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All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Studies of the structure and function of Mms6, a bacterial protein that promotes the formation of magnetic nanoparticles

Here we report structural and functional studies of Mms6, a biomineralization protein that can promote the formation in vitro of magnetic nanoparticles with sizes and morphologies similar to the magnetites synthesized by magnetotactic bacteria. We found the binding pattern of Mms6 to ferric ion to be two-phase and multivalent. We quantatively determined that Mms6 binds one Fe 3+ with a very high affinity (K d = 10 16 M). The second phase of iron binding is multivalent and cooperative with respect to iron with a K d in the μM range and a stoichiometry of about 20 ferric ion per protein molecule. We found that Mms6 exists in large particles of two sizes, one consisting of 20-40 monomeric units and the other of 200 units. From proteolytic digestion, ultracentrifugation and liposome fusion studies, we found that Mms6 forms a large micellar quaternary structure with the N-terminal domain self-assembling into a uniformly sized micelle and the C-terminal domain on the surface. The two-phase iron-binding pattern may be relevant to iron crystal formation. We propose that the first high affinity phase may stabilize a new conformation of the C-terminal domain that allows interaction with other C-terminal domains leading to a structural change in the multimeric protein complex that enables the second low affinity iron binding phase to organize iron and initiate crystal formation. We also observed a dimeric apparent molecular mass of the Mms6 C-terminal peptide (C21Mms6). We speculate that the C-terminal domain may form higher order quaternary arrangements on the surface of the micelle or when anchored to a membrane by the N-terminal domain. The change in fluorescence quenching in the N-terminal domain with iron binding suggests a structural integrity between the C- and N-terminal domains. The slow change in trp fluorescence as a function of time after adding iron suggests a very slow conformational change in the protein that involves both N- and C-terminal domains. We interpret these results to mean that there is a coordinated global change in Mms6 structure that involves multiple Mms6 monomers. Based on our observations, we propose a mechanism by which Mms6 can promote the formation of crystalline nanoparticles. Upon binding ferric iron at very high affinity with a molar ratio of 1, the C-terminal domains undergo a conformational change, coordinated with the N-terminal domain that initiates a slow rearrangement of the multiprotein complex to create a surface on which many iron atoms can organize. This slow rearrangement allows the initiation of a crystal that is propagated on the protein surface to form a crystal seed. We also observed that Mms6 undergoes a periodical structural change with increasing molar ratios of iron to protein. The observed structural change occurs in the N-terminal domain, but reflects iron binding by the C-terminal domain. A mutant Mms6 that does not promote the formation of superparamagnetic magnetite also does not undergo the periodic structural change. The correlation between the ability to form magnetic nanoparticles and the ability to undergo the periodic structural change suggests that this structural change might participate in the mechanism of magnetite formation. Analysis of the quaternary structure of Mms6 protein and its C-terminal domain reveals that the C-terminal domain contributes to the overall stability of the quaternary structure of Mms6. The C-terminal domain of Mms6 displays ferric reductase activity that is diminished in the mutant C-terminus. Although it does not play a role in the in vitro formation of magnetite during which both ferrous and ferric forms of iron are provided, this reductase activity may participate in magnetite formation in vivo. Our results suggest that the iron binding properties and quaternary structure of Mms6 is responsible for formation of magnetic nanoparticles. The ability for Mms6 protein to form a quaternary structure and the ability of that structure to change as iron is incorporated into a crystal may be fundamental aspects of the mechanism by which a small protein such as Mms6 can promote the formation of magnetite crystals.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A DNA molecular printer capable of programmable positioning and patterning in two dimensions

Nanoscale manipulation and patterning usually require costly and sensitive top-down techniques such as those used in scanning probe microscopies or in semiconductor lithography. DNA nanotechnology enables exploration of bottom-up fabrication and has previously been used to design self-assembling components capable of linear and rotary motion. In this work, we combine three independently controllable DNA origami linear actuators to create a nanoscale robotic printer. The two-axis positioning mechanism comprises a moveable gantry, running on parallel rails, threading a mobile sleeve. We show that the device is capable of reversibly positioning a write head over a canvas through the addition of signaling oligonucleotides. We demonstrate “write” functionality by using the head to catalyze a local DNA strand–exchange reaction, selectively modifying pixels on a canvas. Furthermore, this work demonstrates the power of DNA nanotechnology for creating nanoscale robotic components and could find application in surface manufacturing, biophysical studies, and templated chemistry.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2019

Classify QCD phase transition with deep learning

The state-of-the-art pattern recognition method in machine learning (deep convolution neural network) is used to identify the equation of state (EoS) employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering the nature of the phase transition in QCD. The EoS-meter is model independent and insensitive to other simulation inputs including the initial conditions and shear viscosity for hydrodynamic simulations. Through this study we demonstrate that there is a traceable encoder of the dynamical information from the phase structure that survives the evolution and exists in the final snapshot of heavy ion collisions and one can exclusively and effectively decode these information from the highly complex final output with machine learning when traditional methods fail. Besides the deep neural network, the performance of traditional machine learning classifiers are also provided.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2010

From a discrete to a continuous model for interpulse interference with a frequency-comb laser

We have investigated correlation patterns generated by a frequency-comb laser in a dispersive unbalanced Michelson interferometer and apply the developed formalism to the case of distance metrology. Due to group velocity dispersion, the position of the brightest fringe of the correlation pattern, which is used for distance determination, cannot be derived by simply using the definition of group refractive index of the dispersive medium. It is shown that the discrete spectrum of the optical frequency comb gives rise to correlation functions which can be represented by a series, namely a discrete correlation series. We have developed a general formalism, valid for any pulse train, extending the discrete model to a continuous model of cross-correlation functions using the Poisson summation. Our model is relevant for any offset and repetition frequency of the frequency comb. From the continuous cross-correlation model we show that, even for a homogeneous dispersive medium the position of the brightest fringe varies nonlinearly for small delay distances and stabilizes for longer ones. We have compared the theoretical results to measurements of pulse propagation in air for path-lengths up to 200 m.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2010

Higher-order phase shift reconstruction approach

Purpose: Biological soft tissues encountered in clinical and preclinical imaging mainly consists of atoms of light elements with low atomic numbers and their elemental composition is nearly uniform with little density variation. Hence, x-ray attenuation contrast is relatively poor and cannot achieve satisfactory sensitivity and specificity. In contrast, x-ray phase-contrast provides a new mechanism for soft tissue imaging. The x-ray phase shift of soft tissues is about a thousand times greater than the x-ray absorption over the diagnostic x-ray energy range, yielding a higher signal-to-noise ratio than the attenuation contrast counterpart. Thus, phase-contrast imaging is a promising technique to reveal detailed structural variation in soft tissues, offering a high contrast resolution between healthy and malignant tissues. Here the authors develop a novel phase retrieval method to reconstruct the phase image on the object plane from the intensity measurements. The reconstructed phase image is a projection of the phase shift induced by an object and serves as input to reconstruct the 3D refractive index distribution inside the object using a tomographic reconstruction algorithm. Such x-ray refractive index images can reveal structural features in soft tissues, with excellent resolution differentiating healthy and malignant tissues. Methods: A novel phase retrieval approach is proposed to reconstruct an x-ray phase image of an object based on the paraxial Fresnel-Kirchhoff diffraction theory. A primary advantage of the authors' approach is higher-order accuracy over that with the conventional linear approximation models, relaxing the current restriction of slow phase variation. The nonlinear terms in the autocorrelation equation of the Fresnel diffraction pattern are eliminated using intensity images measured at different distances in the Fresnel diffraction region, simplifying the phase reconstruction to a linear inverse problem. Numerical experiments are performed to demonstrate the accuracy and stability of the proposed approach. Results: The proposed reconstruction formula is a generalization of the transport of intensity equation (TIE). It has the second-order accuracy compared to the linear model used in the conventional phase retrieval approach. The numerical experiments demonstrate that the accuracy and stability of the proposed phase reconstruction method outperforms the TIE-based reconstruction method. Conclusions: A novel approach has been proposed to retrieve an x-ray phase shift image induced by an object from intensity images measured at different distances in the Fresnel diffraction region. The authors' approach has the second-order accuracy and is able to retrieve the phase shift of an object stably, overcoming the restriction of slow phase variation assumed by the conventional phase retrieval techniques.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2012

Influence of pH condition on colloidal suspension of exfoliated graphene oxide by electrostatic repulsion

A facile chemical process is described to produce graphene oxide utilizing a zwitterions amino acid intermediate from graphite oxide sheets. 11-aminoundecanoic acid molecules were protonated to intercalate molecules into the graphite oxide sheets to achieve ion exchange, and the carboxyl groups were then ionized in a NaOH solution to exfoliate the graphite oxide sheets. In this way, the produced graphene oxide nanosheets were stably dispersed in water. The delaminated graphene nanosheets were confirmed by XRD, AFM, and TEM. XRD patterns indicated the d{sub 002}-spacing of the graphite greatly increased from 0.380 nm and 0.870 nm. AFM and TEM images showed that the ordered graphite crystal structure of graphene nanosheets was effectively exfoliated by this method. The prepared graphene nanosheets films showed 87.1% transmittance and a sheet resistance of 2.1 Multiplication-Sign 10{sup 3} {Omega}/square. - Graphical abstract: A stable graphene oxide suspension could be quickly prepared by exfoliating a graphite oxide suspension by a host-guest electrostatic repulsion in aqueous solution. Highlights: Black-Right-Pointing-Pointer Graphene nanosheets were prepared by a zwitterions amino acid intermediate from graphite oxide. Black-Right-Pointing-Pointer 11-aminoundecanoic acid was protonated to intercalate molecules into the graphene oxide to achieve ion exchange. Black-Right-Pointing-Pointer The d{sub 002}-spacing of the graphite oxide greatly increased from 0.330 nm to 0.415 nm after 11-aminoundecanoic acid treatment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Characterization of electron-beam recorded microdomain patterns on the nonpolar surface of LiNbO{sub 3} crystal by nondestructive methods

We report on characterization of the electron-beam fabricated planar domain gratings on the nonpolar (Y-) surface of LiNbO{sub 3} crystals performed with the use of AFM and confocal second harmonic generation (SHG) microscopy. The dependence of domain formation on the irradiation conditions was investigated. The relation of domain thicknesses to the electron penetration depth is experimentally proved. In particular, the possibility of controlling the thickness of planar domains by varying acceleration electron-beam voltages is demonstrated. The observed specificity of SHG is analyzed in the framework of the Kleinman-Boyd theory [G. D. Boyd and D. A. Kleinman, J. Appl. Phys. 39, 3597 (1968)] and Uesu approach [Kaneshiro et al., J. Appl. Phys. 104, 054112 (2008); Kaneshiro et al., J. Opt. Soc. Am. B 27, 888 (2010)] extended in our case to reflection geometry. The calculations performed predict the dependence of SHG conversion efficiency η on the domain thickness, which is in a qualitative agreement with the experiment. It is shown that planar domains on top of the nonpolar surface always enhance the value of η as compared with the bare surface.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Magnetization reversal in magnetic dot arrays: Nearest-neighbor interactions and global configurational anisotropy

Various proposals for future magnetic memories, data processing devices, and sensors rely on a precise control of the magnetization ground state and magnetization reversal process in periodically patterned media. In finite dot arrays, such control is hampered by the magnetostatic interactions between the nanomagnets, leading to the non-uniform magnetization state distributions throughout the sample while reversing. In this paper, we evidence how during reversal typical geometric arrangements of dots in an identical magnetization state appear that originate in the dominance of either Global Configurational Anisotropy or Nearest-Neighbor Magnetostatic interactions, which depends on the fields at which the magnetization reversal sets in. Based on our findings, we propose design rules to obtain the uniform magnetization state distributions throughout the array, and also suggest future research directions to achieve non-uniform state distributions of interest, e.g., when aiming at guiding spin wave edge-modes through dot arrays. Our insights are based on the Magneto-Optical Kerr Effect and Magnetic Force Microscopy measurements as well as the extensive micromagnetic simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Simulation and Emulation of X-Ray Diffraction from Dynamic Compression Experiments

Many important aspects of the dynamic thermo-mechanical response of materials occur at the mesoscale, i.e. a physical scale of interactions smaller than what can be adequately described by homogenous behaviors, yet larger than the scale of the atomic lattice. Concurrent advancements in computational power, continuum theory, and experimental diagnostics are enabling unprecedented understanding of such interactions. However, we cannot develop a sufficient level of confidence in such mesoscale capability until the constitutive description of the underlying constituents is reliably representative of their actual physical behavior. Therefore, there is a strong need to combine experimental, modeling, and data-science techniques to validate models of the thermomechanical response of individual single crystals. One experimental diagnostic with high potential impact to shock physics and materials science is in-situ x-ray diffraction. This paper is primarily focused on simulation of x-ray diffraction in shock physics, but with an aim toward quantifying parametric uncertainty of simulation models. Here, we develop and demonstrate a data-science and model-driven approach to constrain the parameterization of continuum models of crystal lattice deformation associated with the shock response of crystalline materials. The framework is built around the connection between continuum hydrodynamic simulations of lattice deformation and a new Bragg diffraction simulation code, BarberShop. The dynamic deformation of a crystal lattice is modeled using the DiscoFlux model within an arbitrary Lagrangian-Eulerian hydrodynamic code, FLAG. These detailed continuum simulations of lattice deformation can be computationally slow, thus a statistical model is used to emulate the evolution of lattice deformation fields in time and across the considered model parameter space. Emulated lattice deformation fields can then be generated rapidly for any combination of physics model parameters. In turn, these fields can be fed into BarberShop to realize a rapid prediction of Bragg diffraction patterns associated with particular values of physics model parameters. The framework enables parameterization of the single crystal model to obtain Bragg diffraction patterns that most closely resemble a corresponding measurement. Furthermore, the framework naturally provides sensitivities of the lattice deformation to the physics parameters. We highlight the utility of this framework through the application to a synthetic closed-loop inverse problem leading to the parameterization of a single crystal material model. As a model problem, we consider the dynamic response of the energetic molecular crystal, cyclotrimethylenetrinitramine (or RDX), under dynamic compression induced by simulated flyer plate impact experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Crystal structure of Kuzel's salt 3CaO.Al{sub 2}O{sub 3}.1/2CaSO{sub 4}.1/2CaCl{sub 2}.11H{sub 2}O determined by synchrotron powder diffraction

The crystal structure of Kuzel's salt has been successfully determined by synchrotron powder diffraction. It crystallizes in the rhombohedral R3-bar symmetry with a = 5.7508 (2) A, c = 50.418 (3) A, V = 1444.04 (11) A{sup 3}. Joint Rietveld refinement was realized using three X-ray powder patterns recorded with a unique wavelength and three different sample-to-detector distances. Kuzel's salt is the chloro-sulfoaluminate AFm phase and belongs to the layered double hydroxide (LDH) large family. Its structure is composed of positively charged main layer [Ca{sub 2}Al(OH){sub 6}]{sup +} and negatively charged interlayer [Cl{sub 0.50}.(SO{sub 4}){sub 0.25}.2.5H{sub 2}O]{sup -}. Chloride and sulfate anions are ordered into two independent crystallographic sites and fill successive interlayer leading to the formation of a second-stage compound. The two kinds of interlayer have the compositions [Cl.2H{sub 2}O]{sup -} and [(SO{sub 4}){sub 0.5}.3H{sub 2}O]{sup -}. The crystal structure explains why chloride and sulfate anions are not substituted and why the formation of extended solid solution in the chloro-sulfate AFm system does not occur.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Prediction of low-Z collinear and noncollinear antiferromagnetic compounds having momentum-dependent spin splitting even without spin-orbit coupling

The over 60 years old Rashba-Dresselhaus effect predicts spin-orbit coupling (SOC) induced momentum-dependent spin splitting and spin polarization in materials with noncentrosymmetric structures. Strong SOC induced effects usually require high-atomic number (Z) elements such as rare-earth elements. It has recently been pointed out that antiferromagnets could hold SOC-independent spin splitting and spin polarization. In the present work we develop the spatial and magnetic symmetry conditions enabling such antiferromagnet (AFM)-induced spin splitting, dividing the 1651 magnetic space groups into seven different spin splitting prototypes (SST-1 to SST-7). This analysis places the physics of AFM spin splitting (SST-4) within the broader context of symmetry conditions that enable the more familiar forms of spin splitting, such as ferromagnetic Zeeman effect (SST-5), nonmagnetic no spin splitting (SST-6), and the nonmagnetic Rashba and Dresselhaus effects (SST-7). The AFM-induced spin splitting and spin polarization do not necessarily require breaking of inversion symmetry or the presence of SOC, hence can exist even in centrosymmetric, low-Z light element compounds, considerably broadening the material base for spin manipulations. We use the “inverse design” approach of first formulating the target property (here, spin splitting in low-Z compounds not restricted to low symmetry structures), then derive the enabling physical design principles—the magnetic symmetry conditions—to search realizable compounds that satisfy these a priori design principles. This process uncovers 422 magnetic space groups (160 centrosymmetric and 262 noncentrosymmetric) that could hold AFM-induced, SOC-independent spin splitting and spin polarization. We then search for stable compounds following such enabling symmetries. We investigate the electronic and spin structures of some selected prototype compounds by density functional theory (DFT) and find spin textures that are different than the traditional Rashba-Dresselhaus patterns and exist even in the absence of SOC effect. We provide the DFT results for all antiferromagnetic spin splitting prototypes (SST-1, SST-2, SST-3, SST-4), and concentrate on two limits of SST-4 that are particularly unusual: When spin splitting is momentum dependent (just like the Rashba effect) but is enabled in antiferromagnets even in the absence of SOC in the Hamiltonian. This includes examples of (a) centrosymmetric SST-4A compounds (e.g., orthorhombic LaMnO 3 illustrating collinear AFM, as well as cubic NiS 2 illustrating noncollinear AFM) and (b) noncentrosymmetric SST-4B compounds (e.g., rhombohedral MnTiO 3 illustrating collinear AFM and hexagonal ScMnO 3 illustrating noncollinear AFM). The symmetry design principles outlined here, along with their transformation into an inverse design material search approach and DFT verification, could open the way to their experimental examination.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Integrated modeling of boron powder injection for real-time plasma-facing component conditioning

An integrated modeling framework for investigating the application of solid boron (B) powder injection for real-time surface conditioning of plasma-facing components (PFCs) in tokamak environments is presented. Utilizing the DIII-D impurity powder dropper (IPD) setup, this study simulates B powder injection scenarios ranging from milligrams to tens of milligrams per second, corresponding to boron flux rates of 10 20 –10 21 B/s in standard L-mode conditions. The comprehensive modeling approach combines EMC3-EIRENE for simulating the deuterium plasma background and the Dust Injection Simulator (DIS) for the ablation and transport of the boron powder particles. EMC3 trace impurity fluid modeling results show substantial boron transport to the inboard lower divertor, predominantly influenced by the main ion plasma flow. The dependency on powder particle size (5-250 µm) was found to be insignificant for the scenario considered. The effects of erosion and redeposition were considered to reconcile the discrepancies with experimental observations, which saw substantial deposition on the outer divertor plasma-facing components. For this purpose, the WallDYN3D code was updated to include boron sources within the plasma domain and integrated into the modeling framework. The mixed-material migration modeling shows evolving boron deposition patterns, suggesting the formation of mixed B-C layers or predominantly B coverage depending on the powder mass flow rate. While the modeling outcomes at lower B injection rates tend to align with DIII-D experimental observations, the prediction of near-pure boron layers at higher rates has yet to be experimentally verified in the carbon environment of the DIII-D tokamak. The extensive reach of boron layers found in the modeling suggests the need for modeling that encompasses the entire wall geometry for more accurate experimental correlations. This integrated approach sets a precedent for analyzing and applying real-time in-situ boron coating techniques in advanced tokamak scenarios, potentially extendable to ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Physical properties of intergrowth compound Eu 2 CuZn 2 P 3

Here, the physical properties of single-crystalline Eu 2 ⁢CuZn 2 ⁢P 3 were inspected via thermodynamic, transport, and neutron diffraction measurements. Eu 2 ⁢ CuZn 2⁢ P 3 is composed of EuCuP and EuZn 2 ⁢ P 2 motifs stacked in a one-to-one ratio. The magnetic response of Eu 2 ⁢ CuZn 2 ⁢ P 3 is similar to that of EuZn 2 ⁢ P 2 in its A-type antiferromagnetic (semiconducting) state. A Néel temperature of T N = 40.3K is obtained from the specific heat capacity. Single-crystal neutron diffraction reveals a (001) magnetic propagation vector, with primarily in-plane moments coupled along [001] in an up-up-down-down pattern. This spin structure retains the ferromagnetic EuCuP motifs and antiferromagnetic coupling across the EuZn 2 ⁢P 2 motifs. The electrical resistivity is characterized by metallic behavior above 100 K, an increase in ρ upon cooling below ≈ 75K, and a large negative magnetoresistance below T N . First principles calculations evidence a narrow band gap for antiferromagnetic ordering and semimetallic behavior for the ferromagnetic state. This is consistent with the observed effect of magnetic field on the electrical resistivity. Hall effect measurements reveal a field-induced, negative anomalous Hall effect that increases on cooling down to 2 K. Also, an unconventional contribution to the Hall effect dominates the low-field Hall signal, particularly near T N , and is similar in appearance to a topological Hall effect. However, further work is necessary to understand if any of the transport properties have topological origins or if magnetism-induced modifications to the Fermi surface induce these unusual Hall effect signals in this and related materials.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Structural and Functional Proteomic Analysis of a Developing Energy Transducing Membrane

While much is known about the light reactions of photosynthesis in purple bacteria, comparatively little information is available on how the requisite integral membrane proteins are assembled, their patterns of cellular localization are established or their apoproteins cooperate with numerous assembly factors in their insertion into the growing intracytoplasmic membrane (ICM). This problem was approached through a detailed structural and functional proteomic analysis of ICM assembly process in the well-characterized purple bacterium Rhodobacter sphaeroides. Proteomic approaches have focused upon identification of membrane proteins temporally expressed during ICM development and spatially localized in both membrane growth initiation sites and in mature ICM vesicles. Protocols were established for ICM induction under reduced aeration and ICM remodeling in cells adapting to low intensity illumination, which permitted isolation, in sucrose density gradients, of ICM growth initiation sites as an upper pigmented band (UPB) and mature ICM vesicles as the main (chromatophore) band. Non-denaturing clear native gel electrophoresis (CNE) of these isolated membrane fractions gave rise to pigmented bands containing the peripheral light-harvesting 2 (LH2) antenna and the reaction center-light-harvesting 1 (RC-LH1) core complex, together with a full array of other ICM proteins, which were subjected to proteomic analysis.

14 SOLAR ENERGY↗
DOE OSTI2012

Oxygen cluster anions revisited: Solvent-mediated dissociation of the core O{sub 4}{sup -} anion

The electronic structure and photochemistry of the O{sub 2n}{sup -}(H{sub 2}O){sub m}, n= 1-6, m= 0-1 cluster anions is investigated at 532 nm using photoelectron imaging and photofragment mass-spectroscopy. The results indicate that both pure oxygen clusters and their hydrated counterparts with n{>=} 2 form an O{sub 4}{sup -} core. Fragmentation of these clusters yields predominantly O{sub 2}{sup -} and O{sub 2}{sup -}{center_dot}H{sub 2}O anionic products, with the addition of O{sub 4}{sup -} fragments for larger parent clusters. The fragment autodetachment patterns observed for O{sub 6}{sup -} and larger O{sub 2n}{sup -} species, as well as some of their hydrated counterparts, indicate that the corresponding O{sub 2}{sup -} fragments are formed in excited vibrational states (v {>=} 4). Yet, surprisingly, the unsolvated O{sub 4}{sup -} anion itself does not show fragment autodetachment at 532 nm. It is hypothesized that the vibrationally excited O{sub 2}{sup -} is formed in the intra-cluster photodissociation of the O{sub 4}{sup -} core anion via a charge-hopping electronic relaxation mechanism mediated by asymmetric solvation of the nascent photofragments: O{sub 4}{sup -}{yields} O{sub 2}{sup -}(X{sup 2}{Pi}{sub g}) + O{sub 2}(a{sup 1}{Delta}{sub g}) {yields} O{sub 2}(X{sup 3}{Sigma}{sub g}{sup -}) + O{sub 2}{sup -}(X{sup 2}{Pi}{sub g}). This process depends on the presence of solvent molecules and leads to vibrationally excited O{sub 2}{sup -}(X{sup 2}{Pi}{sub g}) products.

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

Automated Construction of Potential Energy Surfaces Suitable to Describe van der Waals Complexes with Highly Excited Nascent Molecules: The Rotational Spectra of Ar–CS( v ) and Ar–SiS( v )

Some reactions produce extremely hot nascent products which nevertheless can form sufficiently long-lived van der Waals (vdW) complexes—with atoms or molecules from a bath gas—as to be observed via microwave spectroscopy. Theoretical calculations of such unbound resonance states can be much more challenging than ordinary bound-state calculations depending on the approach employed. One encounters not just the floppy, and perhaps multiwelled potential energy surface (PES) characteristic of vdWs complexes, but in addition, one must contend with excitation of the intramolecular modes and its corresponding influence on the PES. Straightforward computation of the (resonance) rovibrational levels of interest, involves the added complication of the unbound nature of the wave function, often treated with techniques such as introducing a complex absorbing potential. Here, we have demonstrated that a simplified approach of making a series of vibrationally effective PESs for the intermolecular coordinates—one for each reaction product vibrational quantum number of interest—can produce vdW levels for the complex with spectroscopic accuracy. This requires constructing a series of appropriately weighted lower-dimensional PESs for which we use our freely available PES-fitting code AUTOSURF. The applications of this study are the Ar–CS and Ar–SiS complexes, which are isovalent to Ar–CO and Ar–SiO, the latter of which we considered in a previously reported study. Using a series of vibrationally effective PESs, rovibrational levels and predicted microwave transition frequencies for both complexes were computed variationally. A series of shifting rotational transition frequencies were also computed as a function of the diatom vibrational quantum number. The predicted transitions were used to guide and inform an experimental effort to make complementary observations. Comparisons are given for the transitions that are within the range of the spectrometer and were successfully recorded. Calculations of the rovibrational level pattern agree to within 0.2% with experimental measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

What Hinders Electron Transfer Dissociation (ETD) of DNA Cations?

Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a•/w or d/z• ion pairs. This reaction pathway contrasts with previous findings on the dissociation processes after electron capture by DNA cations, suggesting multiple, parallel dissociation channels. However, all these channels merely result in partial fragmentation of the precursor ion because the charge-reduced DNA radical cations are quite stable. Two hypotheses are put forward to explain the low dissociation yield of DNA radical cations: it is either attributed to non-covalent interactions between complementary fragments or to the stabilization of the unpaired electron in stacked nucleobases. MS{sup 3} experiments suggest that the charge-reduced species is the intact oligonucleotide. Moreover, introducing abasic sites significantly increases the dissociation yield of DNA cations. Consequently, the stabilization of the unpaired electron by π–π-stacking provides an appropriate rationale for the high intensity of DNA radical cations after electron transfer. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Accelerating molecular property calculations with nonorthonormal Krylov space methods

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remain small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.

74 ATOMIC AND MOLECULAR PHYSICS↗