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At least 217 records · Page 12

Enhanced Collisional Losses from a Magnetic Mirror Using the Lenard-Bernstein Collision Operator

Collisions are crucial in governing particle and energy transport in plasmas confined in a magnetic mirror trap. Modern gyrokinetic codes model transport in magnetic mirrors, but some utilize approximate model collision operators. This study focuses on a Pastukhov-style method of images calculation of particle and energy confinement times using a Lenard-Bernstein model collision operator. Prior work on parallel particle and energy balances used a different Fokker-Planck plasma collision operator. The method must be extended in non-trivial ways to study the Lenard-Bernstein operator. To assess the effectiveness of our approach, we compare our results with a modern finite element solver. Our findings reveal that the particle confinement time scales like a exp( a 2 ) using the Lenard-Bernstein operator, in contrast to the more accurate scaling that the Coulomb collision operator would yield a 2 exp( a 2 ), where a 2 is approximately proportional to the ambipolar potential. We propose that codes solving for collisional losses in magnetic mirrors utilizing the Lenard-Bernstein or Dougherty collision operator scale their collision frequency of any electrostatically confined species. This study illuminates the collision operator’s intricate role in the Pastukhov-style method of images calculation of collisional confinement.

fusion plasma↗

Drift-cyclotron loss-cone instability in 3-D simulations of a sloshing-ion simple mirror

The kinetic stability of collisionless, sloshing beam-ion (45° pitch angle) plasma is studied in a three-dimensional (3-D) simple magnetic mirror, mimicking the Wisconsin high-temperature superconductor axisymmetric mirror experiment. The collisional Fokker–Planck code CQL3D-m provides a slowing-down beam-ion distribution to initialize the kinetic-ion/fluid-electron code Hybrid-VPIC, which then simulates free plasma decay without external heating or fuelling. Over 1 – 10 μs, drift-cyclotron loss-cone (DCLC) modes grow and saturate in amplitude. The DCLC scatters ions to a marginally stable distribution with gas-dynamic rather than classical-mirror confinement. Sloshing ions can trap cool (low-energy) ions in an electrostatic potential well to stabilize DCLC, but DCLC itself does not scatter sloshing beam-ions into the said well. Instead, cool ions must come from external sources such as charge-exchange collisions with a low-density neutral population. Manually adding cool ∼1keV ions improves beam-ion confinement several-fold in Hybrid-VPIC simulations, which qualitatively corroborates prior measurements from real mirror devices with sloshing ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The gyrokinetic field invariant and electromagnetic temperature-gradient instabilities in ‘good-curvature’ plasmas

Curvature-driven instabilities are ubiquitous in magnetised fusion plasmas. By analysing the conservation laws of the gyrokinetic system of equations, we demonstrate that the well-known spatial localisation of these instabilities to regions of ‘bad magnetic curvature’ can be explained using the conservation law for a sign-indefinite quadratic quantity that we call the gyrokinetic field invariant. Its evolution equation allows us to define the local effective magnetic curvature whose sign demarcates the regions of ‘good’ and ‘bad’ curvature, which, under some additional simplifying assumptions, can be shown to correspond to the inboard (high-field) and outboard (low-field) sides of a tokamak plasma, respectively. We find that, given some reasonable assumptions, electrostatic curvature-driven modes are always localised to the regions of bad magnetic curvature, regardless of the specific character of the instability. More importantly, we also deduce that any mode that is unstable in the region of good magnetic curvature must be electromagnetic in nature. As a concrete example, we present the magnetic-drift mode, a novel good-curvature electromagnetic instability, and compare its properties with the well-known electron-temperature-gradient instability. Finally, we discuss the relevance of the magnetic drift mode for high-β fusion plasmas, and in particular its relationship with microtearing modes.

fusion plasma↗

Detecting shearless phase-space transport barriers in global gyrokinetic turbulence simulations with test particle map models

In magnetically confined fusion plasmas, the role played by zonal 𝐸 x 𝐵 flow shear layers in the suppression of turbulent transport is relatively well understood. However, less is understood about the role played by the weak shear regions that arise in the non-monotonic radial electric field profiles often associated with these shear layers. In electrostatic simulations from the global total-𝑓 gyrokinetic particle-in-cell code XGC, we demonstrate how shearless regions with non-zero flow curvature form zonal ‘jets’ that, in conjunction with neighbouring regions of shear, can act as robust barriers to particle transport and turbulence spreading. By isolating quasi-coherent fluctuations radially localised to the zonal jets, we construct a map model for the Lagrangian dynamics of gyrokinetic test particles in the presence of drift waves. We identify the presence of shearless invariant tori in this model and verify that these tori act as partial phase-space transport barriers in the simulations. We also demonstrate how avalanches impinging on these shearless tori cause eddy detachment events that form ‘cold/warm core ring’ structures analogous to those found in oceanic jets, facilitating transport across the barriers without destroying them completely. We discuss how shearless tori may generically arise from tertiary instabilities or other types of discrete eigenmodes, suggesting their potential relevance to broader classes of turbulent fluctuations.

fusion plasma↗

Mechanistic Insights into Dinitrogen Reduction to Ammonia in Light-Controlled Nanocrystal:Nitrogenase Complexes

Developing systems that can efficiently capture photon energy and convert this energy into fuels and chemicals requires understanding how to assemble molecular components with diverse functions into complete systems possessing selectivity and efficiency in directing charge carriers to catalytic reactions. There are many challenges to achieving this goal. One promising approach is the development of hybrid systems that combine semiconductor nanocrystals (NCs) for light capture and enzymes as efficient catalysts. Such biohybrid systems capitalize on the tunable electronic and optical properties of NCs while leveraging the unmatched specificity and efficiency of enzymes in catalyzing chemical reactions, thereby offering opportunities to surpass the limitations of each component alone. Here, we focus on recent progress in developing a biohybrid system that combines CdS NCs for photon capture with the enzyme nitrogenase to accomplish light-driven dinitrogen (N 2 ) reduction to ammonia (NH 3 ). Integrating light-harvesting materials with biological catalysts requires a deep understanding of NC properties, protein stability, and electron transfer (ET), making it an inherently multidisciplinary problem. The reduction of N 2 to NH 3 is a challenging reaction, with a high demand in both agriculture and industrial chemical production. This reaction is intrinsically energy intensive, due to the need to activate the N≡N triple bond. The current standard industrial approach to N 2 reduction, the Haber−Bosch reaction, obtains the necessary energy input from fossil fuels, whereas biological systems capable of N 2 reduction utilize the hydrolysis of ATP as their energy source. Replacing these costly, energy-intensive inputs with renewable light energy represents a critical step toward sustainable NH 3 production. Recent progress has demonstrated that semiconductor CdS NCs can be coupled to the catalytic component of nitrogenase, the MoFe protein, to form a biohybrid CdS NC:MoFe protein complex, enabling light-driven N 2 reduction rather than energy input from fossil fuels or ATP. This illustrates how inorganic NCs can functionally replace the natural Fe protein partner, yielding a biohybrid catalyst that enables controlled electron delivery and provides not only light-driven NH 3 production but also new approaches for probing enzyme catalytic function. The CdS NC:MoFe protein biohybrid system enables light-initiated electron delivery at ambient temperature, as well as temperatures below freezing, allowing for stabilization and spectroscopic characterization of key reaction intermediates. These findings highlight how photochemical biohybrids can serve as both functional catalysts and mechanistic probes. Beyond studies of the nitrogenase mechanism, studies of the CdS NC:MoFe system reveal how variables such as NC size, electrostatic binding interactions, and sacrificial electron donors (SEDs) govern complex stability, charge transfer efficiency, and catalytic performance. In addition, studies of nitrogenase and the high activation barrier for N 2 reduction are enabling investigations of new and interesting questions regarding the properties and limitations of NC biocatalysis. In this Account, we describe the key features of CdS NC:MoFe protein biohybrids and the parameters for optimal light-driven N 2 reduction, and how controlling ET with light illuminates the path to new insights into the nitrogenase mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ionic Liquids in Analytical Chemistry: Fundamentals, Technological Advances, and Future Outlook

The development of new analytical methods most often focus on novel materials used to impart selectivity or sensitivity to the protocol. Ionic liquids (ILs) are a class of solvents that have been extensively explored as promising materials for various applications and continue to be explored due to their tunable physicochemical properties. These materials possess melting temperatures below 100 °C and can interact with analytes through a multitude of interactions afforded by their readily tunable chemical structure. These interactions include electrostatic, dispersive, hydrogen bonding, π–π, and dipolar interactions and can be modulated or strengthened based on the functional groups present within the chemical structure. ILs consist predominately of organic cations and either inorganic or organic anions, both of which can be functionalized with desired moieties. Common cation and anions found in IL chemical structures are presented in Figure 1. The unique polarity afforded by the ionic structure has also led to their increasing use in areas including sample preparation, chemical separations, electrochemistry, mass spectrometry, and spectroscopy.

Zeger, Victoria R. [Iowa State Univ., Ames, IA (Un↗

Local Electric Field Effects on Water Dissociation in Bipolar Membranes Studied Using Core–Shell Catalysts

The local electric field strength is thought to affect the rate of water dissociation (WD) in bipolar membranes (BPMs) at the catalyst–nanoparticle surfaces. Here, we study core–shell nanoparticles, where the core is metallic, semiconducting, or insulating, to understand this effect. The nanoparticle cores were coated with a WD catalyst layer (TiO2 or HfO2) via atomic layer deposition (ALD), and the morphology was imaged with transmission electron microscopy. Irrespective of the core material, these core–shell catalysts displayed comparable WD overpotentials at optimal mass loading, despite the hypothesized differences in the electric field strength across the catalyst particle suggested by continuum electrostatic simulations. Substantial atomic interdiffusion between the core and shell was ruled out by X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and diffuse reflectance optical measurements. However, the optimal mass loading of catalyst was roughly 1 order of magnitude higher for the conductive and high dielectric core materials than for the low dielectric insulating cores. These findings are consistent with the hypothesis that electric field screening within the core material focuses the electric field drop between particles such that larger film thicknesses can be tolerated. Collectively, these data support the idea that it is the local electric field at the molecular level that controls proton-transfer rates and that the metal core/dielectric-shell constructs introduced here modulate that field. Further materials and synthetic design may enable optimization of the electric field strength across the proton-transfer trajectory at the material surface.

Sarma, Prasad V↗

Expanding Configurational Complexity through Dipole Dilution in Pseudohalide Argyrodite Ion Conductors

The advantageous properties of (pseudo)halide argyrodite ion conductors of the formula Li 6 PS 5 X (X = Cl – , Br – , I – , CN – ) have motivated extensive studies of their structure-transport relationships, particularly as they pertain to the role of atomic site disorder. The argyrodite structure can accommodate additional configurational complexity to promote ion transport via extended three-anion site mixing and the potential for orientational disorder of molecular anions. In this work, we explore a ternary anion system including the cyanide anion, expanding site disorder and introducing dipolar orientations as an additional degree of freedom. We prepared the series Li 6 PS 5 (CN) 1–x Br x , in which the dipolar cyanide anions are systematically diluted with bromide. We find that anion disorder, as determined by synchrotron and neutron diffraction and quantified by configurational entropy (S config ), is correlated with lowered activation barriers and increased lithium ion conductivity. We propose that S config describes the electrostatic heterogeneity of the Li environments, flattening the energetic landscape for ion transport. While anion substitution strongly impacts the activation barrier for transport, the temperature-independent Arrhenius prefactor does not follow the same trend. Through heat-capacity measurements of attempt frequency and deconvolution of terms within the prefactor, we rationalize the apparent decoupling of activation energy and prefactor to strong cyanide-lithium interactions that increase the entropy of migration. Together, these results expand the structure–property relationships in the argyrodite family to encompass multiple facets of disorder and the subsequent impact on lithium ion transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

From Cation Order to Disorder: Unlocking Ion Transport Pathways in Li–Zn–Zr–Cl Halospinels

Lithium metal chloride halospinels of the general formula Li 2 MCl 4 are a promising class of earth-abundant ion conductors for all-solid-state batteries. However, poor roomtemperature ionic conductivity has historically limited their use in practical applications. Here, we substitute Zr 4+ into Li 2 ZnCl 4 along the series Li 2−2x/3 Zn 1−x Zr 2x/3 Cl 4 (x = 0, 0.1, 0.3, 0.4, 0.6, 0.9, and 1.0) to understand how cation disorder and vacancy tuning impact ion transport in “normal” halospinels. Aliovalent Zr 4+ substitution increases ionic conductivity by nearly 5 orders of magnitude, from 1.320(3) × 10 −9 S cm −1 in Li 2 ZnCl 4 to 6.74(1)× 10 −5 S cm −1 for x = 0.6. Average and local structure characterization through synchrotron X-ray diffraction (SXRD) and neutron pair distribution function (nPDF) analysis reveal that Zr 4+ redistributes the Zn 2+ and Li + sublattices into previously unoccupied interstitial sites, which form new low-energy hopping pathways that facilitate ion transport. We rationalize the dramatic rearrangement of the cation local structure by considering the coordination preferences of the cations and the potential electrostatic penalties incurred by the higher-valent Zr 4+ cations. This work delivers an atomistic understanding of substitution-induced cation disorder and ion transport properties in a new family of earth-abundant halospinels.

Cardoza, Abby M. [Colorado School of Mines, Golden↗

Interactions between Per- and Polyfluoroalkyl Substances (PFAS) at the Water–Air Interface

Per- and polyfluoroalkyl substances (PFAS)--so-called “forever chemicals”--contaminate the drinking water of about 100 million people in the U.S. alone and are inefficiently removed by standard treatment techniques. A key property of these compounds that underlies their fate and transport and the efficacy of several promising remediation approaches is that they accumulate at the water−air interface. This phenomenon remains incompletely understood, particularly under conditions relevant to natural and treatment systems where water−air interfaces often carry significant loads of other organic contaminants or natural organic matter. To understand the impact of organic loading on PFAS adsorption, we carried out molecular dynamics simulations of PFAS at varying interfacial densities. We find that adsorbed PFAS form strong mutual interactions (attraction between perfluoroalkyl chains and electrostatic interactions among charged head groups) that give rise to ordered interfacial coatings. Furthermore, these interactions often involve near-cancellation of hydrophobic attraction and Coulomb repulsion. Our findings explain an apparent paradox whereby PFAS adsorption isotherms often suggest minimal mutual interactions while simultaneously displaying a high sensitivity to the composition and density of interfacial coatings. Consideration of the compounds present with PFAS at the interface has the potential to allow for more accurate predictions of fate and transport and the design of more efficient remediation approaches.

54 ENVIRONMENTAL SCIENCES↗

Elucidating Phosphate and Cadmium Cosorption Mechanisms on Mineral Surfaces with Direct Spectroscopic and Modeling Evidence

The simultaneous sorption of cations and anions at the mineral–water interface can substantially alter their individual sorption characteristics; however, this phenomenon lacks a mechanistic understanding. Our study provides direct spectroscopic and modeling evidence of the molecular cosorption mechanisms of the cadmium ion (Cd 2+ ) and phosphate (P) on goethite and layered manganese (Mn) oxide of birnessite, through in situ attenuated total reflection Fourier-transform infrared (ATR-FTIR), P K-edge X-ray absorption near-edge structure (XANES) spectroscopy, and surface complexation modeling. Phosphate synergistically cosorbed with Cd on goethite predominantly through P-bridged ternary complexes (≡Fe–P–Cd) and electrostatic interactions at wide pH conditions. Likewise, P and Cd exhibited synergistic cosorption on birnessite by forming P-bridged ternary complexes (≡Mn–P–Cd) and weak competitive sorption at the layer edge sites. As pH and Cd loading increased, the surface P species transitioned from a binary complex to a ternary complex and/or Cd 3 (PO 4 ) 2 precipitate for both goethite and birnessite. Compared to that in solution at pH 8, the formation of Cd 3 (PO 4 ) 2 was inhibited by the presence of goethite and birnessite, ascribed to the specific adsorption of P and Cd, more pronounced in birnessite due to the stronger sorption of Cd at its vacant sites. Finally, the discovered cosorption mechanisms of P and Cd have important implications for understanding and predicting their mobility and availability in Cd-contaminated settings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational Investigation of the Chemical Bond between An(III) Ions and Soft-Donor Ligands

The chemical bonding of actinide ions with arene and borohydride ligands is explored via quantum chemical methods to understand how the transuranium elements interact with softdonor ligands. Specifically, the [An(C 6 Me 6 )(BH 4 ) 3 ] complexes (An = U, Np, and Pu) and their reduced congeners are studied. Density functional theory (DFT) shows that the metal–ligand interactions in the neutral complexes are governed by electrostatic interactions. Both DFT and complete active space (CASSCF) results show that as one moves from U to Pu, the 5f-orbitals are stabilized leading to a poorer energy match with the ligand orbitals. This contributes to progressively weaker metal-arene and metal-borohydride interactions across the series due to a decrease in energy-driven covalency. A reduction in orbital contributions to bonding is obtained for the transuranium-arene interactions as well. Upon reduction, the arene is reduced, forming a δ-bond. This causes the An–arene distances to contract by 0.1–0.2 Å compared to the neutral complexes. The ground state is assigned as the intermediate-spin state where the arene radical is antiferromagnetically coupled to the metal-centered f-electrons in Np and Pu. On the other hand, the ferromagnetically and antiferromagnetically coupled states are close in energy in the uranium complex, but do not mix when spin– orbit coupling is included using a state-interaction approach (SO-CASPT2). The population of the CASSCF δ*-antibonding natural orbital increases from U to Pu consistent with the increased An–arene distances, weaker interactions, and decreasing covalency across the series. Although the An–B distance increases by ca. 0.06 Å upon reduction, both the neutral and reduced species involve an An(III)–borohydride bond and as such are qualitatively similar. The Np complexes can be assigned to have slightly weaker bonding than the uranium analogs but are overall “uranium-like”. The Pu complexes are predicted to have less covalent contributions to bonding in both the Pu–arene and Pu–borohydride interactions; however, the Pu–arene interaction is predicted to be particularly weak.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Alkali Metal Control of Triplet-Mediated C–H Activation in Iron-Mediated Coupling of Dinitrogen and Benzene

Direct coupling of N 2 with abundant feedstocks like benzene to form N-containing organic compounds is a promising strategy for N 2 fixation pathways. The challenge of coupling N 2 activation and C–H bond oxidative addition was recently solved by introducing a reversible benzene C–H bond activation process mediated by a low-valent Fe(0) complex, which gave an organometallic product that could couple with partially reduced N 2 . Interestingly, the energetics of the C–H oxidative addition/reductive elimination step depends on the choice of alkali metal. However, the reason why the alkali metal influences the C–H bond activation remained elusive. In this work, we present a comprehensive study on this Fe(0)-mediated reversible C–H activation. Through density functional theory combined with high-level coupled cluster calculations, we discovered that the intermediate-spin triplet (S = 1) controls the energy of the transition state for C–H cleavage, while the high-spin quintet (S = 2) controls the position of the equilibrium. Na + drives the equilibrium toward oxidative addition due to an electrostatic effect, while K + and Rb + are dominated by a steric effect that favors the iron(0) species. The key role played by nonbonding interactions in the Fe-mediated C–H activation provides a conceptual model for alkali control over organometallic transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hybrid Quantum Mechanical, Molecular Mechanical, and Machine Learning Potential for Computing Aqueous-Phase Adsorption Free Energies on Metal Surfaces

Performing reliable computer simulations of elementary processes occurring at metal–water interfaces is pivotal for novel catalyst design in sustainable energy applications. Computational catalyst design hinges on the ability to reliably and efficiently compute the potential energy surface (PES) of the system. Here, due to the large system sizes needed for studying processes at liquid water–metal interfaces, these systems can currently not be described using density functional theory (DFT). In this work, we used a hybrid quantum mechanical, molecular mechanical, and machine learning potential for studying the adsorption behavior of phenol, atomic hydrogen, 2-butanol, and 2-butanone on the (0001) facet of Ru under reducing conditions when Ru is not oxidized. Specifically, we describe the adsorbate and the surrounding metal atoms at the DFT level of theory. Here, we also considered the electrostatic field effect of the water molecules on adsorbate–metal interactions. Next, for the water–water and water–adsorbate interactions, we used established classical force fields. Finally, for the water–Ru surface interaction, for which no reliable force fields have been published, we used Behler–Parrinello high-dimensional neural network potentials (HDNNPs). Employing this setup, we used our explicit solvation for metal surface (eSMS) approach to compute the aqueous-phase effect on the low-coverage adsorption of selected molecules and atoms on the (0001) facet of Ru. In agreement with previous experimental and computational studies of oxygenated molecules over transition metal facets, we found that liquid water destabilizes the tested adsorbates on Ru(0001). Interestingly, our findings indicate that adsorbates on Ru are less affected by the presence of an aqueous phase than on other transition metals (e.g., Pt), highlighting the necessity of experimental investigations of Ru-based catalytic systems in liquid water.

Adsorption↗

Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors

SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (K dimer ) 2–3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ~10 to 30%, relative to that of the wild-type enzyme, without altering K dimer . Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MPro WT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MPro WT -ensitrelvir. In conclusion, chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.

60 APPLIED LIFE SCIENCES↗

Water Dielectric Function at Finite Wavelength and the Convergence of Its Large Wavelength Limit (Static Dielectric) by Fluctuation Formulas

Here we provide a general analysis of the longitudinal dielectric function ε l (k) via fluctuation formulas at finite wavelength k, including the static dielectric constant ε w = ε l (k → 0), and analyze the different sources of errors, deriving explicit formulas. Simulations with the SPC/E water model show that the convergence of fluctuation formulas to compute the static dielectric constant is slow and requires long simulations. The analysis of ε l (k) allows us to identify the long- and short-wavelength limits and provide a precise determination of the location of the poles as well as the zeros in the complex plane, which determine the short-distance form of the electrostatic (Coulomb) interaction among charged particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Restoring Symmetry and Enhancing Exchange via Chiral Molecular-Magnetic Hexagons

Modified behaviors of molecules, designed for device or energy applications, can occur due to lattice-molecule incompatibilities in point-group symmetries (PGS), long-range interactions between neighboring molecules, or latticemolecule charge transfer. Such sensitivities are prerequisite for the use of quantum molecules as devices, but removing certain broken symmetries is desirable from the standpoint of simplifying their behaviors. Here, we demonstrate symmetry restoration to molecular-magnetic lattices and show that it leads to strengthened exchange-coupling due to dipolar electrostatic interactions between neighboring molecules and due to manifestations of an earlier identification of a spin-sensitive slightly mobile electron by Hooshmand et al. Starting with a broken symmetry molecular magnet of current interest, we demonstrate a more robust structure composed of six molecular magnets on a h-BN-like surface. The broken point-group symmetry is healed by constructing interpenetrating equilateral triangular structures that are appropriately ratcheted to preserve three-fold rotational symmetry and inversion symmetry.

Pederson, Mark R.↗

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗