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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Lowering the Activation Barriers for Lithium-Ion Conductivity through Orientational Disorder in the Cyanide Argyrodite Li6PS5CN

Rapid advancements in safe and high-energy-density energy storage are predicated on identifying new solid-state ion conductors with low activation energies and high ionic conductivities for all-solid-state battery technologies. Halide argyrodites are among some of the top candidates for solid-state electrolytes, as they can achieve ionic conductivities that approach liquid electrolytes. Incorporating dynamic pseudohalide species in argyrodite solid electrolytes presents an exciting opportunity to exploit lattice dynamics as a design principle to modulate the ion conduction properties of solid-state ion conductors. In the present study, we have prepared the new argyrodite Li 6 PS 5 CN containing orientationally disordered cyanide ions. The new cyanide argyrodite Li 6 PS 5 CN exhibits an activation barrier to Li-ion transport of 471 ± 25 meV and a room-temperature ionic conductivity of 6(2) × 10 –5 S cm –1 in comparison to the activation barrier of 502 ± 16 meV and an ionic conductivity of 2.3(1) × 10 –4 S cm –1 measured for the bromide analogue Li 6 PS 5 Br. Structural studies of both compounds by high-resolution X-ray diffraction indicate that Li 6 PS 5 CN and Li 6 PS 5 Br adopt nearly identical crystal structures with similar lattice parameters, which indicates that lower activation barriers in Li 6 PS 5 CN arise due to the cyanide ion itself rather than due to changes in the geometry of conduction pathways in the local lithium environment. The orientational disorder of the quadrupolar cyanide ion in Li 6 PS 5 CN points to a complex interplay of lattice polarizability and molecular dynamics that lower the activation barrier for lithium-ion conductivity in the cyanide argyrodite.

25 ENERGY STORAGE↗
DOE OSTI2020

Li 5 VF 4 (SO 4 ) 2 : A Prototype High-Voltage Li-Ion Cathode.

A Li-rich polyanionic compound based on V 3+ with a previously unknown structure, Li 5 VF 4 (SO 4 ) 2 , has been developed as a high-voltage cathode material for Li-ion batteries. The solvothermal preparation of this material, crystal structure solution, and initial electrochemical characterization are presented. An analysis based on density functional theory electronic structure calculations suggests that a high voltage close to 5 V is required to extract two Li ions and to reach the oxidation state of V 5+ . However, the use of conventional carbonate-based electrolytes, which exhibit increasing degradation above a potential of 4.3 V, does not permit the full capacity of this compound to be achieved at this time.

25 ENERGY STORAGE↗
DOE OSTI2020

Resolving the Atomic Structure of Sequential Infiltration Synthesis Derived Inorganic Clusters

Sequential infiltration synthesis (SIS) is a route to the precision deposition of inorganic solids in analogy to atomic layer deposition but occurs within (vs upon) a soft material template. SIS has enabled exquisite nanoscale morphological complexity in various oxides through selective nucleation in block copolymers templates. However, the earliest stages of SIS growth remain unresolved, including the atomic structure of nuclei and the evolution of local coordination environments, before and after polymer template removal. We employed In K-edge extended X-ray absorption fine structure and atomic pair distribution function analysis of high-energy X-ray scattering to unravel (1) the structural evolution of InO x H y clusters inside a poly(methyl methacrylate) (PMMA) host matrix and (2) the formation of porous In 2 O 3 solids (obtained after annealing) as a function of SIS cycle number. Early SIS cycles result in InO x H y cluster growth with high aspect ratio, followed by the formation of a three-dimensional network with additional SIS cycles. That the atomic structures of the InO x H y clusters can be modeled as multinuclear clusters with bonding patterns related to those in In 2 O 3 and In(OH) 3 crystal structures suggests that SIS may be an efficient route to 3D arrays of discrete-atom-number clusters. As a result, annealing the mixed inorganic/polymer films in air removes the PMMA template and consolidates the as-grown clusters into cubic In 2 O 3 nanocrystals with structural details that also depend on SIS cycle number.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structure-function analysis of microRNA 3'-end trimming by Nibbler

Nibbler (Nbr) is a 3'-to-5' exoribonuclease whose catalytic 3'-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis. Here, we report on structural and functional studies to decipher the contributions of Nbr’s N-terminal domain (NTD) and exonucleolytic domain (EXO) in miRNA 3'-end trimming. We have solved the crystal structures of the NTD core and EXO domains of Nbr, both in the apo-state. The NTD-core domain of Aedes aegypti Nbr adopts a HEAT-like repeat scaffold with basic patches constituting an RNA-binding surface exhibiting a preference for binding double-strand RNA (dsRNA) over single-strand RNA (ssRNA). Structure-guided functional assays in Drosophila S2 cells confirmed a principal role of the NTD in exonucleolytic miRNA trimming, which depends on basic surface patches. Gain-of-function experiments revealed a potential role of the NTD in recruiting Nbr to Argonaute-bound small RNA substrates. The EXO domain of A. aegypti and Drosophila melanogaster Nbr adopt a mixed α/β-scaffold with a deep pocket lined by a DEDDy catalytic cleavage motif. We demonstrate that Nbr’s EXO domain exhibits Mn2+-dependent ssRNA-specific 3'-to-5' exoribonuclease activity. Modeling of a 3' terminal Uridine into the catalytic pocket of Nbr EXO indicates that 2'-O-methylation of the 3'-U would result in a steric clash with a tryptophan side chain, suggesting that 2'-O-methylation protects small RNAs from Nbr-mediated trimming. Overall, our data establish that Nbr requires its NTD as a substrate recruitment platform to execute exonucleolytic miRNA maturation, catalyzed by the ribonuclease EXO domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nanoscale structural correlations in a model cuprate superconductor

Understanding the extent and role of inhomogeneity is a pivotal challenge in the physics of cuprate superconductors. While it is known that structural and electronic inhomogeneity is prevalent in the cuprates, it has proven difficult to disentangle compound-specific features from universally relevant effects. Here, in this study, we combine advanced neutron and x-ray diffuse scattering with numerical modeling to obtain insight into bulk structural correlations in HgBa 2 ⁢ CuO 4+δ . This cuprate exhibits a high optimal transition temperature of nearly 100 K, pristine charge-transport behavior, and a simple average crystal structure without long-range structural instabilities, and is therefore uniquely suited for investigations of intrinsic inhomogeneity. We uncover diffuse reciprocal-space patterns that correspond to prominent nanoscale correlations of atomic displacements perpendicular to the CuO 2 planes. The real-space nature of the correlations is revealed through three-dimensional pair distribution function analysis and complementary numerical refinement. We find that relative displacements of ionic and CuO 2 layers play a crucial role, and that the structural inhomogeneity is not directly caused by the presence of conventional point defects. The observed correlations are therefore intrinsic to HgBa 2 ⁢ CuO 4+δ , and thus likely important for the physics of cuprates more broadly. It is possible that the structural correlations are closely related to the unusual superconducting fluctuations and Mott-localization in these complex oxides. As advances in scattering techniques yield increasingly comprehensive data, the experimental and analysis tools developed here for large volumes of diffuse scattering data can be expected to aid future investigations of a wide range of materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Influence of Ga doping on magnetic properties, magnetocaloric effect, and electronic structure of pseudobinary GdZn 1 - x Ga x ( x = 0 - 0.1 )

Here, we explore the impact of introducing IIIA-group element Ga in place of IIB-group element Zn in binary intermetallic GdZn on its magnetic and magnetocaloric properties, as well as explicate the modified electronic band structure of the compound. The magnetic transition temperature of the compound decreases with the increase of Ga concentration in GdZn 1-x ⁢Ga x ⁢(x = 0–0.1) while the crystal structure (CsCl prototype) and lattice parameters remain unchanged. Our detailed analysis of magnetization and magnetocaloric data conclusively proves that long-ranged magnetic ordering exists in the sample, despite the magnetic interaction considerably weakening with the increase of Ga. The experimental data are rationalized using both a theoretical machine-learning model and first-principle density functional theory. The electronic band structure of GdZn is manifested with some unusual complex features which gradually diminish with Ga doping and the conventional sinusoidal feature of Ruderman-Kittel-Kasuya-Yosida-type interactions also disappears. A mean-field theory model is developed and can successfully describe the overall magnetocaloric behavior of the GdZn 1-x⁢ Ga x series of samples.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Humidity Disrupts Structural and Chiroptical Properties of Chiral 2D Perovskites

Chiral two-dimensional (2D) hybrid organic–inorganic metal halide perovskite semiconductors have emerged as an exceptional material platform with many design opportunities for spintronic applications. However, a comprehensive understanding of changes to the crystal structure and chiroptical properties upon exposure to atmospheric humidity has not been established. We demonstrate phase degradation to the 1D (MBA)PbI 3 (MBA = methylbenzylammonium) and the hypothetical (MBA) 3 PbI 5 ·H 2 O hydrate phases, accompanied by a reduction and disappearance of the chiroptical response. Firstprinciple simulations show that water molecules preferentially locate at the interface between the organic cations and the inorganic framework, thereby disrupting the hydrogen bonding, impacting both the structural chirality and stability of the material. These findings provide critical insights into phase degradation mechanisms and their impact on chiroptical activity in chiral 2D perovskites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Synthesis, structure, and stability of a novel 2 H -azirine under pressure

We have synthesized 2,3-diphenyl-2H-azirine, a strained unsaturated heterocyclic compound, and examined its high-pressure behavior to above 10 GPa using diamond anvil cell techniques. Single crystal X-ray diffraction at ambient conditions reveals that the crystal structure is hexagonal and consists of interesting helices surrounding voids in the structure. A continuous shift of the Raman and infrared vibrational spectra with increasing pressure is observed, indicating that the molecular structure is preserved to at least 8 GPa at room temperature. High-pressure synchrotron powder X-ray diffraction shows that the hexagonal structure persists, with a smooth compression of the a and c parameters to 10 GPa. The structural stability under pressure is attributed to the reduction in void size within the helical framework despite the inherent strain and reactivity of the molecule. The channels in the structure could encapsulate small molecules for gas or energy storage applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Real-space imaging of periodic nanotextures in thin films via phasing of diffraction data

New properties and exotic quantum phenomena can form due to periodic nanotextures, including Moire patterns, ferroic domains, and topologically protected magnetization and polarization textures. Despite the availability of powerful tools to characterize the atomic crystal structure, the visualization of nanoscale strain-modulated structural motifs remains challenging. Here, we develop nondestructive real-space imaging of periodic lattice distortions in thin epitaxial films and report an emergent periodic nanotexture in a Mott insulator. Specifically, we combine iterative phase retrieval with unsupervised machine learning to invert the diffuse scattering pattern from conventional X-ray reciprocal-space maps into real-space images of crystalline displacements. Our imaging in PbTiO 3 /SrTiO 3 superlattices exhibiting checkerboard strain modulation substantiates published phase-field model calculations. Furthermore, the imaging of biaxially strained Mott insulator Ca 2 RuO 4 reveals a strain-induced nanotexture comprised of nanometer-thin metallic-structure wires separated by nanometer-thin Mott-insulating-structure walls, as confirmed by cryogenic scanning transmission electron microscopy (cryo-STEM). The nanotexture in Ca 2 RuO 4 film is induced by the metal-to-insulator transition and has not been reported in bulk crystals. We expect the phasing of diffuse X-ray scattering from thin crystalline films in combination with cryo-STEM to open a powerful avenue for discovering, visualizing, and quantifying the periodic strain-modulated structures in quantum materials.

Science & Technology - Other Topics↗
DOE OSTI2022

Crystalline phase transitions and water-soluble complexes of copper(Ⅰ) 2-hydroxyethanethiolate

We report the coordination polymer copper(I) 2-hydroxyethanethiolate, (CuSCH 2 CH 2 OH) n , though insoluble in all common solvents, dissolved readily in basic aqueous solutions of the thiolate anion (HOCH 2 CH 2 S – ) of 2-mercaptoethanol to form a single species: the tetranuclear cluster [Cu 4 (μ-SCH 2 CH 2 OH) 6 ] 2– . From this solution were grown X-ray quality single crystals of copper(I) 2-hydroxyethanethiolate. This compound underwent a hitherto unknown crystal phase transition at ca. 6 °C, from point group P2 1 2 1 2 1 to Pna2 1 , with noticeable changes in the geometry of the Cu-S layer and in the orientation of the alkylthiolate side chains. When the bulky base tetrabutylammonium hydroxide was employed in the aqueous thiolate solution used to dissolve (CuSCH 2 CH 2 OH) n , the water-soluble polynuclear copper(I) complex bis(tetrabutylammonium) hexakis(μ-2-hydroxyethanethiolato) tetracuprate(I), [(C 4 H 9 ) 4 N] 2 [Cu 4 (μ-SCH 2 CH 2 OH) 6 ], could be isolated as X-ray quality crystals. Structural characterization of this complex revealed a tetrahedral arrangement of copper(I) centers with thiolates bridging the edges of the tetrahedra. On standing, this complex degraded to a larger polynuclear Cu(I) sulfide cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Energetics of hydroxylbastnäsite solid solutions, La 1-$\chi$ Nd $\chi$ CO 3 OH

Bastnäsites (LnCO 3 (F,OH)) are a group of common rare earth elements (REE)-bearing minerals and are one of the primary global sources of REE. Due to the chemical similarities among REE, bastnӓsites tend to occur as solid solutions instead of end members in REE containing ores. To better understand the processes and the mechanisms of formation of such deposits, it is essential to determine the thermodynamic properties of bastnӓsites, including hydroxylbastnӓsite (LnCO 3 OH) solid solutions. In this work, we performed detailed structural and calorimetric investigations on synthetic hexagonal La–Nd hydroxylbastnӓsite (La 1-$\chi$ NdCO 3 OH, $\chi$ = 0, 0.25, 0.5, 0.75, 1) solid solutions. X-ray diffraction confirms the crystal structure of the solid solution series in the $\ P$6 space group, and pair distribution function (PDF) analysis reveals local bonding environments characterized by three different types of 9-coordinated metal-oxygen polyhedra. Unit cell parameters of La1–xNdxCO3OH exhibit a nearly linear relation with the Nd content x, suggesting a random distribution of La and Nd in the structure. Their standard enthalpies of formation (Δ$\ H$° f ) were determined by high temperature oxide melt drop solution calorimetry, from which the enthalpies of mixing (Δ$\ H$ mix ) were derived. The Δ$\ H$ mix can be fitted by a regular solution model with an interaction parameter of 12.58 ± 0.16 kJ/mol, suggesting enthalpic metastability of La1–xNdxCO3OH relative to the two endmembers. Combining entropy and enthalpy, we further estimated the Gibbs free energies of mixing (Δ$\ G$ mix ) at relevant temperatures, revealing favorable temperatures under which the intermediate La 1-$\chi$ NdCO 3 OH phases can be stabilized. Such entropy-driven stabilization, as is consistent with our geochemical modeling results, may explain the enhancement of thermal stability of the solid solutions in nature. Additionally, the temperature range constrained from this study may be used to estimate the thermal history of REE bastnӓsite deposit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Stabilization of NbTe 3 , VTe 3 , and TiTe 3 via Nanotube Encapsulation

The structure of MX 3 transition metal trichalcogenides (TMTs, with M a transition metal and X a chalcogen) is typified by one-dimensional (1D) chains weakly bound together via van der Waals interactions. This structural motif is common across a range of M and X atoms (e.g. NbSe 3 , HfTe 3 , TaS 3 ), but not all M and X combinations are stable. We report here that three new members of the MX 3 family which are not stable in bulk, specifically NbTe 3 , VTe 3 , and TiTe 3 , can be synthesized in the few- to single-chain limit via nano-confined growth within the stabilizing cavity of multi-walled carbon nanotubes. Transmission electron microscopy (TEM) and atomic-resolution scanning transmission electron microscopy (STEM) reveal the chain-like nature and the detailed atomic structure. The synthesized materials exhibit behavior unique to few-chain quasi-1D structures, such as multi-chain spiraling and a trigonal anti-prismatic rocking distortion in the single-chain limit. Density functional theory (DFT) calculations provide insight into the crystal structure and stability of the materials, as well as their electronic structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles

$RAD51C$ is an enigmatic predisposition gene for breast, ovarian, and prostate cancer. Currently, missing structural and related functional understanding limits patient mutation interpretation to homology-directed repair (HDR) function analysis. Here we report the RAD51C-XRCC3 (CX3) X-ray co-crystal structure with bound ATP analog and define separable RAD51C replication stability roles informed by its three-dimensional structure, assembly, and unappreciated polymerization motif. Mapping of cancer patient mutations as a functional guide confirms ATP-binding matching RAD51 recombinase yet highlights distinct CX3 interfaces. Analyses of CRISPR/Cas9-edited human cells with $RAD51C$ mutations combined with single-molecule, single-cell and biophysics measurements uncover discrete CX3 regions for DNA replication fork protection, restart and reversal, accomplished by separable functions in DNA binding and implied 5’ RAD51 filament capping. Collective findings establish CX3 as a cancer-relevant replication stress response complex, show how HDR-proficient variants could contribute to tumor development, and identify regions to aid functional testing and classification of cancer mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A single diiron enzyme catalyses the oxidative rearrangement of tryptophan to indole nitrile

Abstract Nitriles are uncommon in nature and are typically constructed from oximes through the oxidative decarboxylation of amino acid substrates or from the derivatization of carboxylic acids. Here we report a third nitrile biosynthesis strategy featuring the cyanobacterial nitrile synthase AetD. During the biosynthesis of the eagle-killing neurotoxin, aetokthonotoxin, AetD transforms the 2-aminopropionate portion of 5,7-dibromo-l-tryptophan to a nitrile. Employing a combination of structural, biochemical and biophysical techniques, we characterized AetD as a non-haem diiron enzyme that belongs to the emerging haem-oxygenase-like dimetal oxidase superfamily. High-resolution crystal structures of AetD together with the identification of catalytically relevant products provide mechanistic insights into how AetD affords this unique transformation, which we propose proceeds via an aziridine intermediate. Our work presents a unique template for nitrile biogenesis and portrays a substrate binding and metallocofactor assembly mechanism that may be shared among other haem-oxygenase-like dimetal oxidase enzymes.

Chemistry↗
DOE OSTI2025

Structural and magnetic properties of CoTeMo⁢O 6

Here, we have conducted a comprehensive investigation into the magnetic properties of the chiral multiferroic material CoTeMo⁢O 6 . In contrast with the previous claim of canted antiferromagnetic order with ferromagnetic components [Y. Doi et al., J. Solid State Chem. 182, 3232 (2009)], our investigation reveals an antiferromagnetic ground state with compensated moments, providing an interesting platform for exploring exotic material properties. Through careful measurements of magnetization under a series of applied fields, we demonstrate that there exist two sequential field-induced magnetic transitions in CoTeMo⁢O 6 , with one occurring at 𝐻 𝑐⁢1 =460 Oe along the 𝑎 axis, and the other at 𝐻 𝑐⁢2 =1.16 T with the field along the 𝑏 axis. The values of 𝐻 𝑐⁢1 and 𝐻 𝑐⁢2 exhibit strong angular dependence and diverge with different rates as the applied field is rotated 90 ° within the 𝑎⁢𝑏 plane. This reflects the distinct nature of these transitions, which is further supported by the different critical behavior of 𝐻 𝑐⁢1 and 𝐻 𝑐⁢2 , characterized by the values of 𝛾, in the function of 𝐻 𝑐 =𝐻 0 ⁡(1−𝑇/𝑇 𝑐 ) 𝛾 . Furthermore, we have demonstrated that there exist structural and magnetic twin domains in CoTeMo⁢O 6 that strongly affect the experimental measurement of their macroscopic properties. Intriguingly, these twin domains can be related to the orthorhombicity/chirality of the crystal structure with the space group 𝑃⁢2 1 ⁢2 1⁢ 2. We further explored the magnetic and structural domains with uniaxial pressure and polarized light microscopy. Our results suggest that CoTeMo⁢O 6 could be used as a unique platform for investigating the intriguing physics involving intertwined degrees of freedom. The tunability of the underlying domain distribution and its strong anisotropy could also be useful for developing functional devices and applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Phonon-Driven Femtosecond Dynamics of Excitons in Crystalline Pentacene from First Principles

Nonradiative exciton relaxation processes are critical for energy transduction and transport in optoelectronic materials, but how these processes are connected to the underlying crystal structure and the associated electron, exciton, and phonon band structures, as well as the interactions of all these particles, is challenging to understand. Here, in this work, we present a first-principles study of exciton-phonon relaxation pathways in pentacene, a paradigmatic molecular crystal and optoelectronic semiconductor. We compute the momentum- and band-resolved exciton-phonon interactions, and use them to analyze key scattering channels. We find that both exciton intraband scattering and interband scattering to parity-forbidden dark states occur on the same ~100 fs timescale as a direct consequence of the longitudinal-transverse splitting of the bright exciton band. Consequently, exciton-phonon scattering exists as a dominant nonradiative relaxation channel in pentacene. We further show how the propagation of an exciton wave packet is connected with crystal anisotropy, which gives rise to the longitudinal-transverse exciton splitting and concomitant anisotropic exciton and phonon dispersions. Our results provide a framework for understanding the role of exciton-phonon interactions in exciton nonradiative lifetimes in molecular crystals and beyond.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure

The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. Here, to clarify the mechanism, we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ~18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme–substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗