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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Neutron Diffraction Study of Significant sp 3 and sp 2 C–H Bond Shortening in a Fluorinated Pyridinium Saccharinate

Here we have experimentally shown by neutron diffraction significant shortening of both $sp^3$- and $sp^2$-hybridized C–H bonds to 1.092(2) and 1.081(1) Å in a hydrogen-bonded crystal of a difluorinated compound, 4-((2,2-difluoroethoxy)methyl)pyridinium saccharinate. Both MP2 and DFT calculations affirmed the C–H bond shrinkages. Sanderson’s electronegativity equalization principle provides insight into the shortening of the C–H covalent bond lengths for both $sp^3$- and $sp^2$-hybridized carbon atoms. To the best of our knowledge, this neutron diffraction study has revealed the largest extents of $sp^3$ and $sp^2$ C–H bond shrinkages with a 3-sigma rule being satisfied.

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

Mechanism of Nitrogen-Carbon Bond Formation from Iron(IV) Disilylhydrazido Intermediates during N 2 Reduction

We recently reported a reaction sequence that activates C–H bonds in simple arenes as well as the N–N triple bond in N 2 , delivering the aryl group to N 2 to form a new N–C bond ( Nature 2020 , 584, 221). This enables the transformation of abundant feedstocks (arenes and N 2 ) into N-containing organic compounds. The key N–C bond forming step occurs upon partial silylation of N 2 . However, the pathway through which reduction, silylation, and migration occurred was unknown. Here, in this work, we describe synthetic, structural, magnetic, spectroscopic, kinetic, and computational studies that elucidate the steps of this transformation. N 2 must be silylated twice at the distal N atom before aryl migration can occur, and sequential silyl radical and silyl cation addition is a kinetically competent pathway to a formally iron(IV)–NN(SiMe 3 ) 2 intermediate that can be isolated at low temperature. Kinetic studies show its first-order conversion to the migrated product, and DFT calculations indicate a concerted transition state for migration. The electronic structure of the formally iron(IV) intermediate is examined using DFT and CASSCF calculations, which reveal contributions from iron(II) and iron(III) resonance forms with oxidized NNSi 2 ligands. The depletion of electron density from the Fe-coordinated N atom makes it electrophilic enough to accept the incoming aryl group. This new pathway for the N–C bond formation offers a method for functionalizing N 2 using organometallic chemistry.

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

Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands

In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O 2 is reduced to H 2 O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. Here, this study focused on the ~350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255–285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90–150 mV for anionic charge and ~100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.

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

Enhancing Substrate–Metal Catalyst Affinity via Hydrogen Bonding: Pd(II)-Catalyzed β-C(sp 3 )–H Bromination of Free Carboxylic Acids

Achieving sufficient substrate-metal catalyst affinity is a fundamental challenge for developing synthetically useful C–H activation reactions of weakly coordinating native substrates. While hydrogen bonding has been harnessed to bias site selectivity in existing C(sp 2 )–H activation reactions, the potential for designing catalysts with hydrogen bond donors (HBDs) to enhance catalyst substrate affinity, and thereby facilitate otherwise unreactive C(sp 3 )–H activation, remains to be demonstrated. Herein, we report the discovery of a ligand scaffold containing a remote amide motif that can form a favorable meta-macrocyclic hydrogen bonding interaction with the aliphatic acid substrate. The utility of this ligand scaffold is demonstrated through the development of an unprecedented C(sp 3 )–H bromination of α-tertiary and α-quaternary free carboxylic acids, which proceeds in exceedingly high mono-selectivity. Furthermore, the geometric relationship of the NHAc hydrogen bond donor and the coordinating quinoline ligand is crucial for forming the meta-macrocyclophane-like hydrogen bonding interaction, providing a guideline for the future design of catalysts employing secondary interactions.

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

Cerium Dimer Anion and the Contribution of 4f Electrons to Lanthanide Metal–Metal Bonds

Direct metal−metal bonding between lanthanide atoms has been challenging to observe. We report on the first spectroscopic characterization of the cerium dimer anion (Ce 2 − ) and its neutral analog (Ce 2 ) in the gas phase, achieved using photoelectron and ultrafast spectroscopy combined with high-level quantum chemistry calculations. The electron affinity of Ce 2 is 0.24 eV, from which a dissociation energy of 2.21 eV is derived for Ce 2 − . The wave-packet dynamics upon photodetachment are studied and yield vibrational frequencies for electronically excited Ce 2 . Ce 2 − exhibits a conventional metal−metal triple bond with minimal contribution from 4f electrons. However, evidence of 4f-electron participation in bonding is identified for the low-energy excited states only 0.1 eV higher. The results challenge the assumption of inert 4f electrons in metal−metal bonding, and we propose a promising strategy for forming stable lanthanide−lanthanide bonds involving significant 4f-electron contributions.

Anions↗
DOE OSTI2025

Symmetrization of Strong Hydrogen Bond under High Pressure in Bihydroxide-Ion-Containing NaCu 2 (SO 4 ) 2 ·H 3 O 2 Revealed by Experimental Charge Density, Single-Crystal Electron Diffraction, and Neutron Diffraction Studies

In minerals and inorganic compounds, strong hydrogen bonding can lead to the formation of complex ionic species such as the H 3 O 2 – bihydroxide anion and Zundel cation H 5 O 2 + . We studied [NaCu 2 (SO 4 ) 2 ·H 3 O 2 ] natrochalcite, which contains bihydroxide anions and undergoes hydrogen bond symmetrization at the lowest pressure reported so far among inorganic compounds. Hydrogen bond symmetrization leads to changes in the bulk modulus, seismic wave velocities, and proton mobility and plays a primary role in high-temperature superconductivity, but its characteristics are not well understood due to a lack of systematic studies and limitations of experimental methods sensitive to this subtle change. In this work, we applied experimental charge density analysis based on in situ single-crystal X-ray diffraction data, along with the single-crystal neutron and electron diffraction experiments, to probe the behavior of hydrogen atoms during the hydrogen bond symmetrization process under high-pressure conditions. On the way to the symmetrical H-bonding, natrochalcite undergoes a series of complex redistributions of electron density, which we trace with multipole refinement and detailed analysis of changes in the Laplacian of electron density values. Additionally, we deconvoluted the equation of state (volume of the unit cell vs pressure relation) into the atomic equation of states describing dependencies of atomic charges or volumes vs pressure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Mechanistic Examination of Cβ–Cγ Bond Cleavages of Tryptophan Residues during Dissociations of Molecular Peptide Radical Cations

In this study, we used collision-induced dissociation (CID) to examine the gas-phase fragmentations of [GnW]•+ (n = 2-4) and [GXW]•+ (X = C, S, L, F, Y, Q) species. The Cβ–Cγ bond cleavage of a C-terminal decarboxylated tryptophan residue ([M - CO2]•+) can generate [M - CO2 - 116]+, [M - CO2 - 117]•+, and [1H-indole]•+ (m/z 117) species as possible product ions. Competition between the formation of [M - CO2 - 116]+ and [1H-indole]•+ systems implies the existence of a proton-bound dimer formed between the indole ring and peptide backbone. Formation of such a proton-bound dimer is facile via a protonation of the tryptophan γ-carbon atom as suggested by density functional theory (DFT) calculations. DFT calculations also suggested the initially formed ion 2--the decarboxylated species that is active against Cβ–Cγ bond cleavage -can efficiently isomerize to form a more-stable -radical isomer (ion 9) as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. The Cβ–Cγ bond cleavage of a tryptophan residue also can occur directly from peptide radical cations containing a basic residue. CID of [WGnR]•+ (n = 1-3) radical cations consistently resulted in predominant formation of [M-116]+ product ions. It appears that the basic arginine residue tightly sequesters the proton and allows the charge-remote Cβ–Cγ bond cleavage to prevail over the charge-directed one. DFT calculations predicted the barrier for the former is 6.2 kcal mol -1 lower than that of the latter. Furthermore, the pathway involving a salt-bridge intermediate also was accessible during such a bond cleavage event.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2017

Elucidating bonding preferences in tetrakis(imido)uranate(VI) dianions

Actinyl species, [AnO 2 ] 2+ , are well-known derivatives of the f-block because of their natural occurrence and essential roles in the nuclear fuel cycle. Along with their nitrogen analogues, [An(NR) 2 ] 2+ , actinyls are characterized by their two strong trans-An–element multiple bonds, a consequence of the inverse trans influence. We report that these robust bonds can be weakened significantly by increasing the number of multiple bonds to uranium, as demonstrated by a family of uranium(VI) dianions bearing four U–N multiple bonds, [M] 2 [U(NR) 4 ] (M = Li, Na, K, Rb, Cs). Their geometry is dictated by cation coordination and sterics rather than by electronic factors. Multiple bond weakening by the addition of strong π donors has the potential for applications in the processing of high-valent actinyls, commonly found in environmental pollutants and spent nuclear fuels.

Anderson, Nickolas H.↗
DOE OSTI2014

Resolving the molecular mechanism of cadherin catch bond formation

Classical cadherin Ca(2+)-dependent cell-cell adhesion proteins play key roles in embryogenesis and in maintaining tissue integrity. Cadherins mediate robust adhesion by binding in multiple conformations. One of these adhesive states, called an X-dimer, forms catch bonds that strengthen and become longer lived in the presence of mechanical force. Here we use single-molecule force-clamp spectroscopy with an atomic force microscope along with molecular dynamics and steered molecular dynamics simulations to resolve the molecular mechanisms underlying catch bond formation and the role of Ca(2+) ions in this process. Our data suggest that tensile force bends the cadherin extracellular region such that they form long-lived, force-induced hydrogen bonds that lock X-dimers into tighter contact. When Ca(2+) concentration is decreased, fewer de novo hydrogen bonds are formed and catch bond formation is eliminated

36 MATERIALS SCIENCE↗
DOE OSTI2018

Controlling reaction pathways of selective C–O bond cleavage of glycerol

The selective hydrodeoxygenation (HDO) reaction is desirable to convert glycerol into various value-added products by breaking different numbers of C–O bonds while maintaining C–C bonds. Here we combine experimental and density functional theory (DFT) results to reveal that the Cu modifier can significantly reduce the oxophilicity of the molybdenum carbide (Mo 2 C) surface and change the product distribution. The Mo 2 C surface is active for breaking all C–O bonds to produce propylene. As the Cu coverage increases to 0.5 monolayer (ML), the Cu/Mo 2 C surface shows activity towards breaking two C–O bonds and forming ally-alcohol and propanal. As the Cu coverage further increases, the Cu/Mo 2 C surface cleaves one C–O bond to form acetol. DFT calculations reveal that the Mo 2 C surface, Cu-Mo interface, and Cu surface are distinct sites for the production of propylene, ally-alcohol, and acetol, respectively. This study explores the feasibility of tuning the glycerol HDO selectivity by modifying the surface oxophilicity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Visible light enables catalytic formation of weak chemical bonds with molecular hydrogen

The synthesis of weak chemical bonds at or near thermodynamic potential is a fundamental challenge in chemistry, with applications ranging from catalysis to biology to energy science. Proton-coupled electron transfer using molecular hydrogen is an attractive strategy for synthesizing weak element–hydrogen bonds, but the intrinsic thermodynamics presents a challenge for reactivity. Here we describe the direct photocatalytic synthesis of extremely weak element–hydrogen bonds of metal amido and metal imido complexes, as well as organic compounds with bond dissociation free energies as low as 31 kcal mol –1 . Key to this approach is the bifunctional behaviour of the chromophoric iridium hydride photocatalyst. Activation of molecular hydrogen occurs in the ground state and the resulting iridium hydride harvests visible light to enable spontaneous formation of weak chemical bonds near thermodynamic potential with no by-products. In conclusion, photophysical and mechanistic studies corroborate radical-based reaction pathways and highlight the uniqueness of this photodriven approach in promoting new catalytic chemistr

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

Interleaved bond frustration in a triangular lattice antiferromagnet

Frustration of long-range order via lattice geometry amplifies fluctuations and generates ground states that are highly sensitive to perturbations. Traditionally, geometric frustration is used to engineer unconventional magnetic states; however, the charge degree of freedom and bond order can be similarly frustrated. Finding materials that host both frustrated magnetic and bond networks holds promise for engineering structural and magnetic states with the potential of coupling to one another via either magnetic or strain fields. Here we identify an unusual instance of this coexistence in the triangular lattice antiferromagnets LnCd 3 P 3 (Ln = lanthanides). These compounds feature two-dimensional planes of unique trigonal planar CdP 3 units with an underlying bond instability that is frustrated via emergent kagome ice correlations. This bond instability is interleaved in between layers of frustrated magnetic moments. Furthermore, our results establish LnCd 3 P 3 as a rare materials class in which frustrated magnetism is embedded within a dopable semiconductor with a frustrated bond order instability.

Gomez Alvarado, S. J. [University of California, S↗
DOE OSTI2021

Direct Observation of Ultrafast Hydrogen Bond Strengthening in Liquid Water

Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network, including unusually efficient vibrational energy redistribution and relaxation. An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here we measured the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04 Å on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of ~1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on the femtosecond timescales. Our experiment and simulations unveiled the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Importance of interlayer H bonding structure to the stability of layered minerals

Layered (oxy) hydroxide minerals often possess out-of-plane hydrogen atoms that form hydrogen bonding networks which stabilize the layered structure. However, less is known about how the ordering of these bonds affects the structural stability and solubility of these minerals. Here, we report a new strategy that uses the focused electron beam to probe the effect of differences in hydrogen bonding networks on mineral solubility. In this regard, the dissolution behavior of boehmite (γ-AlOOH) and gibbsite (γ-Al(OH)3) were compared and contrasted in real time via liquid cell electron microscopy. Under identical such conditions, 2D-nanosheets of boehmite (γ-AlOOH) exfoliated from the bulk and then rapidly dissolved, whereas gibbsite was stable. Further, substitution of only 1% Fe(III) for Al(III) in the structure of boehmite inhibited delamination and dissolution. Factors such as pH, radiolytic species, and knock on damage were systematically studied and eliminated as proximal causes for boehmite dissolution. Instead, the creation of electron/hole pairs was considered to be the mechanism that drove dissolution. The widely disparate behaviors of boehmite, gibbsite, and Fe-doped boehmite are discussed in the context of differences in the OH bond strengths, hydrogen bonding networks, and the presence or absence of electron/hole recombination centers.

58 GEOSCIENCES↗
DOE OSTI2016

Activation of carbon dioxide by a terminal uranium–nitrogen bond in the gas-phase: a demonstration of the principle of microscopic reversibility

Activation of CO 2 is demonstrated by its spontaneous dissociative reaction with the gas-phase anion complex NUOCl 2 - , which can be considered as NUO + coordinated by two chloride anion ligands. This reaction was previously predicted by density functional theory to occur exothermically, without barriers above the reactant energy. In this paper, the present results demonstrate the validity of the prediction of microscopic reversibility, and provide a rare case of spontaneous dissociative addition of CO 2 to a gas-phase complex. The activation of CO 2 by NUOCl 2 - proceeds by conversion of a U[triple bond]N bond to a U[double bond]O bond and creation of an isocyanate ligand to yield the complex UO 2 (NCO)Cl 2 - , in which uranyl, UO 2 2+ , is coordinated by one isocyanate and two chloride anion ligands. This activation of CO 2 by a uranium(VI) nitride complex is distinctive from previous reports of oxidative insertion of CO 2 into lower oxidation state U(III) or U(IV) solid complexes, during which both C–O bonds remain intact. This unusual observation of spontaneous addition and activation of CO 2 by NUOCl 2 - is a result of the high oxophilicity of uranium. If the computed Gibbs free energy of the reaction pathway, rather than the energy, is considered, there are barriers above the reactant asymptotes such that the observed reaction should not proceed under thermal conditions. Finally, this result provides a demonstration that energy rather than Gibbs free energy determines reactivity under low-pressure bimolecular conditions.

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

Selective bond formation triggered by short optical pulses: quantum dynamics of a four-center ring closure

Here we report bond formation induced by an ultrashort UV pulse. The photochemical process is described by quantum dynamics as coherent electronic and nuclear motions during the ultrashort pulse induced ring closure of norbornadiene to quadricyclane. Norbornadiene consists of two ethylene moieties connected by a rigid (CH 2 ) 3 bridge. Upon photoexcitation, two new sigma bonds are formed, resulting in the closure of a four-atom ring. As a medium-sized polyatomic molecule, norbornadiene exhibits a high density of strongly coupled electronic states from about 6 eV above the ground state. We report on inducing the formation of the new bonds using a short femtosecond UV pulse to pump a non-equilibrium electronic density in the open form that evolves towards the closed ring form. As the coherent electronic-nuclear coupled dynamics unfold, the excited states change character through non-adiabatic interactions and become valence states for the two new C–C bonds of quadricyclane. Our three-dimensional fully quantum dynamical grid simulations during the first 200 fs show that short UV pulses of different polarization initiate markedly different initial non-equilibrium electronic densities that follow different dynamical paths to the S 0 /S 1 conical intersection. They lead to different initial relative yields of quadricyclane, thereby opening the way to controlling bond-making with attopulses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Relevance of hydrogen bonded associates to the transport properties and nanoscale dynamics of liquid and supercooled 2-propanol

2-Propanol was investigated, in both the liquid and supercooled states, as a model system to study how hydrogen bonds affect the structural relaxation and the dynamics of mesoscale structures, of approximately several Ångstroms, employing static and quasi-elastic neutron scattering and molecular dynamics simulation. Dynamic neutron scattering measurements were performed over an exchanged wave-vector range encompassing the pre-peak, indicative of the presence of H-bonding associates, and the main peak. The dynamics observed at the pre-peak is associated with the formation and disaggregation of the H-bonded associates and is measured to be at least one order of magnitude slower than the dynamics at the main peak, which is identified as the structural relaxation. Additionally, the measurements indicate that the macroscopic shear viscosity has a similar temperature dependence as the dynamics of the H-bonded associates, which highlights the important role played by these structures, together with the structural relaxation, in defining the macroscopic rheological properties of the system. Importantly, the characteristic relaxation time at the pre-peak follows an Arrhenius temperature dependence whereas at the main peak it exhibits a non-Arrhenius behavior on approaching the supercooled state. The origin of this differing behavior is attributed to an increased structuring of the hydrophobic domains of 2-propanol accommodating a more and more encompassing H-bond network, and a consequent set in of dynamic cooperativity.

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

A crossed molecular beams and computational study on the unusual reactivity of banana bonds of cyclopropane (c-C 3 H 6 ; X 1 A$^{'}_{1}$ ) through insertion by ground state carbon atoms (C( 3 P j ))

The mechanism and chemical dynamics of the reaction of ground electronic state atomic carbon C( 3 P j ) with cyclopropane c-C 3 H 6 (X 1 A$^{'}_{1}$) have been explored by combining crossed molecular beams experiments with electronic structure calculations of the pertinent triplet C 4 H 6 potential energy surface and statistical computations of product branching ratios under single-collision conditions. The experimental findings suggest that the reaction proceeds via indirect scattering dynamics through triplet C 4 H 6 reaction intermediate(s) leading to C 4 H 5 product(s) plus atomic hydrogen via a tight exit transition state, with the overall reaction exoergicity evaluated as 231 ± 52 kJ mol –1 . The calculations indicate that C( 3 P j ) can easily insert into one of the three equivalent C–C ‘banana’ bonds of cyclopropane overcoming a low barrier of only 2 kJ mol –1 following the formation of a van der Waals reactant complex stabilized by 15 kJ mol –1 . The carbon atom insertion into one of the six C–H bonds is also feasible via a slightly higher barrier of 5 kJ mol –1 . Here, these results highlight an unusual reactivity of cyclopropane's banana C–C bonds, which behave more like unsaturated C–C bonds with a π-character than saturated σ C–C bonds, which are known to be generally unreactive toward the ground electronic state atomic carbon such as in ethane (C 2 H 6 ). The statistical theory predicts the overall product branching ratios at the experimental collision energy as 50% for 1-butyn-4-yl, 33% for 1,3-butadien-2-yl, i-C 4 H 5 , and 11% for 1,3-butadien-1-yl, n-C 4 H 5 , with i-C 4 H 5 (230 kJ mol –1 below the reactants) favored by the C–C insertion providing the best match with the experimentally observed reaction exoergicity. The C( 3 P j ) + c-C 3 H 6 reaction is predicted to be a source of C 4 H 5 radicals under the conditions where its low entrance barriers can be overcome, such as in planetary atmospheres or in circumstellar envelopes but not in cold molecular clouds. Both i- and n-C 4 H 5 can further react with acetylene eventually producing the first aromatic ring and hence, the reaction of the atomic carbon with c-C 3 H 6 can be considered as an initial step toward the formation of benzene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗