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Science (New York, N.Y.) Aug 2023Ergodicity, the central tenet of statistical mechanics, requires an isolated system to explore all available phase space constrained by energy and symmetry. Mechanisms...
Ergodicity, the central tenet of statistical mechanics, requires an isolated system to explore all available phase space constrained by energy and symmetry. Mechanisms for violating ergodicity are of interest for probing nonequilibrium matter and protecting quantum coherence in complex systems. Polyatomic molecules have long served as a platform for probing ergodicity breaking in vibrational energy transport. Here, we report the observation of rotational ergodicity breaking in an unprecedentedly large molecule, C, determined from its icosahedral rovibrational fine structure. The ergodicity breaking occurs well below the vibrational ergodicity threshold and exhibits multiple transitions between ergodic and nonergodic regimes with increasing angular momentum. These peculiar dynamics result from the molecule's distinctive combination of symmetry, size, and rigidity, highlighting its relevance to emergent phenomena in mesoscopic quantum systems.
PubMed: 37590361
DOI: 10.1126/science.adi6354 -
The Journal of Physical Chemistry. A Mar 2023Charge migration (CM) is a coherent attosecond process that involves the movement of localized holes across a molecule. To determine the relationship between a...
Charge migration (CM) is a coherent attosecond process that involves the movement of localized holes across a molecule. To determine the relationship between a molecule's structure and the CM dynamics it exhibits, we perform systematic studies of para-functionalized bromobenzene molecules (X-CH-R) using real-time time-dependent density functional theory. We initiate valence-electron dynamics by emulating rapid strong-field ionization leading to a localized hole on the bromine atom. The resulting CM, which takes on the order of 1 fs, occurs via an X localized → CH delocalized → R localized mechanism. Interestingly, the hole contrast on the acceptor functional group increases with increasing electron-donating strength. This trend is well-described by the Hammett σ value of the group, which is a commonly used metric for quantifying the effect of functionalization on the chemical reactivity of benzene derivatives. These results suggest that simple attochemistry principles and a density-based picture can be used to predict and understand CM.
PubMed: 36791088
DOI: 10.1021/acs.jpca.3c00568 -
International Journal of Physiology,... 2019Membrane fusion is a universal event in all living organism. It is at the heart of intracellular organelle biogenesis and membrane traffic processes such as endocytosis... (Review)
Review
Membrane fusion is a universal event in all living organism. It is at the heart of intracellular organelle biogenesis and membrane traffic processes such as endocytosis and exocytosis, and is also used by enveloped viruses to enter hosting cells. Regarding the cellular mechanisms underlying membrane fusion, pioneering studies by Randy Schekman, James Rothman, Thomas C. Südhof and their colleagues have demonstrated the function of specific proteins and protein-protein interactions as essential fusogenic factor to initiate membrane fusion. Since then, function of lipids and protein-lipid interaction has also been identified as important players in membrane fusion. Based on that NSF (NEM-sensitive factor where NEM stands for -ethyl-maleimide) and acyl-CoA are required for the membrane fusion of transporting vesicles with Golgi cisternae, it is further suggested that the transfer of the acyl chain to a molecule(s) is essential for membrane fusion. Among the previously identified fusogens, phosphatidic acid (PA) is found as an acyl chain recipient. Functionally, acylation of PA is required for tethering the membranes of Rab5a vesicles and early endosomes together during membrane fusion. As certain threshold of proximity between the donor and acceptor membrane is required to initiate membrane fusion, fusogenic factors beyond protein-protein and protein-lipid interaction need to be identified.
PubMed: 31993099
DOI: No ID Found -
Nature Chemistry Jun 2022For molecular collisions, the deflection of a molecule's trajectory provides one of the most sensitive probes of the interaction potential and there are general rules of...
For molecular collisions, the deflection of a molecule's trajectory provides one of the most sensitive probes of the interaction potential and there are general rules of thumb that relate the direction of deflection to precollision conditions. Following intuition, forward scattering results from glancing collisions, whereas near head-on collisions result in back scattering. Here we present the observation of forward scattering in inelastic processes that defies this common wisdom. For deeply inelastic collisions between NO radicals and CO or HD molecules, we observed forward scattering in fully resolved pair-correlated differential cross-sections, despite the low impact parameters that are needed to induce a sufficient energy transfer. We rationalized these findings by extending the textbook model of hard-sphere scattering-taking inelastic energy transfer into account-and attribute the forward scattering to glory-type trajectories caused by attractive forces. This phenomenon, which we refer to as hard-collision glory scattering, is predicted to be ubiquitous. We derive under which conditions hard-collision glory scattering occurs and retrospectively identify such behaviour in previously studied systems.
Topics: Energy Transfer; Quantum Theory; Retrospective Studies
PubMed: 35315436
DOI: 10.1038/s41557-022-00907-2 -
PloS One 2019Dextranol, a reduced dextran, prevents damage to stored dry protein samples that unmodified dextran would otherwise cause. Desiccation protectants (xeroprotectants) like...
Dextranol, a reduced dextran, prevents damage to stored dry protein samples that unmodified dextran would otherwise cause. Desiccation protectants (xeroprotectants) like the polysaccharide dextran are critical for preserving dried protein samples by forming a rigid glass that protects entrapped protein molecules. Stably dried proteins are important for maintaining critical information in clinical samples like blood serum as well as maintaining activity of biologic drug compounds. However, we found that dextran reacts with both dried serum proteins and lyophilized purified proteins during storage, producing high-molecular weight Amadori-product conjugates. These conjugates appeared in a matter of days or weeks when stored at elevated temperatures (37° or 45°C), but also appeared on a timescale of months when stored at room temperature. We synthesized a less reactive dextranol by reducing dextran's anomeric carbon from an aldehyde to an alcohol. Serum samples dried in a dextranol-based matrix protected the serum proteins from forming high-molecular weight conjugates. The levels of four cancer-related serum biomarkers (prostate specific antigen, neuropilin-1, osteopontin, and matrix-metalloproteinase 7) decreased, as measured by immunoassay, when serum samples were stored for one to two weeks in dextran-based matrix. Switching to a dextranol-based xeroprotection matrix slightly reduced the damage to osteopontin and completely stopped any detectable damage during storage in the other three biomarkers when stored for a period of two weeks at 45°C. We also found that switching from dextran to dextranol in a lyophilization formulation eliminates this unwanted reaction, even at elevated temperatures. Dextranol offers a small and easy modification to dextran that significantly improves the molecule's function as a xeroprotectant by eliminating the potential for damaging protein-polysaccharide conjugation.
Topics: Blood Proteins; Desiccation; Dextrans; Drug Compounding; Oxidation-Reduction; Preservation, Biological; Protein Stability; Temperature
PubMed: 31490977
DOI: 10.1371/journal.pone.0222006 -
Physical Review Letters Sep 2021We report on a joint experimental and theoretical study of photoelectron circular dichroism (PECD) in methyloxirane. By detecting O 1s photoelectrons in coincidence with...
We report on a joint experimental and theoretical study of photoelectron circular dichroism (PECD) in methyloxirane. By detecting O 1s photoelectrons in coincidence with fragment ions, we deduce the molecule's orientation and photoelectron emission direction in the laboratory frame. Thereby, we retrieve a fourfold differential PECD clearly beyond 50%. This strong chiral asymmetry is reproduced by ab initio electronic structure calculations. Providing such a pronounced contrast makes PECD of fixed-in-space chiral molecules an even more sensitive tool for chiral recognition in the gas phase.
PubMed: 34533326
DOI: 10.1103/PhysRevLett.127.103201 -
Journal of Chemical Information and... Aug 2022Synthesis planning and reaction outcome prediction are two fundamental problems in computer-aided organic chemistry for which a variety of data-driven approaches have... (Review)
Review
Synthesis planning and reaction outcome prediction are two fundamental problems in computer-aided organic chemistry for which a variety of data-driven approaches have emerged. Natural language approaches that model each problem as a SMILES-to-SMILES translation lead to a simple end-to-end formulation, reduce the need for data preprocessing, and enable the use of well-optimized machine translation model architectures. However, SMILES representations are not efficient for capturing information about molecular structures, as evidenced by the success of SMILES augmentation to boost empirical performance. Here, we describe a novel Graph2SMILES model that combines the power of Transformer models for text generation with the permutation invariance of molecular graph encoders that mitigates the need for input data augmentation. In our encoder, a directed message passing neural network (D-MPNN) captures local chemical environments, and the global attention encoder allows for long-range and intermolecular interactions, enhanced by graph-aware positional embedding. As an end-to-end architecture, Graph2SMILES can be used as a drop-in replacement for the Transformer in any task involving molecule(s)-to-molecule(s) transformations, which we empirically demonstrate leads to improved performance on existing benchmarks for both retrosynthesis and reaction outcome prediction.
Topics: Molecular Structure; Neural Networks, Computer
PubMed: 35881916
DOI: 10.1021/acs.jcim.2c00321 -
Biotechnology Advances Dec 2019Lignin holds tremendous potential as a renewable feedstock for upgrading to a number of high-value chemicals and products that are derived from the petroleum industry at... (Review)
Review
Lignin holds tremendous potential as a renewable feedstock for upgrading to a number of high-value chemicals and products that are derived from the petroleum industry at present. Since lignin makes up a significant fraction of lignocellulosic biomass, co-utilization of lignin in addition to cellulose and hemicelluloses is vital to the economic viability of cellulosic biorefineries. The recalcitrant nature of lignin, originated from the molecule's compositional and structural heterogeneity, however, poses great challenges toward effective and selective lignin depolymerization and valorization. Ionic liquid (IL) is a powerful solvent that has demonstrated high efficiency in fractionating lignocellulosic biomass into sugar streams and a lignin stream of reduced molecular weight. Compared to thermochemical methods, biological lignin deconstruction takes place at mild temperature and pressure while product selectivity can be potentially improved via the specificity of biocatalysts (lignin degrading enzymes, LDEs). This review focuses on a lignin valorization strategy by harnessing the biomass fractionating capabilities of ILs and the substrate and product selectivity of LDEs. Recent advances in elucidating enzyme-IL interactions as well as strategies for improving enzyme activity in IL are discussed, with specific emphases on biocompatible ILs, thermostable and IL-tolerant enzymes, enzyme immobilization, and surface charge engineering. Also reviewed is the protein engineering toolsets (directed evolution and rational design) to improve the biocatalysts' activity, stability and product selectivity in IL systems. The alliance between IL and LDEs offers a great opportunity for developing a biocatalytic route for lignin valorization.
Topics: Biocatalysis; Biomass; Ionic Liquids; Lignin; Solvents
PubMed: 31326521
DOI: 10.1016/j.biotechadv.2019.107418 -
Journal of the American Chemical Society Oct 2023Fullerenes offer versatile functionalities and are promising materials for a widespread range of applications from biomedicine and energy to electronics. Great efforts...
Fullerenes offer versatile functionalities and are promising materials for a widespread range of applications from biomedicine and energy to electronics. Great efforts have been made to manipulate the symmetries of fullerene and its derivatives for studying material properties and novel effects, such as ferroelectricity with polar symmetry; however, no documentary report has been obtained to realize their ferroelectricity. Here, for the first time, we demonstrated clear ferroelectricity in a fullerene adduct formed by C and S. More is different: the combination of the most symmetric molecule C with the highest symmetry and molecule S with high symmetry resulted in the polar CS adduct with a low crystallographic symmetry of the (2) point group at room temperature. The presented CS undergoes polar-to-polar ferroelectric phase transition with the 2F notation, whose ferroelectricity was confirmed by a ferroelectric hysteresis loop and ferroelectric domain switching. This finding opens up a new functionality for fullerenes and sheds light on the exploration of more ferroelectric fullerenes.
PubMed: 37819908
DOI: 10.1021/jacs.3c08419