Common Organic Molecules Research Articles

Enhancing Understanding of Siloxane Surface Properties and Functional Group Effects on Water Deoxygenation

The deoxygenation process in water used in well injection operations is an important matter to eliminate corrosion in the petroleum industry. This study used molecular dynamics simulations to understand the behavior of siloxane surfaces by studying the surface properties with two functional groups attached to the end of siloxane and their effect on the deoxygenation process. The simulations were performed using LAMMPS to characterize surface properties. Jmol software version 14 was used to generate siloxane chains with (8, 20, and 35) repeat units. We evaluated properties such as total energy, surface tension, and viscosity. Then, we used siloxane as a membrane to compare the efficiency of deoxygenation for both types of functional groups. The results indicated that longer chain lengths increased the total energy and viscosity while decreasing surface tension. Replacing methyl groups with trifluoromethyl (CF3) groups increased all the above mentioned properties in varying proportions. Trifluoromethyl (CF3) groups showed better removal efficiency than methyl (CH3) groups but allowed more water to pass. Furthermore, the simulations were run using the class II potential developed by Sun, Rigby, and others within an explicit-atom (EA) model. This force field is universally applicable to the atomistic simulation of polymers, inorganic small molecules, and common organic molecules.

Photostimulus-Responsive Peptide Dot-Centered Covalent Organic Polymers: Effective Pesticide Sensing via Enhancing Accessibility.

Pesticide detection and monitoring are necessary for human health as the overapplication has serious consequences for environmental pollution. Herein, a proper modulation strategy was implemented to construct the photostimulus-responsive peptide-dot-centered covalent organic polymer (P-PCOP) nanoarchitecture for selective sensing of pesticides. The as-constructed P-PCOP was prepared at room temperature by using amino-containing peptide dots as a building block instead of common organic molecules, and the merits of P-PCOP enable it to reduce the steric hindrance of recognition, enhance the interfacial contact of the target, and facilitate the accessibility of sites, which promises to improve the sensitivity. The P-PCOF exhibited a low detection limit of 0.38 μg L-1 to cartap over the range of 1-80 μg L-1 (R2 = 0.9845), and the recoveries percentage in real samples was estimated to be 93.39-105.82%. More importantly, the DFT calculation confirmed the selective recognition ability of P-PCOP on chemical pesticides. In conjunction with a smartphone-integrated portable reading device, on-site chemical sensing is achieved. The proper modulation strategy of fixing a functional guest on the COP system contributes to the advanced structure-chemical properties that are conducive to their applications in chemical sensing.

Organic Molecules Mimic Alkali Metals Enabling Spontaneous Harpoon Reactions with Halogens.

The harpoon mechanism has been a milestone in molecular reaction dynamics. Until now, the entity from which electron harpooning occurs has been either alkali metal atoms or non-metallic analogs in their excited states. In this work, we demonstrate that a common organic molecule, octamethylcalix[4] pyrrole (omC4P), behaves just like alkali metal atoms, enabling the formation of charge-separated ionic bonding complexes with halogens omC4P+ ⋅ X- (X=F-I, SCN) via the harpoon mechanism. Their electronic structures and chemical bonding were determined by cryogenic photoelectron spectroscopy of the corresponding anions and confirmed by theoretical analyses. The omC4P+ ⋅ X- could be visualized to form from the reactants omC4P+X via electron harpooning from omC4P to X at a distance defined by the energy difference between the ionization potential of omC4P and electron affinity of X.

Triboelectric Spectroscopy for In Situ Chemical Analysis of Liquids.

Chemical analysis of ions and small organic molecules in liquid samples is crucial for applications in chemistry, biology, environmental sciences, and health monitoring. Mainstream electrochemical and chromatographic techniques often suffer from complex and lengthy sample preparation and testing procedures and require either bulky or expensive instrumentation. Here, we combine triboelectrification and charge transfer on the surface of electrical insulators to demonstrate the concept of triboelectric spectroscopy (TES) for chemical analysis. As a drop of the liquid sample slides along an insulating reclined plane, the local triboelectrification of the surface is recorded, and the charge pattern along the sample trajectory is used to build a fingerprinting of the charge transfer spectroscopy. Chemical information extracted from the charge transfer pattern enables a new nondestructive and ultrafast (<1 s) tool for chemical analysis. TES profiles are unique, and through an automated identification, it is possible to match against standard and hence detect over 30 types of common salts, acids, bases and organic molecules. The qualitative and quantitative accuracies of the TES methodology is close to 93%, and the detection limit is as low as ppb levels. Instruments for TES chemical analysis are portable and can be further miniaturized, opening a path to in situ and rapid chemical detection relying on inexpensive, portable low-tech instrumentation.

Multiconfigurational Pair-Density Functional Theory Is More Complex than You May Think.

Multiconfigurational pair-density functional theory (MC-PDFT) is a promising way to describe both strong and dynamic correlations in an inexpensive way. The functionals in MC-PDFT are often "translated" from standard spin density functionals. However, these translated functionals can in principle lead to "translated spin densities" with a nonzero imaginary component. Current developments so far neglect this imaginary part by simply setting it to zero. In this work, we show how this imaginary component is actually needed to reproduce the correct physical behavior in a range of cases, especially low-spin open shells. We showcase the resulting formalism on both local density approximation and generalized gradient approximation functionals and illustrate the numerical behavior by benchmarking a number of singlet-triplet splittings (ST gaps) of organic diradicals and low-lying excited states of some common organic molecules. The results demonstrate that this scheme improves existing translated functionals and gives more accurate results, even with minimal active spaces.

Conformational analysis of simple oxygenated hydrocarbons in a solid parahydrogen matrix

Acetone, acetaldehyde, propylene oxide, propionaldehyde, and 2-propanol are all simple oxygen-containing organic molecules, and play an important role in combustion chemistry, atmospheric chemistry, and astrochemistry. These small molecules are often produced by chemical reactions or UV photolysis of larger molecules containing oxygen atoms. Thus, knowing the IR spectrum of these molecules is important for the identification of (photo)chemical processes of various molecules. In this study, the IR spectra of these five common organic molecules were studied using parahydrogen (pH2) matrix isolation with Fourier transform infrared spectroscopy. Conformational analysis of the IR spectra revealed two conformers of propionaldehyde and 2-propanol exist in the pH2 matrix at 3.8 K. This work will be useful for the identification of products in future pH2 photochemistry experiments.

Therapeutic Effects of Coumarins with Different Substitution Patterns.

The use of derivatives of natural and synthetic origin has gained attention because of their therapeutic effects against human diseases. Coumarins are one of the most common organic molecules and are used in medicine for their pharmacological and biological effects, such as anti-inflammatory, anticoagulant, antihypertensive, anticonvulsant, antioxidant, antimicrobial, and neuroprotective, among others. In addition, coumarin derivates can modulate signaling pathways that impact several cell processes. The objective of this review is to provide a narrative overview of the use of coumarin-derived compounds as potential therapeutic agents, as it has been shown that substituents on the basic core of coumarin have therapeutic effects against several human diseases and types of cancer, including breast, lung, colorectal, liver, and kidney cancer. In published studies, molecular docking has represented a powerful tool to evaluate and explain how these compounds selectively bind to proteins involved in various cellular processes, leading to specific interactions with a beneficial impact on human health. We also included studies that evaluated molecular interactions to identify potential biological targets with beneficial effects against human diseases.

Acetaldehyde binding energies: a coupled experimental and theoretical study

ABSTRACT Acetaldehyde is one of the most common and abundant gaseous interstellar complex organic molecules found in cold and hot regions of the molecular interstellar medium. Its presence in the gas-phase depends on the chemical formation and destruction routes, and its binding energy (BE) governs whether acetaldehyde remains frozen on to the interstellar dust grains or not. In this work, we report a combined study of the acetaldehyde BE obtained via laboratory temperature programmed desorption (TPD) experiments and theoretical quantum chemical computations. BEs have been measured and computed as a pure acetaldehyde ice and mixed with both polycrystalline and amorphous water ice. Both calculations and experiments found a BE distribution on amorphous solid water that covers the 4000–6000 K range when a pre-exponential factor of $1.1\times 10^{18}\, \mathrm{s}^{-1}$ is used for the interpretation of the experiments. We discuss in detail the importance of using a consistent couple of BE and pre-exponential factor values when comparing experiments and computations, as well as when introducing them in astrochemical models. Based on the comparison of the acetaldehyde BEs measured and computed in the present work with those of other species, we predict that acetaldehyde is less volatile than formaldehyde, but much more than water, methanol, ethanol, and formamide. We discuss the astrochemical implications of our findings and how recent astronomical high spatial resolution observations show a chemical differentiation involving acetaldehyde, which can easily explained due to the different BEs of the observed molecules.

Fluorescent Covalent Organic Frameworks: A Promising Material Platform for Explosive Sensing.

Covalent organic frameworks (COFs) are a novel class of porous crystalline organic materials with organic small molecule units connected by strong covalent bonds and extending in two- or three-dimension in an ordered mode. The tunability, porosity, and crystallinity have endowed covalent organic frameworks the capability of multi-faceted functionality. Introduction of fluorophores into their backbones or side-chains creates emissive covalent organic frameworks. Compared with common fluorescent organic solid materials, COFs possess several intrinsic advantages being as a type of irreplaceable fluorescence materials mainly because its highly developed pore structures can accommodate various types of guest analytes by specific or non-specific chemical bonding and non-bonding interaction. Developments in fluorescent COFs have provided opportunities to enhance sensing performance. Moreover, due to its inherent rigidified structures and fixed conformations, the intramolecular rotation, vibration, and motion occurred in common organic small molecules, and organic solid systems can be greatly inhibited. This inhibition decreases the decay of excited-state energy as heat and blocks the non-radiative quenching channel. Thus, fluorescent COFs can be designed, synthesized, and precisely tuned to exhibit optimal luminescence properties in comparison with common homogeneous dissolved organic small molecule dyes and can even compete with the currently mainstream organic solid semiconductor-based luminescence materials. This mini-review discusses the major design principle and the state-of-the-art paragon examples of fluorescent COFs and their typical applications in the detection and monitoring of some key explosive chemicals by fluorescence analysis. The challenges and the future direction of fluorescent COFs are also covered in detail in the concluding section.

Effect of beeswax and combinations of its fractions on the oxidative stability of oleogels

Beeswax can be a good structuring agent for edible oleogels. There is controversy about its role in the oleogel oxidation processes. This study investigated the oxidative stability of oleogels and the impact of their composition and texture on this stability. Oleogels were created by structuring sunflower oil with beeswax or combinations of its fractions (6% w/w gelator). Preparative flash chromatography was used to obtain beeswax fractions, which had a diverse composition according to TLC and HPLS-ELSD (hydrocarbons, wax esters, free fatty acids, and alcohols). Different oxidation indices (PV, AV, CDV, TOTOX, volatile organic compounds) of oleogels were evaluated, as well as their textural properties (firmness and Young's modulus) after 20 days of storage at 35 °C. Among the tested samples, unstructured sunflower oil demonstrated the highest oxidative stability. The sample based on hydrocarbons and monoesters was the most stable of the oleogels tested. Hexanal is the most common volatile organic molecule generated during the oxidation of sunflower oil. Oleogels have a more complex profile of volatile compounds, including ketones, alcohols, and terpenes. Beeswax based oleogel's induction period was the shortest. The oxidation rate of oleogels and Young's modulus (r2 = 0.9511, negative), as well as the concentration of free fatty acids (r2 = 0.8195, positive) had a strong correlations. The results show that oleogels structured with beeswax fractions could be beneficial in fat-containing products with improved oxidation resistance.

Organic solvent assisted laser processing of transparent polymer films based on the swelling and penetration behavior

The laser processing of polymer films has significant importance due to the wide applications in various fields. The problems in laser processing of transparent polymer films caused by the poor absorption and current doping methods have prevailed. In this paper, a simple, efficient, and low-cost doping and laser processing method based on polymers’ swelling and penetration behavior was applied to improve the laser processing of transparent polymer films: organic solvent assisted laser processing (SALP). In the SALP method, various common organic solvent molecules (Ethanol, Acetone, N, N-dimethylformamide, Chloroform) were introduced into transparent polydimethylsiloxane (PDMS) films through the swelling and penetration (SP) pretreatment and acted as the dopant to improve the efficiency, capability, and quality of laser processing. Experimental results showed that the SALP method performed higher efficiency and capability (kerf depth: 296.79 ± 11.98 μm, kerf width: 16.59 ± 1.46 μm, kerf aspect ratio: 18.02 ± 1.98) under the same processing conditions compared to the typical laser processing (TLP) method (kerf depth: 137.36 ± 6.47 μm, kerf width: 27.30 ± 1.11 μm, kerf aspect ratio: 5.04 ± 0.31). The roughness of the kerf inner surface and the debris and microcracks on the kerf surface were also significantly reduced. More importantly, this method hardly influenced the original properties of the native polymer films due to the removability of organic solvents. On the one hand, the introduction of organic solvent molecules improved the optical absorption of PDMS films and the heat transfer during laser processing. On the other hand, the excitation, ionization, and dissociation of organic solvent molecules under laser irradiation improved the decomposition process of PDMS, which improved photochemical reaction and promoted the complete and uniform decomposition in laser processing. The SALP method has enlightening significance for improving the laser processing of polymers and investigating the laser ablation mechanism.

Facile synthesis of AgNPs@SNCDs nanocomposites as a fluorescent 'turn on' sensor for detection of glutathione.

The present study illustrates the facile synthesis of silver nanoparticles capped with sulfur and nitrogen co-doped carbon dots (AgNPs@SNCDs) nanocomposites and their application towards the sensitive and selective detection of glutathione (GSH) using a spectrofluorimetry method. SNCDs were synthesized using solvothermal treatment of cysteamine hydrochloride and p-phenylenediamine. The as-fabricated SNCDs were then utilized as capping and stabilizing agents for the preparation of AgNPs@SNCDs nanocomposites using wet chemistry. The size of AgNPs@SNCDs nanocomposites was characterized to be ~37.58 nm or even larger aggregates. Particularly, the quenched fluorescence of AgNPs@SNCDs nanocomposites could be significantly restored upon addition of GSH, and the colour of its solution changed to some extent. The fluorescence intensity ratio of AgNPs@SNCDs nanocomposites at ~450 nm and 550 nm was directly proportional to the GSH concentration within the ranges 8.35-66.83 μM and 66.83-200.5 μM, and the detection limit was 0.52 μM. Furthermore various common organic molecules had no obvious interference in the detection mode. The proposed nanosensor was successfully applied for GSH assay in actual water samples.

High accuracy machine learning identification of fentanyl-relevant molecular compound classification via constituent functional group analysis

Fentanyl is an anesthetic with a high bioavailability and is the leading cause of drug overdose death in the U.S. Fentanyl and its derivatives have a low lethal dose and street drugs which contain such compounds may lead to death of the user and simultaneously pose hazards for first responders. Rapid identification methods of both known and emerging opioid fentanyl substances is crucial. In this effort, machine learning (ML) is applied in a systematic manner to identify fentanyl-related functional groups in such compounds based on their observed spectral properties. In our study, accurate infrared (IR) spectra of common organic molecules which contain functional groups that are constituents of fentanyl is determined by investigating the structure–property relationship. The average accuracy rate of correctly identifying the functional groups of interest is 92.5% on our testing data. All the IR spectra of 632 organic molecules are from National Institute of Standards and Technology (NIST) database as the training set and are assessed. Results from this work will provide Artificial Intelligence (AI) based tools and algorithms increased confidence, which serves as a basis to detect fentanyl and its derivatives.

Quantum Chemical Support on the Two-Dimensional Assembly of Porphyrin Rings in the Application of Energy-Storage Devices

Metal-ion batteries are the revolutionary gadgets of the present decade which still need improvement in efficiency and stability. Porphyrin, a common organic molecule, is considered in the present ...

Melt-salt-assisted direct transformation of solid oxide into atomically dispersed FeN4 sites on nitrogen-doped porous carbon

Abstract Emerging heterogeneous catalysts with metal atomically dispersed on supports (tentatively termed single-atom catalysts, SACs) exhibit many appealing features in a wide variety of catalytic reactions, such as high activity and nearly 100% atom utilization. However, the synthesis of SACs currently requires not only multiple procedures but also appropriate precursors with special structures. Herein, the molten-salt assistance is presented as an effective means that enables the use of common metal oxides (such as Fe2O3 and Co2O3) and small organic molecules as precursors for the preparation of carbon-supported SACs through one-pot pyrolysis. Molten salts as templates that can be easily removed after synthesis also contribute to the formation of porous and nitrogen-doped carbon with a high specific area. More importantly, benefiting from the strong polarizing force of molten salts, the ionic bonds in oxides can be destabilized at high temperature. Subsequently, metal ions released from solid oxides are transformed into atomically dispersed active sites after being trapped by nitrogen (N) atoms on the carbon support. The as-prepared SAC with atomically dispersed Fe–N4 sites demonstrates high activity, outstanding stability and good methanol tolerance in the oxygen reduction reaction (ORR) in both alkaline and acidic media.

Determination of a thiol-based ionic liquid using ultrathin graphitic carbon nitride nanosheets as a nanofluoroprobe

Herein, a simple and green “ON-OFF-ON” sensing system was developed using ultrasonic-exfoliated g-C3N4 nanosheets (CNNS) for the determination of a thiol-based ionic liquid (THIL), which was prominently different from common organic or biothiol molecules in terms of physico-chemical properties. After addition of THIL ([HSBMIM]Br used as an example), the Ag+-quenched CNNS fluorescence (“OFF” state) was recovered to the “ON” state due to reaction between THIL and Ag+ that led to functional group activation on CNNS surfaces. This phenomenon can be explained by competition of THIL with Ag+ because of the strong and specific affinity of –SH groups in THIL for Ag+ and by the reversibility of the Ag+-CNNS coordination reaction. Relevant factors influencing fluorescent recovery were rigorously optimized, including solution pH, incubation time as well as CNNS and THIL concentrations. THIL-recovered fluorescence intensities increased with increasing THIL concentrations providing a linear range of 15–360 nM and limit of detection (LOD) of 4.28 nM (1.07 μg L−1). Testing a series of conventional imidazole-based ionic liquids indicated high specificity for the target analyte and negligible interference effects for the determination of nM-level THIL. The proposed fluorescent sensing method demonstrated excellent feasibility for trace THIL determination in real-world fresh and marine water matrices with high extraction recovery (90.3–107.9%) and high inter- and intra-day precisions (2.3–5.6% relative standard deviations). As far as our information goes, it is the first report on the development of g–C3N4–based “ON-OFF-ON” sensing platform for fast, sensitive and cost-effective determination of nM-level ionic liquids in natural waters.

AMOEBA+ Classical Potential for Modeling Molecular Interactions

Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration, and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model based on the AMOEBA+ framework captures various liquid-phase properties in molecular dynamics simulations while remaining consistent with SAPT energy decompositions, utilizing both ab initio data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.

Heavy atom free 1,1,4,4-tetraphenylbuta-1,3-diene with aggregation induced emission for photodynamic cancer therapy

Common organic molecules usually suffer from aggregation caused quenching (ACQ), which is disadvantageous for imaging guided phototherapy.

Construction of Highly Efficient Carbazol-9-yl-Substituted Benzimidazole Bipolar Hosts for Blue Phosphorescent Light-Emitting Diodes: Isomer and Device Performance Relationships.

Four isomers of carbazol-9-yl-substituted 1,2-diphenylbenzimidazole at 7, 6, 5, and 4 positions, named as 1-CbzBiz, 2-CbzBiz, 3-CbzBiz, and 4-CbzBiz, respectively, have been synthesized. Instead of having an identical molecular weight, the CbzBiz's have their glass transition temperatures ( Tg) spanning a large range from 53 to 90 °C. Their Tg and melting point ( Tm) basically obey the Boyer-Kauzmann rule ( Tg = g· Tm with g ≈ 0.7) on the absolute temperature scale (in kelvins). However, while 1-CbzBiz and 4-CbzBiz demonstrate a small g value of 0.66, which is significantly smaller than other common organic glass molecules, 3-CbzBiz shows an unexpectedly high g value of 0.73, implying higher intermolecular interactions in the glass. These CbzBiz's are suitable hosts for bis[2-(4,6-difluorophenyl)pyridinato- C2, N](picolinato)iridium(III) (FIrpic) in phosphorescence organic light-emitting diodes (PhOLEDs). The optimized PhOLED of indium tin oxide/4,4'-cyclohexylidenebis[ N, N-bis(4-methylphenyl)benzenamine]/4Cbz/4-CbzBiz-FIrpic(15%)/diphenylbis(4-(pyridin-3-yl)phenyl)silane/LiF-Al shows a maximum brightness of 18 760 cd/m2, a current efficiency of 64.1 cd/A, and the external quantum efficiency of 30.9%.

Facile coupling of content design and efficient modulation on the activity of CNT-supported PdAgCu nanoparticle electrocatalysts: Leaching lift-up and annealing fall-off

In the present study, carbon nanotubes (CNTs) decorated with Pd, PdAg and PdAgCu nanocatalysts with various Cu content have been synthesized by a wet chemical route. These catalysts are characterized by X-ray diffraction (XRD), transmission electron spectroscopy (TEM), high-resolution transmission electron spectroscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV) and chronoamperometry (CA). After suffering an efficient electrochemical leaching activation, the post-activated Pd25Ag25Cu50/CNTs catalyst demonstrates the best catalytic activities toward common small organic molecules oxidation reaction including methanol, ethanol and formic acid. Apart from the triggered high electrochemical active surface area (SEAS) owing to surface reconstruction via Cu depletion, the widespread geometric donation (i.e., lattice mismatch, strain, defect and/or dislocations) and strengthened electronic interaction between Pd, Ag and residual buried Cu should play significant roles in the catalytic activity enhancement. It also evidences that the annealing toward as-synthesized catalyst results in a significant decrease of SEAS value, thus engendering a degradation on the mass activities of electrocatalytic oxidation reaction toward small organic molecules.