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Forty-one isomers of Al[sub.2] C[sub.4] H[sub.2] that lie within 50 kcal mol[sup.−1] are theoretically identified in this work using density functional theory. Among these, isomers 3 and 14 contain a planar tetracoordinate carbon (ptC) atom that lies at 3.3 and 16.9 kcal mol[sup.−1] , respectively, and are above the global minimum geometry 1 at the ωB97XD/6-311++G(2d,2p) level of theory. The other ten isomers that also contain unique bonding features are isomers 4, 18, 20, 21, 22, 27, 28, 31, 34, and 40. Out of these isomers, 4, 18, 20, 22, 27, 28, and 34 contain planar tetracoordinate aluminum (ptAl) whereas isomers 31 and 40 contain both ptC and ptAl atoms. Chemical bonding characteristic features are thoroughly analyzed for all these eleven isomers with various bonding and topological quantum chemical tools, such as NBO, AdNDP, WBI, and ELF, except isomer 27 due to the observed elongated Al-Al bond length. The current results indicate that ptC isomer 3 is more stable than other isomers because electron delocalization is more prevalent and it also has double aromaticity as observed from the ELF, NICS, and AdNDP analysis. Further, the structural stability of these isomers is investigated through ab initio molecular dynamics (AIMD) simulation. Isomer 21 shows the planar pentacoordinate aluminum but it is observed as a kinetically unstable geometry from AIMD and, further, one could notice that it isomerizes to isomer 12.

Computational modeling of chemical and biological systems at atomic resolution is a crucial tool in the chemist’s toolset. The use of computer simulations requires a balance between cost and accuracy: quantum-mechanical methods provide high accuracy but are computationally expensive and scale poorly to large systems, while classical force fields are cheap and scalable, but lack transferability to new systems. Machine learning can be used to achieve the best of both approaches. Here we train a general-purpose neural network potential (ANI-1ccx) that approaches CCSD(T)/CBS accuracy on benchmarks for reaction thermochemistry, isomerization, and drug-like molecular torsions. This is achieved by training a network to DFT data then using transfer learning techniques to retrain on a dataset of gold standard QM calculations (CCSD(T)/CBS) that optimally spans chemical space. The resulting potential is broadly applicable to materials science, biology, and chemistry, and billions of times faster than CCSD(T)/CBS calculations. Computational modelling of chemical systems requires a balance between accuracy and computational cost. Here the authors use transfer learning to develop a general purpose neural network potential that approaches quantum-chemical accuracy for reaction thermochemistry, isomerization, and drug-like molecular torsions.

Glycans have diverse physiological functions, ranging from energy storage and structural integrity to cell signalling and the regulation of intracellular processes 1 . Although biomass-derived carbohydrates (such as d -glucose, d -xylose and d -galactose) are extracted on commercial scales, and serve as renewable chemical feedstocks and building blocks 2 , 3 , there are hundreds of distinct monosaccharides that typically cannot be isolated from their natural sources and must instead be prepared through multistep chemical or enzymatic syntheses 4 , 5 . These ‘rare’ sugars feature prominently in bioactive natural products and pharmaceuticals, including antiviral, antibacterial, anticancer and cardiac drugs 6 , 7 . Here we report the preparation of rare sugar isomers directly from biomass carbohydrates through site-selective epimerization reactions. Mechanistic studies establish that these reactions proceed under kinetic control, through sequential steps of hydrogen-atom abstraction and hydrogen-atom donation mediated by two distinct catalysts. This synthetic strategy provides concise and potentially extensive access to this valuable class of natural compounds. Various rare sugars that cannot be isolated from natural sources are synthesized using light-driven epimerization, a process which may find application in other synthetic scenarios.

Unlike proteins, glycan chains are not directly encoded by DNA, but by the specificity of the enzymes that assemble them. Theoretical calculations have proposed an astronomical number of possible isomers (> 10 12 hexasaccharides) but the actual diversity of glycan structures in nature is not known. Bacteria of the Bacteroidetes phylum are considered primary degraders of polysaccharides and they are found in all ecosystems investigated. In Bacteroidetes genomes, carbohydrate-degrading enzymes (CAZymes) are arranged in gene clusters termed polysaccharide utilization loci (PULs). The depolymerization of a given complex glycan by Bacteroidetes PULs requires bespoke enzymes; conversely, the enzyme composition in PULs can provide information on the structure of the targeted glycans. Here we group the 13,537 PULs encoded by 964 Bacteroidetes genomes according to their CAZyme composition. We find that collectively Bacteroidetes have elaborated a few thousand enzyme combinations for glycan breakdown, suggesting a global estimate of diversity of glycan structures much smaller than the theoretical one. Bacteroidetes genomes contain polysaccharide utilization loci (PULs), each of which encodes enzymes for the breakdown of one particular glycan. By analyzing the enzyme composition of 13,537 PULs, the authors suggest that the natural glycan diversity is orders of magnitude lower than previously proposed.

The C[sub.3] H[sub.3] NO family of isomers is relevant in astrochemistry, even though its members are still elusive in the interstellar medium. To identify the best candidate for astronomical detection within this family, we developed a new computational protocol based on the minimum-energy principle. This approach aims to identify the most stable isomer of the family and consists of three steps. The first step is an extensive investigation that characterizes the vast number of compounds having the C[sub.3] H[sub.3] NO chemical formula, employing density functional theory for this purpose. The second step is an energy refinement, which is used to select isomers and relies on coupled cluster theory. The last step is a structural improvement with a final energy refinement that provides improved energies and a large set of accurate spectroscopic parameters for all isomers lying within 30 kJ mol[sup.−1] above the most stable one. According to this protocol, vinylisocyanate is the most stable isomer, followed by oxazole, which is about 5 kJ mol[sup.−1] higher in energy. The other stable species are pyruvonitrile, cyanoacetaldehyde, and cyanovinylalcohol. For all of these species, new computed rotational and vibrational spectroscopic data are reported, which complement those already available in the literature or fill current gaps.

The phosphates in the backbones of DNA and RNA are often drawn like crosses but are in fact tetrahedral. Sulfur is sometimes substituted for one of the phosphate oxygens during development of nucleotide-based drugs. Because of the geometry, this swap can lead to two different isomers. Knouse et al. report a pair of phosphorus reagents that conveniently produce either isomer selectively. This ability depended on the configuration of appended limonene substituents that are subsequently jettisoned. In addition to simplifying the route to sulfur-substituted oligonucleotides, these reagents will enable more precise studies of each isomer's distinct bioactivity. Science , this issue p. 1234 Limonene-substituted phosphorus reagents offer a simplified and stereoselective route to nucleotide-based drug candidates. Phosphorothioate nucleotides have emerged as powerful pharmacological substitutes of their native phosphodiester analogs with important translational applications in antisense oligonucleotide (ASO) therapeutics and cyclic dinucleotide (CDN) synthesis. Stereocontrolled installation of this chiral motif has long been hampered by the systemic use of phosphorus(III) [P(III)]–based reagent systems as the sole practical means of oligonucleotide assembly. A fundamentally different approach is described herein: the invention of a P(V)-based reagent platform for programmable, traceless, diastereoselective phosphorus-sulfur incorporation. The power of this reagent system is demonstrated through the robust and stereocontrolled synthesis of various nucleotidic architectures, including ASOs and CDNs, via an efficient, inexpensive, and operationally simple protocol.

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

Ginsenosides are the major bioactive constituents of Panax ginseng, which have pharmacological effects. Although there are several reviews in regards to ginsenosides, new ginsenosides have been detected continually in recent years. This review updates the ginsenoside list from P. ginseng to 170 by the end of 2019, and aims to highlight the diversity of ginsenosides in multiple dimensions, including chemical structure, tissue spatial distribution, time, and isomeride. Protopanaxadiol, protopanaxatriol and C17 side-chain varied (C17SCV) manners are the major types of ginsenosides, and the constitute of ginsenosides varied significantly among different parts. Only 16 ginsenosides commonly exist in all parts of a ginseng plant. Protopanaxadiol-type ginsenoside is dominant in root, rhizome, leaf, stem, and fruit, whereas malonyl- and C17SCV-type ginsenosides occupy a greater proportion in the flower and flower bud compared with other parts. In respects of isomeride, there are 69 molecular formulas corresponding to 170 ginsenosides, and the median of isomers is 2. This is the first review on diversity of ginsenosides, providing information for reasonable utilization of whole ginseng plant, and the perspective on studying the physiological functions of ginsenoside for the ginseng plant itself is also proposed.

The development of synthetic structures that mimic mechanical actuation in living matter such as autonomous translation and shape changes remains a grand challenge for materials science. In living systems the integration of supramolecular structures and covalent polymers contributes to the responsive behaviour of membranes, muscles and tendons, among others. Here we describe hybrid light-responsive soft materials composed of peptide amphiphile supramolecular polymers chemically bonded to spiropyran-based networks that expel water in response to visible light. The supramolecular polymers form a reversibly deformable and water-draining skeleton that mechanically reinforces the hybrid and can also be aligned by printing methods. The noncovalent skeleton embedded in the network thus enables faster bending and flattening actuation of objects, as well as longer steps during the light-driven crawling motion of macroscopic films. Our work suggests that hybrid bonding polymers, which integrate supramolecular assemblies and covalent networks, offer strategies for the bottom-up design of soft matter that mimics living organisms. Peptide amphiphile supramolecular polymers with a crosslinked spiropyran network respond to light by expelling water, enabling the fabrication of soft actuators or light-driven crawlers.

The development of sustainable polymers that possess useful material properties competitive with existing petroleum-derived polymers is a crucial goal but remains a formidable challenge for polymer science. Here we demonstrate that irreversible ring-opening polymerization (IROP) of biomass-derived five-membered thionolactones is an effective and robust strategy for the polymerization of non-strained five-membered rings—these polymerizations are commonly thermodynamically forbidden under ambient conditions, at industrially relevant temperatures of 80–100 °C. Computational studies reveal that the selective IROP of these thionolactones is thermodynamically driven by S/O isomerization during the ring-opening process. IROP of γ-thionobutyrolactone, a representative non-strained thionolactone, affords a sustainable polymer from renewable resources that possesses external-stimuli-triggered degradability. This poly(thiolactone) also exhibits high performance, with its key thermal and mechanical properties comparing well to those of commercial petroleum-based low-density polyethylene. This IROP strategy will enable conversion of five-membered lactones, generally unachievable by other polymerization methods, into sustainable polymers with a range of potential applications. Five-membered lactones are common in nature and are produced in large quantities from biomass, but a lack of ring strain means that ring-opening polymerization is usually thermodynamically unfavourable at ambient conditions. Now, an irreversible ring-opening polymerization of biomass-derived five-membered thionolactones—driven by S/O isomerization—has been developed, enabling their conversion into sustainable polymers at industrially relevant temperatures.