Formation Of Molecules Research Articles

Formation of CN and CO Molecules in the Envelope of Nova V1391 Cas During the Near-maximum Phase

Moderate-resolution spectra (R ≈ 2700) of the classical nova V1391 Cas were obtained in the near-infrared wavelength range of 0.95–2.45 μm on UT 2020 August 14.41 using the Keck II telescope and the NIRES spectrograph. The spectral analysis revealed simultaneous detection of CO and CN molecular features. The CN red-system band was observed solely in absorption, while the CO first overtone bands, encompassing both 12CO and 13CO, displayed a combination of emission and absorption features at different velocities, resembling a P-Cygni profile. This specific CO profile is unprecedented in classical novae observations. Additionally, the negative velocity shifts in the absorption bands of both CN and CO were found to be consistent with each other.

Formation mechanism of soot in pyrolysis of 2-methylfuran under high temperature based on ReaxFF molecular dynamics simulation

In this study, the detailed mechanism of soot formation under high temperature pyrolysis of 2-methylfuran (2-MF) has been investigated by using Reactive force field molecular dynamics (ReaxFF MD) simulation. The MD analysis shows that 2-MF undergoes ring cleavage and the removal of CO/HCO/CH2CO/CH3CO, which results in the production of the C2-C4 species, promoting the formation of the initial ring molecules. The clustering of hydrocarbons by radical-chain reaction (CHRCR) mechanism plays a significant role in the mass growth of both polycyclic aromatic hydrocarbons (PAHs) and initial soot particles. The main contributors to this process are C2H2 and resonance-stabilized free radicals of C3 and C4. The H-abstraction-C2H2-addition (HACA) mechanism is important for the formation of surface active sites for PAHs and initial soot to some extent. In addition, the soot formation capacity of 2,5-dimethylfuran (25DMF) and 2-MF are compared. Under the same simulation conditions, 25DMF exhibits a higher capacity to form soot. Compared with 2-MF, 25DMF pyrolysis forms more ring-containing species at the initial stage, particularly cyclopentadiene and its derivatives. These compounds have the ability to promote the formation of PAHs, thus providing further support to the experimental-based theory.

In situ visualisation of zeolite anisotropic framework flexibility during catalysis

Zeolites exhibit framework flexibility driving their chemical and catalytic properties. Since the zeolitic pores are extremely small, a slight strain generated in the crystal induces compelling changes in shape, connectivity, accessibility, and the framework chemical properties. These modifications affected the adsorption and desorption of reactants/products and the diffusion within the channels during reaction. Using in situ 3D Bragg coherent X-ray diffraction imaging, we unveil the dynamics of the zeolite structure during catalysis, contraction and/or expansion of its framework also known as zeolite framework flexibility. We imaged three-dimensionally a single faujasite zeolite crystal during the ethanol dehydration reaction revealing anisotropic lattice dynamics simultaneously to guest molecules formation. Understanding zeolite flexibility could permit to tune zeolites properties towards potentially higher adsorption and selectivity.

Non-Adiabatic Excited-State Time-Dependent GW (TDGW) Molecular Dynamics Simulation of Nickel-Atom Aided Photolysis of Methane to Produce a Hydrogen Molecule

Methane photolysis is a very important initiation reaction from the perspective of hydrogen production for alternative energy applications. In our recent work, we demonstrated using our recently developed novel method, non-adiabatic excited-state time-dependent GW (TDGW) molecular dynamics (MD), how the decomposition reaction of methane into a methyl radical and a hydrogen atom was captured accurately via the time-tracing of all quasiparticle levels. However, this process requires a large amount of photoabsorption energy (PAE ∼10.2 eV). Moreover, only one hydrogen atom is produced via a single photon absorption. Transition metal atoms can be used as agents for photochemical reactions, to reduce this optical gap and facilitate an easier pathway for hydrogen production. Here, we explore the photolysis of methane in the presence of a Ni atom by employing TDGW-MD. We show two possibilities for hydrogen-atom ejection with respect to the location of the Ni atom, towards the Ni side or away from it. We demonstrate that only the H ejection away from the Ni side facilitates the formation of a hydrogen molecule with the quasiparticle level corresponding to it having an energy close to the negative ionization potential of an isolated H2 molecule. This is achieved at a PAE of 8.4 eV which is lower compared to that of pristine methane. The results obtained in this work are an encouraging step towards transition metal-mediated hydrogen production via photolysis of hydrocarbons.

Emergence of Optical Activity and Surface Morphology Changes in Racemic Amino Acid Films Under Circularly Polarized Lyman-α Light Irradiation.

The homochirality of life remains one of the most enigmatic issues in the study of the origin of life. A proposed mechanism for symmetry breaking involves irradiation by circularly polarized light (CPL). To investigate the photoreaction of amino acids under CPL irradiation, a vacuum ultraviolet (VUV) CPL irradiation system was developed at the synchrotron light source UVSOR-III. Hydrogen Lyman-α CPL (121.6 nm) is considered a potential asymmetric source in space. Therefore, racemic alanine film samples were irradiated with Lyman-α CPL to explore the photoreaction of biomolecules. Circular dichroism (CD) spectra measurements revealed that irradiation with right- (left-) handed CPL induced a positive (negative) anisotropy factor g in the wavelength range of 180-240 nm. However, the spectra differed from those of enantiopure alanine, exhibiting broad wavelength ranges and no sign change. Liquid chromatography-mass spectrometry (LC-MS) measurements indicate formation of larger molecules, such as oligomeric alanine adducts or modified oligomers after the Lyman-α CPL irradiation. Additionally, CPL irradiation considerably changes the microstructure of the alanine film surface, leading to the formation of circular network aggregates on the scale of 100 nm. The morphology changes in the alanine film and/or the formation of the larger molecules could be possible causes of the modified anisotropy factor spectra compared to those of enantiopure alanine. These findings highlight the need for further research on the photoreaction of biomolecules in solid states under VUV CPL irradiation, particularly in the photoionization energy range, to validate the cosmic scenario of homochirality.

Azole Derivatives: Cutting‐Edge Agents in Cancer Therapy

AbstractMonocyclic 5‐membered heterocycles including imidazoles, thiazoles, oxazoles, and their related compounds have gained significant attention in medicinal chemistry because of their potent anticancerous activity. These small heterocyclic molecules possess versatile properties, including biological activity, absorption, distribution, metabolism, excretion, and chemical diversity that give them immense potential as anticancer agents. It is also a fact that inherent characteristic of azoles to combine with many biological molecules through hydrogen bond, stacking, and hydrophobic interaction makes them effective against almost all cancer types. In the present paper the author discusses the way which is connected with chemical structure of monocyclic azoles and their anticancer activity namely the ability of these compounds to intercalate with DNA, to inhibit some enzymes and to interfere cellular signaling pathways. Interestingly, several azole derivatives have been seen to be effective in preclinical efficacy studies as well as in clinical trials and are considered to be potent in overcoming the problem of resistance and side effects of the common anticancer agents. As the synthetic chemistry progresses, the structural system of the azoles has diversified and development in the pharmacology has become more specific. This has helped in enhancing the formation of new molecules in the azole class with improved selectivity and efficacy. Furthermore, the comprehensive review explains how computational chemistry and structure‐activity relationship (SAR) approaches are applied to the design of future‐generation azole compounds. In light of these facts, this article is designed to give a broad overview of the current state of monocyclic azole‐based anticancer agents in an attempt to further assert its therapeutic promise and spur further attempts at infusing the said agents into the cancer therapeutics fray. The discoveries made in this study may allow the development the radical different therapeutic approaches, which could lead to improved and targeted treatment of cancer.

Journey of complex organic molecules: Formation and transport in protoplanetary disks

Complex organic molecules serve as indicators of molecular diversity. Their detection on comets, planets, and moons has prompted inquiries into their origins, particularly the conditions conducive to their formation. One hypothesis suggests that the UV irradiation of icy grains in the protosolar nebula generates significant molecular complexity, a hypothesis supported by experiments on methanol ice irradiation. We investigated the irradiation of methanol ice particles as they migrate through the protosolar nebula. Our objective is to ascertain whether the encountered conditions facilitate the formation of complex organics molecules, and we leverage experimental data in our analysis. We developed a two-dimensional model that describes the transport of pebbles during the evolution of the protosolar nebula, employing a Lagrangian scheme. This model computes the interstellar UV flux received by the particles along their paths, which we compared with experimental values. On average, particles ranging from 1 to 100 mu m in size, released at a local temperature of 20 K, undergo adequate irradiation to attain the same molecular diversity as methanol ice during the experiments within timescales of 25 kyr of protosolar nebula evolution. In contrast, 1 cm sized particles require 911 kyr of irradiation to reach similar molecular diversity, making comparable molecular complexity unlikely. Similarly, particles ranging from 1 to 100 mu m in size, released at a local temperature of 80 K, receive sufficient irradiation after 141 and 359 kyr. In contrast, 1 cm sized particles would require several million years to receive this level of irradiation, which is infeasible since they cross the iceline within approximately 500 kyr. The particles readily receive the irradiation dose necessary to generate the molecular diversity observed in the experiments within the outer regions of the disk. Our model, combined with future irradiation experiments, can provide additional insights into the specific regions where the building blocks of planets form.

Revisiting the Vertical Distribution of H i Absorbing Clouds in the Solar Neighborhood. II. Constraints from a Large Catalog of 21 cm Absorption Observations at High Galactic Latitudes

The cold neutral medium (CNM) is where neutral atomic hydrogen (H i) is converted into molecular clouds, so the structure and kinematics of the CNM are key drivers of galaxy evolution. Here we provide new constraints on the vertical distribution of the CNM using the recently developed kinematic_scaleheight software package and a large catalog of sensitive H i absorption observations. We estimate the thickness of the CNM in the solar neighborhood to be σ z ∼ 50–90 pc, assuming a Gaussian vertical distribution. This is a factor of ∼2 smaller than typically assumed, indicating that the thickness of the CNM in the solar neighborhood is similar to that found in the inner Galaxy, consistent with recent simulation results. If we consider only structures with H i optical depths τ > 0.1 or column densities N(H i) > 1019.5 cm−2, which recent work suggests are thresholds for molecule formation, we find σ z ∼ 50 pc. Meanwhile, for structures with τ < 0.1 or column densities N(H i) < 1019.5 cm−2, we find σ z ∼ 120 pc. These thicknesses are similar to those derived for the thin- and thick-disk molecular cloud populations traced by CO emission, possibly suggesting that cold H i and CO are well mixed. Approximately 20% of CNM structures are identified as outliers, with kinematics that are not well explained by Galactic rotation. We show that some of these CNM structures—perhaps representing intermediate-velocity clouds—are associated with the Local Bubble wall. We compare our results to recent observations and simulations, and we discuss their implications for the multiphase structure of the Milky Way’s interstellar medium.

Carbon‐ and Nitrogen‐Based Complexes as Photocatalysts for Prebiotic and Oxygen Chemistry during Earth Evolution

AbstractSunlight has long served as primary energy source on our planet, shaping the behavior of living organisms. Extensive research has been dedicated to unraveling the evolutionary pathways involved. When the formation of Earth atmosphere, it primarily consisted of small gas molecules, which are considered crucial for the emergence of life. Recent demonstrations have shown that these molecules can also be transformed into semiconductors, with the potential to harness solar energy and catalyze chemical reactions as photocatalysts. Building upon this research, this minireview focuses on the potential revolutionary impact of photocatalysis on Earth. Initially, it examines key reactions, such as the formation of prebiotic molecules and the oxygen evolution reaction via water oxidation. Additionally, various C−N complexes in photocatalysts are explored, showcasing their roles in catalyzing chemical reactions. The conclusion and outlook provide a potential pathway for the evolution of Earth, shedding light on the significance of metal‐free photocatalysts in development of Earth.

A rapid and scalable method for visible light induced bromination of uracil derivatives in a falling film looping photoreactor.

Visible light induced green synthesis of 5-bromouracil derivatives using N-bromosuccinimide (NBS) in acetonitrile under batch operation with a constant photon flux of 46 μmol s-1 is reported. This methodology has shown excellent tolerance with various 6-substituted and N-substituted uracils and is also applicable for various pyrimidine and arene derivatives. The reaction proceeded through the formation of a bromine molecule via a radical pathway followed by an electrophilic substitution reaction, and this hybrid nature of the reaction pathway in the presence of light made the process faster. We successfully synthesized twenty-one derivatives and characterized them using various spectroscopic methods. Finally, the three different modules of the looping falling film reactor were used to show the successive scalability of the process with comparable photonic characteristics and reaction conditions. We achieved milligram to multigram scale reaction with almost equal efficiency and maximum productivity up to 1.2 kg per day.

Deciphering Doping Effects in a V-Doped Ni Catalyst for Hydrogen Electrooxidation.

The improved performance of soluble metal-doped Ni catalysts is perplexed by the evolvable surface structures in the alkaline electrolytes for hydrogen oxidation reaction (HOR). Herein, V-doped Ni nanoparticles, as a proof of concept, were carefully evaluated to explore the intrinsic function of the enthetic V-species in assisting the HOR kinetic improvement. As expected, it exhibits a mass-normalized kinetic current density of 50.34 mA mgNi-1, more than 12 times that of the Ni counterpart without the introduction of V. Systematic investigations prove that the surface V-species, including the V-oxides and the doped V atoms at the outmost layer, would be dissolved into the electrolytes during the alkaline HOR process. The remaining V-dopants inside the nanoparticles would rationally weaken the hydroxyl binding energy (OHBE) of the Ni-based surfaces, thereby accelerating the formation of water molecules. We also uncover that Ni is located at the overstrong branch of the OHBE-described volcano plot through theoretical calculations and alkali-metal cation probe experiments, and weakening the OHBE by internal V-doping can leave the activity to the volcanic apex.

Hippo pathway in cancer cells induces NCAM1+αSMA+ fibroblasts to modulate tumor microenvironment

Cancer cells adeptly manipulate the tumor microenvironment (TME) to evade host antitumor immunity. However, the role of cancer cell-intrinsic signaling in shaping the immunosuppressive TME remains unclear. Here, we found that the Hippo pathway in cancer cells orchestrates the TME by influencing the composition of cancer-associated fibroblasts (CAFs). In a 4T1 mouse breast cancer model, Hippo pathway kinases, large tumor suppressor 1 and 2 (LATS1/2), promoted the formation of neural cell adhesion molecule 1 (NCAM1)+alpha-smooth muscle actin (αSMA)+ CAFs expressing the transforming growth factor-β, which is associated with T cell inactivation and dysfunction. Depletion of LATS1/2 in cancer cells resulted in a less immunosuppressive TME, indicated by the reduced proportions of NCAM1+αSMA+ CAFs and dysfunctional T cells. Notably, similar Hippo pathway-induced NCAM1+αSMA+ CAFs were observed in human breast cancer, highlighting the potential of TME-manipulating strategies to reduce immunosuppression in cancer immunotherapy.

Nearly linear orbital molecules on a pyrochlore lattice.

The interplay of spin-orbit coupling with other relevant parameters gives rise to the rich phase competition in complex ruthenates featuring octahedrally coordinated Ru4+. While locally, spin-orbit coupling stabilizes a nonmagnetic Jeff = 0 state, intersite interactions resolve one of two distinct phases at low temperatures: an excitonic magnet stabilized by the magnetic exchange of upper-lying Jeff = 1 states or Ru2 molecular orbital dimers driven by direct orbital overlap. Pyrochlore ruthenates A2Ru2O7 (A = rare earth, Y) are candidate excitonic magnets with geometrical frustration. We synthesized In2Ru2O7 with covalent In─O bonds. This pyrochlore ruthenate hosts a local Jeff = 0 state at high temperatures; however, at low temperatures, it forms a unique nonmagnetic ground state with nearly linear Ru─O─Ru molecules, in stark contrast to other A2Ru2O7 compounds. The disproportionation of covalent In─O bonds drives Ru2O molecule formation, quenching not only the local spin-orbit singlet but also geometrical frustration.

Spontaneous Formation of π-Conjugated Polymeric Colloidal Molecules Through Stepwise Coacervation and Symmetric Compartmentalization.

Coacervation, the phase separation of liquid induced by polymeric solutes, sometimes results in the formation of oligomeric clusters of droplets. The morphology of the clusters is non-uniform because the clustering is a consequence of the random collisions of the drifting droplets. Herewereportdistinctively organized coacervation, yielding colloidal molecules with monodisperse size, morphological symmetry, and compositional heterogeneity.Weinvestigate the coacervation of a mixture of two types of synthetic polymers and find that one of the polymers coacervates first and serves as a core droplet, on which the other polymer coacervates subsequently to form satellite droplets. The satellite droplets arrange themselves symmetrically around the core and solidify without losing the morphology. The number of satellites and their symmetry are modulable depending on the chemical affinity and the diameter of the droplets. This finding highlights the capability of coacervation as a non-templated and non-covalent pathway to form aspherical colloidal materials with structural and functional complexity.

Novel Dissymmetric Formal Quinoidal Molecules End-Capped by Dicyanomethylene and Triphenylphosphonium.

A number of quinoidal molecules with symmetric end-capping groups, particularly dicyanomethylene units, have been synthesized for organic optoelectronic materials. In comparison, dissymmetric quinoidal molecules, characterized by end-capping with different groups, are less explored. In this paper, we present the unexpected formation of new formal quinoidal molecules, which are end-capped with both dicyanomethylene and triphenylphosphonium moieties. The structures of these dissymmetric quinoidal molecules were firmly verified by single crystal structural analyses. On the basis of the control experiments and DFT calculations, we proposed the reaction mechanism for the formation of these dissymmetric quinoidal molecules. The respective zwitterionic forms should make contributions to the ground state structures of these quinoidal molecules based on the analysis of their bond lengths and aromaticity and Mayer Bond Orbital (MBO) calculation. This agrees well with the fact that negative solvatochromism was observed for these quinoidal molecules. Although these new quinoidal molecules are non-emissive both in solutions and crystalline states, they become emissive with quantum yields up to 51.4 % after elevating the solvent viscosity or dispersing them in a PMMA matrix. Interestingly, their emissions can also be switched on upon binding with certain proteins, in particular with human serum albumin.

Novel Dissymmetric Formal Quinoidal Molecules End‐Capped by Dicyanomethylene and Triphenylphosphonium

AbstractA number of quinoidal molecules with symmetric end‐capping groups, particularly dicyanomethylene units, have been synthesized for organic optoelectronic materials. In comparison, dissymmetric quinoidal molecules, characterized by end‐capping with different groups, are less explored. In this paper, we present the unexpected formation of new formal quinoidal molecules, which are end‐capped with both dicyanomethylene and triphenylphosphonium moieties. The structures of these dissymmetric quinoidal molecules were firmly verified by single crystal structural analyses. On the basis of the control experiments and DFT calculations, we proposed the reaction mechanism for the formation of these dissymmetric quinoidal molecules. The respective zwitterionic forms should make contributions to the ground state structures of these quinoidal molecules based on the analysis of their bond lengths and aromaticity and Mayer Bond Orbital (MBO) calculation. This agrees well with the fact that negative solvatochromism was observed for these quinoidal molecules. Although these new quinoidal molecules are non‐emissive both in solutions and crystalline states, they become emissive with quantum yields up to 51.4 % after elevating the solvent viscosity or dispersing them in a PMMA matrix. Interestingly, their emissions can also be switched on upon binding with certain proteins, in particular with human serum albumin.

Mechanistic Insights into the Evolution of Graphitic Carbon from Sulfur Containing Polar Aromatic Feedstock.

In the realm of carbon fiber research, a variety of structural configurations is noted, comprising crystalline, noncrystalline, and semicrystalline forms. Recent investigations into this domain have revealed an array of intriguing phases of carbon, among which amorphous graphite is the most notable for its unique mechanical, thermal, and electrical properties that arise from its inherent topological disorders. In this study, we utilized the ReaxFF molecular dynamics (MD) simulations to investigate the carbonization and graphitization processes involved in the production of amorphous graphite from benzothiophene, a sulfur-containing polar aromatic precursor. We developed C/H/S ReaxFF force field parameters to describe the high-temperature chemistry of benzothiophene. Our investigation reveals the reaction mechanisms, providing critical insights into the underlying chemical processes toward the formation of amorphous graphite and the structural characteristics of the end products. The formation of volatile gaseous molecules and their continuous elimination led to the development of noncontinuous layered graphite structures analogous to amorphous graphite consisting of pentagons, hexagons, and heptagons. These findings offer unprecedented insights into the carbonization and graphitization processes of sulfur-containing heavy-end aromatic feedstock. This knowledge lays the groundwork for advancing synthesis methods and developing amorphous graphite materials with specific properties.

Power of molecules: The morphological-informational content of matter

Among the many questions that have occupied scholars of all historical periods for thousands of years, the question regarding the origin and evolution of matter is the most debated and far from having obtained a definitive answer. If we exclude the theories proposed by quantum physics, which are considered the most plausible, for the rest we are groping in the dark. In this article I’m going to try to give some answers, both on the mechanism of formation of molecules, and on their functional significance, without having the presumption of giving positive answers. It should be considered an invitation to discussion, a rational comparison, among those interested in the topic. In the article, I draw attention to an aspect, which I consider fundamental, and on which I have published several works. This is the mode of iteration, communication and recognition between molecules, which is the fundamental stage to obtain any materially detectable and significant result for the emergence of new entities. It is also the event that allows random evolution and without an apparent preordained or pre-established end. Even if the ultimate goal of this complex evolutionary activity is unknown to us, we cannot avoid seeking it.

Similarity of Near-Threshold Energy Dependence of Positronium Formation and Photoionization in Molecules.

High-resolution measurements of the positronium formation cross sections for positron energies from threshold to 10eV are presented for aniline (C_{6}H_{5}NH_{2}), pyridine (C_{5}H_{5}N), and cyclopentane (C_{5}H_{10}). The data reveal that the measured energy dependence of the cross sections on the excess energy in the near-threshold region (1-2eV) is nearly identical to that of the corresponding photoionization cross sections. This similarity occurs despite the difference between the basic threshold laws for processes without and with a Coulomb interaction between the final-state particles. It is proposed here that the near-threshold behavior of these two different ionization processes is governed by the vibrational dynamics of the final-state cation. This is supported by comparison of the data with the calculated spectrum of vibronic intensities for the pyridine cation [Trofimov etal., J. Chem. Phys. 153, 164307 (2020)JCPSA60021-960610.1063/5.0024446].

Development of a ReaxFF Reactive Force Field for Pt/Cl Systems with Application to Platinum Metal Etching with Chlorine and Hydrogen Chloride Gases.

In this study, we present the development of a ReaxFF Pt/Cl/H reactive force field designed to elucidate the etching process by Cl for Pt surfaces. The ReaxFF force field parameters were optimized based on a quantum mechanical training set, which included adsorption energies of Cl and dissociation of HCl on Pt(100) and Pt(111) surfaces, energy/volume relations of PtCl2 crystals, and Cl diffusion on Pt(100) and Pt(111) surfaces. The predictive capability of the force field was further established through molecular dynamics simulations, which investigated the interactions of Cl2 and HCl molecules with the (100) and (111) surfaces of c-Pt crystalline solid slabs. A comparative analysis revealed that the Pt (100) surface exhibited higher susceptibility to chlorination and etching, leading to a more dominant removal of surface Pt atoms, whereas the Pt (111) surface showed greater resistance to these processes. This resistance impeded the access of Cl atoms to the Pt surface, resulting in a slower formation of PtxCly molecules. The etching ratios between HCl and Cl2 were compared with experimental results, yielding satisfactory agreement. This indicates that the developed ReaxFF protocol serves as a valuable tool for studying atomistic-scale details of the etching process in platinum metal systems.