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DENDRAL program used to construct all possible acyclic structural isomers of C, H, N and O
Ab initio infrared intensities and dipole moment derivatives expressed in atomic polar tensor form are calculated using the 4-31 and 6-31G(double asterisk) basis sets for the isoelectronic HCN, HNC, CO, HCO(+), and HOC(+) series of molecules. The calculated atomic polar tensors are analyzed in terms of the charge-charge flux-overlap model, which is found to be useful in explaining some of the trends observed in the dipole moment derivatives for this series of molecules. A detailed examination of the dipole moment derivatives for the structural isomers indicates some of the ways in which experimental atomic polar tensors for one isomer should be modified to predict infrared intensities for the other isomer. The absolute intensities calculated for the HCO(+) and HOC(+) ions are believed to be accurate to within a factor of 2 and thus should be useful in astrophysical applications.
All of the eighteen possible seven-carbon acyclic primary alpha-amino alkanoic acids have been positively identified in a hot-water extract of the Murchison meteorite by the combined use of gas chromatography-mass spectrometry, ion exchange chromatography and reversed-phase chromatography. None of these amino acids has previously been found in meteorites or in any other natural material. They range in concentration from less than or equal to 0.5 to 5.3 nmol/g. Configuration assignments were made for 2-amino-3,4-dimethylpentanoic acid and allo-2-amino-3,4-dimethylpentanoic acid and the diasteromer ratio was determined. Fifty-five amino acids have now been positively identified in the Murchison meteorite, 36 of which are unknown in terrestrial materials. This unique suite of amino acids is characterized by the occurrence of all structural isomers within the two major classes of amino acids represented, by the predominance of branched chain isomers, and by an exponential decline in amount with increasing carbon chain length within homologous series. These characteristics of the Murchison amino acids are suggestive of synthesis before incorporation into a parent body.
Several thermally stable tough linear polyimides containing amide linkages were synthesized which have application as matrix resins in graphite reinforced structures. Isomers of diaminobenzanilide were reacted with 3,3-prime,4,4-prime-benzophenonetetracarboxylic dianhydride, and then thermally converted to the polyamide-imide. Polymers prepared from unsubstituted amide diamines and from N-substituted amide diamines exhibited high inherent viscosities and glass transition temperatures. The mechanical properties of these polymers were found to be superior to those of LARC-TPI.
Evaluating the water-soluble organic composition of carbonaceous chondrites is key to understanding the inventory of organic matter present at the origins of the solar system and the subsequent processes that took place inside asteroid parent bodies. Here, we present a side-by-side analysis and comparison of the abundance and molecular distribution of aliphatic amines, aldehydes, ketones, mono- and dicarboxylic acids, and free and acid-releasable cyanide species in the CM2 chondrites Aguas Zarcas and Murchison. The Aguas Zarcas meteorite is a recent fall that occurred in central Costa Rica and constitutes the largest recovered mass of a CM-type meteorite after Murchison. The overall content of organic species we investigated was systematically higher in Murchison than in Aguas Zarcas. Similar to previous meteoritic organic studies, carboxylic acids were one to two orders of magnitude more abundant than other soluble organic compound classes investigated in both meteorite samples. We did not identify free cyanide in Aguas Zarcas and Murchison; however, cyanide species analyzed after acid-digestion of the water-extracted meteorite mineral matrix were detected and were quantified at slightly higher abundances in Aguas Zarcas compared to Murchison. Although there were differences in the total abundances of specific compound classes, these two carbonaceous chondrites showed similar isomeric distributions of aliphatic amines and carboxylic acids, with common traits such as a complete suite of structural isomers that decreases in concentration with increasing molecular weight. These observations agree with their petrologic CM type-2 classification, suggesting that these meteorites experienced similar organic formation processes and/or conditions during parent body aqueous alteration.
The lack of pyrimidine diversity in meteorites remains a mystery since prebiotic chemical models and laboratory experiments have predicted that these compounds can also be produced from chemical precursors found in meteorites. Here we report the detection of nucleobases in three carbonaceous meteorites using state-of-the-art analytical techniques optimized for small-scale quantification of nucleobases down to the range of parts per trillion (ppt). In addition to previously detected purine nucleobases in meteorites such as guanine and adenine, we identify various pyrimidine nucleobases such as cytosine, uracil, and thymine, and their structural isomers such as isocytosine, imidazole-4-carboxylic acid, and 6-methyluracil, respectively. Given the similarity in the molecular distribution of pyrimidines in meteorites and those in photon-processed interstellar ice analogues, some of these derivatives could have been generated by photochemical reactions prevailing in the interstellar medium and later incorporated into asteroids during solar system formation. This study demonstrates that a diversity of meteoritic nucleobases could serve as building blocks of DNA and RNA on the early Earth.
The chirality of amino acids in extraterrestrial materials may provide an insight into the origin of the essential L-enantiopure amino acids in the terrestrial biosphere. In 2020, the Hayabusa2 mission succeeded in bringing back surface materials from the C-type asteroid (162173) Ryugu to the Earth. Amino acids were one of the targeted organic molecules to be studied in the Ryugu samples. To analyze the various structural isomers of amino acids, which were expected to be present, from the limited amount of the returned samples, the development of a highly-sensitive and selective analytical method was necessary. In the present study, a three-dimensional high-performance liquid chromatography (3D-HPLC) system has been developed for the enantioselective determination of five proteinogenic and three non-proteinogenic amino acids in the Ryugu samples, in which amino acids in the sample were separated by reversed-phase, anion-exchange and enantioselective columns after the fluorescence derivatization with 4-fluoro-7-nitro-2,1,3-benzoxadiozole. The applicability of the analytical system to the extraterrestrial samples was evaluated by analyzing several types of carbonaceous meteorites before applying the system to the Ryugu samples. In the analysis of the Ryugu samples, all of the target amino acids were successfully determined quantitatively. Non-proteinogenic amino acids including 2-amino-n-butyric acid, isovaline and norvaline, rarely present in the terrestrial environment, were found as almost racemic mixtures with 47.1 to 55.2%L.
We report primordial aqueous alteration signatures in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu by the Hayabusa2 spacecraft of JAXA. Newly identified low-molecular-weight hydroxy acids (HO-R-COOH) and dicarboxylic acids (HOOC-R-COOH), such as glycolic acid, lactic acid, glyceric acid, oxalic acid, and succinic acid, are predominant in samples from the two touchdown locations at Ryugu. The quantitative and qualitative profiles for the hydrophilic molecules between the two sampling locations shows similar trends within the order of ppb (parts per billion) to ppm (parts per million). A wide variety of structural isomers, including α- and β-hydroxy acids, are observed among the hydrophilic molecules. We also identify pyruvic acid and dihydroxy and tricarboxylic acids, which are biochemically important intermediates relevant to molecular evolution, such as the primordial TCA (tricarboxylic acid) cycle. Here, we find evidence that the asteroid Ryugu samples underwent substantial aqueous alteration, as revealed by the presence of malonic acid during keto–enol tautomerism in the dicarboxylic acid profile. The comprehensive data suggest the presence of a series for water-soluble organic molecules in the regolith of Ryugu and evidence of signatures in coevolutionary aqueous alteration between water and organics in this carbonaceous asteroid.
A series of hybrid thiosemicarbazone-alkylthiocarbamate copper complexes with similar electronic environments but distinct physical structures have been prepared, characterized, and evaluated for antiproliferation activity. The complexes include the constitutional isomers (1-phenylpropane-1-imine-(O-ethylthiocarbamato)-2-one-(N-methylthiosemicarbazonato))copper(II) (CuL 1 ) and (1-phenylpropane-1-one-(N-methylthiosemicarbazonato)-2-imine-(O-ethylthiocarbamato))copper(II) (CuL 2 ) along with (1-propane-1-imine-(O-ethylthiocarbamato)-2-one-(N-methylthiosemicarbazonato))copper(II) (CuL 3 ). Complexes CuL 1 and CuL 2 differ in the positions of the pendent thiosemicarbazone (TSC) and alkylthiocarbamate (ATC) moieties on the 1-phenylpropane backbone. Complex CuL 3 employs a propane backbone with the TSC in the 2-position as in CuL 1 . The isomer pair CuL 1 and CuL 2 have equivalent electronic environments with indistinguishable Cu II/I potentials (E 1/2 = -0.86 V vs. ferrocenium/ferrocene) and electron paramagnetic resonance (EPR) spectra (g ∥ = 2.26, g ⊥ = 2.08). The electronic structure of CuL 3 has a similar E 1/2 of -0.84 V and identical EPR parameters to CuL 1, 2 . Single crystal X-ray diffraction studies confirm a consistent donor environment with no substantial variation in the Cusingle bondN or Cusingle bondS bond distances and angles between the complexes. The antiproliferation activities of the CuL 1–3 were evaluated against the lung adenocarcinoma cell line (A549) and nonmalignant lung fibroblast cell line (IMR-90) using the MTT assay. CuL 1 had the highest A549 activity ( A549 EC 50 = 0.065 μM) and selectivity ( IMR-90 EC 50 / A549 EC 50 = 20). The constitutional isomer CuL 2 displayed decreased A549 activity (0.18 μM) and selectivity (10.6). The complex CuL 3 displayed activity (0.009 μM) similar to CuL 1 but with a lack of selectivity (1.0). Cellular copper loading determined by ICP-MS was consistent with the activity and selectivity trends. The complexes CuL 1–3 did not induce reactive oxygen species (ROS) generation.
Structural identification of geometric isomer of tetrameric phenylphosphonitrilic chloride via IR SPECTROSCOPY and proton nuclear magnetic resonance
Despite their widespread use, the mechanisms governing the synthesis of zeolite catalysts are still poorly understood. A notable example of this problem is the uncertainty surrounding the influence of synthesis conditions on the placement of Al atoms in the zeolite framework which determines the active sites available for catalytic species. In this work, the role of the cis to trans isomer ratio of the OSDA N,N-dimethyl-3-5-dimethylpiperidinium on the energetics of 26 distinct Al pair distributions in SSZ-39 is examined both in the presence and absence of Na using density functional theory calculations. The initial orientation of the OSDA was found to have a significant impact on the final energies present, necessitating the screening of a large number of initial orientations with force field calculations and single point DFT calculations. Ground state energies were found to vary significantly with the ratio of cis to trans OSDAs with a Boltzmann distribution revealing the most likely Al pair distributions shift from sharing the same 8 membered rings to sharing the same double six membered rings to having no shared subunits as one increases the amount of cis OSDA present within the framework. The presence of Na was found to favor Al pair distributions where both Als occupied the same 6-membered ring. When an implicit solvent model was used to evaluate ground state energies the ideal Na sites shifted from 6-membered rings to empty SSZ-39 cages while OSDA positions and orientations remained largely the same. To provide insight on how kinetic factors may influence Al distributions, formation energies we calculated for connected double six membered rings. Further, these formation energies revealed a preference for Al pairs to occupy the same 4-membered ring which indicates kinetic and thermodynamic control may lead to different Al distributions in SSZ-39.
Nuclear isomers correspond to excited states in nuclides with finite lifetimes. Here, after the discovery of isotopes–different nuclides of the same element–in 1913 by Frederick Soddy [Citation1], Otto Hahn postulated in 1921 [Citation2] that there are even different metastable states within one isotope. In analogy to chemical isomers, which are the same compounds with distinct structures, nuclear isomers have the same number of protons and neutrons but in different configurations.
Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.
Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.
Efficient separation of physicochemically similar alkanes is of vital importance. Adsorptive separation utilizing porous materials such as metal–organic frameworks with tunable pore structure and surface functionality represents an energy-efficient technology. In this study, we demonstrate successful separation of alkanes with varying degree of branching using a microporous nickel isonicotinate framework, Ni(4-PyC) 2 . Its 2-fold interpenetrated diamondoid structure with well-suited pore size enables selective adsorption of linear and monobranched hexane isomers, while excluding dibranched isomer. Breakthrough experiments validated its capability to completely discriminate all three hexane isomers. Ab initio calculations combined with in situ infrared spectroscopic analysis unveiled the nature of host–guest interactions and differences in the binding energies and diffusion barriers among the isomers. Furthermore, having well-balanced adsorption uptakes (146 and 79 mg g –1 of nHEX and 3MP), high nHEX/DMB uptake ratio (12.2) and fast kinetics, Ni(4-PyC) 2 stands out as a promising adsorbent for complete separation of hexane isomers under ambient conditions.
The tungsten carbide α-WC(0001) surface, an active system for the activation of H 2 and important hydrogenation processes involving unsaturated hydrocarbons, can serve as a support of bimetallic clusters to produce materials with unique catalytic properties, opening routes for a wide range of technical applications. In particular, Cu x Pd y clusters are of particular interest because they combine metals with different properties. A stochastic method was applied to obtain the geometry of Cu x Pd y (x + y = 4) bare clusters, evaluating thousands of possibilities to obtain stable structures, yielding one isomer for Cu 4 , Cu 2 Pd 2 , Cu 1 Pd 3 , and Pd 4 and two isomers for Cu 3 Pd 1 . These clusters were supported on C and W terminations of the tungsten carbide (0001) surface, exploring all of the binding possibilities. The adsorption energies on the C and W terminations are in the ranges from −2.51 to −3.02 eV and from −2.26 to −3.30 eV, respectively. The strongest and weakest binding was seen for monometallic Cu 4 and Pd 4 clusters on both C and W terminations, while the Cu-Pd bimetallics have intermediate adsorption energies but lack a clear trend in terms of composition. The location of Cu x Pd y clusters over the (0001) surface induces a decrease in the work function relative to the pristine surface, while the cluster-surface Bader charge transfer and variations in the partial density of states point to changes in the electronic structure of the carbide atoms upon binding of the metallic clusters. The d-band center of the Cu x Pd y deposited on WC(0001) indicates an intermediate reactivity among Cu(111) and Pd(111) surfaces, modulating the reactivity with small numbers of Cu and Pd atoms, i.e., atom economy in catalyst design. The likelihood of existence of the most stable Cu x Pd y (x + y = 4) clusters in the temperature range of 298-400 K is 100%. The composite Cu x Pd y /α-WC(0001) (x + y = 4), is a nontrivial system since 22 isomers are needed to completely describe its structural properties. Among the isomers, seven structures are necessary to represent Cu 3 Pd 1 /α-WC(0001), five for Pd 4 /α-WC(0001), two for Cu 4 /α-WC(0001), and four for Cu 2 Pd 2 /α-WC(0001) and Cu 1 Pd 3 /α-WC(0001). The large number of cluster isomers supported on the tungsten carbide surface opens the door for several applications in the heterogeneous catalysis of the Cu x Pd y /α-WC(0001) composite, with the possibility of modulating the geometric, electronic, and chemical properties according to a desired application. Test studies for the adsorption of CO 2 indicate that the Cu x Pd y /α-WC(0001) composites are highly active for the adsorption and decomposition of the molecule, with bimetallic and admetal-carbide interactions playing a key role in the binding performance. In conclusion, this high activity indicates that these systems should be useful as catalysts for the conversion of CO 2 to oxygenates or light alkanes.
High-efficiency separation of hexane isomers through selective molecular exclusion represents an important yet challenging task in the petrochemical industry. It has stringent requirements on the adsorbents' pore shape and dimensions. Here we report the complete exclusion of branched hexanes from their linear isomer by an aluminum metal-organic framework, CAU-21-ODB (ODB = 4,4'-oxydibenzoate) with high stability. The unique gourd-shaped channels with suitable pore aperture lead to substantial uptake of nHEX (141 mg/g at 30 °C) but negligible adsorption of its branched isomers under identical conditions. Furthermore, the capability of CAU-21-ODB for the separation of hexane isomers has been verified by multicomponent breakthrough experiments. DFT calculations further confirm the size-exclusion based separation mechanism.
Excited structures in 104 Mo were populated by β decays of the ground and isomeric states in the neutron-rich nucleus 104 Nb. The beams were produced by the CARIBU facility at Argonne National Laboratory, re-accelerated by the ATLAS accelerator and implanted on a moving-tape system in the middle of the GAMMASPHERE array. Separate decay schemes for the two β-decaying states in 104 Nb were constructed for the first time. The structure of the isomers are discussed in the framework of the deformed Nilsson model and systematics of known quasiparticle structures in neighboring nuclei.