanism is not fully understood in the literature. In this context, our foamability experiments, coupled with film stability experiments conducted via ethanol drop impact on varying concentration ethanol-water mixture pools, indicate that the surface-active nature of ethanol is observed up to a maximum of 10% molar ethanol concentration in water. We next employ all-atom molecular dynamics simulations to reveal that the surface tension and other interfacial properties are most significantly affected only up to the molar concentration in the range of 0-10% of ethanol in water. This observation is further supported by free energy analyses, indicating that the stabilization free energy of an ethanol molecule at the interface becomes comparable to that in the bulk region beyond this concentration range. The transition from surface-active to a behavior resembling a homogeneous solution occurs when the molar concentration of ethanol in water exceeds 10%. This transition is attributed to distinctive alterations in the number and strength of ethanol-water hydrogen bonds. These findings provide valuable insights into the interfacial molecular structure, which can be suitably exploited to modulate interfacial properties and dynamic behavior in a wide array of industrial and scientific applications.

Molecular folding governs switchable singlet oxygen photoproduction in porphyrin-decorated bistable rotaxanes

Rotaxanes are mechanically interlocked molecules where a ring (macrocycle) is threaded onto a linear molecule (thread). The position of the macrocycle on different stations on the thread can be controlled in response to external stimuli, making rotaxanes applicable as molecular switches. Here we show that bistable rotaxanes based on the combination of a Zn(II) tetraphenylporphyrin photosensitizer, attached to the macrocycle, and a black-hole-quencher, attached to the thread, are capable of singlet oxygen production which can be switched on/off by the addition of base/acid. However, we found that only a sufficiently long linker between both stations on the thread enabled switchability, and that the direction of switching was inversed with regard to the original design. This unexpected behavior was attributed to intramolecular folding of the rotaxanes, as indicated by extensive theoretical calculations. This evidences the importance to take into account the conformational flexibility of large molecular structures when designing functional switchable systems.

Structure of the human dopamine transporter in complex with cocaine.

The dopamine transporter (DAT) is crucial for regulating dopamine signalling and is the prime mediator for the rewarding and addictive effects of cocaine1. As part of the neurotransmitter sodium symporter family, DAT uses the Na+ gradient across cell membranes to transport dopamine against its chemical gradient2. The transport mechanism involves both intra- and extracellular gates that control substrate access to a central site. However, the molecular intricacies of this process and the inhibitory mechanism of cocaine have remained unclear. Here, we present the molecular structure of human DAT in complex with cocaine at a resolution of 2.66 Å. Our findings reveal that DAT adopts the expected LeuT-fold, posing in an outward-open conformation with cocaine bound at the central (S1) site. Notably, while an Na+ occupies the second Na+ site (Na2), the Na1 site seems to be vacant, with the side chain of Asn82 occupying the presumed Na+ space. This structural insight elucidates the mechanism for the cocaine inhibition of human DAT and deepens our understanding of neurotransmitter transport. By shedding light on the molecular underpinnings of how cocaine acts, our study lays a foundation for the development of targeted medications to combat addiction.

Relationships of Prodiginins Mechanisms and Molecular Structures to their Antiproliferative Effects.

The Prodiginins (PGs) natural pigments are secondary metabolites produced by a broad spectrum of gram-negative and gram-positive bacteria, notably by species within the Serratia and Streptomyces genera. These compounds exhibit diverse and potent biological activities, including anticancer, immunosuppressive, antimicrobial, antimalarial, and antiviral effects. Structurally, PGs share a common tripyrrolic core but possess variable side chains and undergo cyclization, resulting in structural diversity. Studies have investigated their antiproliferative effects on various cancer cell lines, with some PGs advancing to clinical trials for cancer treatment. This review aims to illuminate the molecular mechanisms underlying PG-induced apoptosis in cancer cells and explore the structure-activity relationships pertinent to their anticancer properties. Such insights may serve as a foundation for further research in anticancer drug development, potentially leading to the creation of novel, targeted therapies based on PGs or their derivatives.

Electromagnetic Enantiomer: Chiral Nanophotonic Cavities for Inducing Chemical Asymmetry.

Chiral molecules, a cornerstone of chemical sciences with applications ranging from pharmaceuticals to molecular electronics, come in mirror-image pairs called enantiomers. However, their synthesis often requires complex control of their molecular geometry. We propose a strategy called "electromagnetic enantiomers" for inducing chirality in molecules located within engineered nanocavities using light, eliminating the need for intricate molecular design. This approach works by exploiting the strong coupling between a nonchiral molecule and a chiral mode within a nanocavity. We provide evidence for this strong coupling through angular emission patterns verified by numerical simulations and with complementary evidence provided by luminescence lifetime measurements. In simpler terms, our hypothesis suggests that chiral properties can be conveyed on to a molecule with a suitable chromophore by placing it within a specially designed chiral nanocavity that is significantly larger (hundreds of nanometers) than the molecule itself. To demonstrate this concept, we showcase an application in display technology, achieving efficient emission of circularly polarized light from a nonchiral molecule. The electromagnetic enantiomer concept offers a simpler approach to chiral control, potentially opening doors for asymmetric synthesis.

Curing kinetics and mechanical properties of the epoxy vitrimer based on transesterification and its composite laminates

AbstractThe resin is a fundamental factor in determining the performance and usage conditions of its composites. The epoxy vitrimer, which combines both thermoplastic and thermosetting properties, shows significant potential in extending the service life of material. The curing process significantly affects the macroscopic properties of the vitrimer and the resulting carbon fiber reinforced plastics (CFRP). Effective control of curing parameters constitutes the critical factor for the assurance of product quality. In the study, a differential scanning calorimetry (DSC) was utilized to establish a curing kinetics model for a modified, self‐healable epoxy vitrimer based on transesterification. Then the molecular structure, thermodynamic, and mechanical properties of the cured vitrimer were analyzed. Next vitrimeric CFRP (vCFRP) laminates were fabricated, and the tensile and bending properties of the vCFRP laminates were investigated. The results showed the curing process was obtained: 95°C/1 h + 150°C/2 h + 170°C/2 h. The thermodynamic and mechanical properties of cured vitrimer could meet practical requirements. The minimal differences observed in the stress–strain curves of the specimens indicated that the curing process was appropriately configured. The prepared laminates exhibited performance comparable to that of commercial thermosetting composites.

Photoelectron momentum distributions of triatomic CO2 molecules by circularly polarized attosecond pulses

Abstract Molecular-frame photoelectron momentum distributions (MF-PMDs) have been studied for imaging molecular structures. We investigate the MF-PMDs of CO2 molecules exposed to circularly polarized (CP) attosecond laser pulses by solving the time-dependent Schrödinger equations based on the single-active-electron approximation frames. Results show that high-frequency photons lead to photoelectron diffraction patterns, indicating molecular orbitals, these diffraction patterns can be illustrated by the ultrafast photoionization models. However, for the driving pulses with 30 nm, a deviation between MF-PMDs and theoretically predicted results of the ultrafast photoionization models is produced because the Coulomb effect strongly influences the molecular photoionization. Meanwhile, the MF-PMDs rotates in the same direction as the helicity of driving laser pulses. Our results also demonstrate that the MF-PMDs in a CP laser pulse are the superposition of those in the parallel and perpendicular linearly polarized cases. The simulations efficiently visualize molecular orbital geometries and structures by ultrafast photoelectron imaging. Furthermore, we determine the contribution of HOMO and HOMO-1 orbitals to ionization by varying the relative phase and the ratio of these two orbitals.

Molecular Structure and Rotational Dynamics in the Acetonitrile:Acetylene (1:2) Plastic Co-crystal at Titan Conditions

Molecular Structure and Rotational Dynamics in the Acetonitrile:Acetylene (1:2) Plastic Co-crystal at Titan Conditions

Effects of Oxygen Concentration on Soot Formation in Ethylene and Ethane Fuel Laminar Diffusion Flames

In studying the effects of oxygen concentration and molecular structure on the morphologies of the soot particles produced by hydrocarbon fuels, ethylene and ethane were chosen as experimental fuels. With a Gülde laminar coaxial diffusion flame device, a soot particle device was used to sample soot particles at different oxygen concentrations (21%, 24%, 26%, 28%, and 31%) and at different heights above a burner (HABs = 10 mm, 20 mm, 30 mm, 40 mm, and 50 mm). High-resolution transmission electron microscopy (HRTEM) was used to scrutinize and analyze the soot particles at varying oxygen concentrations. The findings suggest that at the same oxygen concentration, ethylene produces brighter and taller flames. With an increase in the oxygen concentration, ethylene flames and ethane flames gradually decrease in height and become brighter. With an increase in the HAB, the average primary soot particle diameter (Dp) increases initially and then decreases, the fractal dimension (Df) increases, and the aggregates transition from strips and chains to clusters. At the same flame height (HAB = 30 mm), the Dp decreases, the Df increases, the carbon layer torsion resistance (Tf) and the carbon layer spacing (Ds) increase, and the carbon layer changes from a parallel arrangement to a curved arrangement to form denser network aggregations.

Elevating Skincare Science: Grape Seed Extract Encapsulation for Dermatological Care

The skin is the largest organ in the human body and serves multiple functions such as barrier protection and thermoregulation. The maintenance of its integrity and healthy structure is of paramount importance. Accordingly, technological advances in cosmetic sciences have been directed towards optimizing these factors. Plant-derived ingredients have been explored for their bioactivity profiles and sustainable sources. Grape by-products contain a group of bioactive molecules that display important biological activities. Nonetheless, many of these molecules (e.g., phenolic compounds) are unstable and susceptible to degradation. So, their encapsulation using nano/microsystems (i.e., microdispersions) has been explored as a promising solution. In this work, two grape seed extracts were obtained, one from a single grape variety (GSE-Ov) and another from a mix of five grape varieties (GSE-Sv). These extracts were analysed for their antioxidant and antimicrobial activities, as well as their chemical composition and molecular structure. The extract that showed the most promising properties was GSE-Ov with a DPPH IC50 of 0.079 mg mL−1. This extract was encapsulated in soy lecithin microdispersions coated with pectin, with an encapsulation efficiency of 88.8%. They showed an in vitro release of polyphenols of 59.4% during 24 h. The particles displayed a zeta potential of −20.3 mV and an average diameter of 13.6 µm. Microdispersions proved to be safe under 5 and 2.5 mg mL−1 in HaCaT and HDF cell models, respectively. Additionally, they demonstrated anti-inflammatory activity against IL-1α when tested at 2 mg mL−1. This work enabled the valorisation of a by-product from the wine industry by using natural extracts in skincare products.