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At least 1,657 records · Page 92
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Protonated Bilin Ring System in Both Photostates

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors distantly related to phytochromes. Both CBCRs and phytochromes use photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert between two states with distinct spectral and biochemical properties, the dark state and the photoproduct. The isolated CBCR domain NpR6012g4 from Nostoc punctiforme is a well-characterized member of the canonical red/green CBCR subfamily, photosensory domains that can function as sensors for light color or intensity to regulate phototactic responses of filamentous cyanobacteria. Such red/green CBCRs utilize conserved Phe residues to tune the photoproduct for green light absorption, but conflicting interpretations of the photoproduct chromophore structure have been proposed. In the hydration model, the proposed photoproduct state is extensively solvated, with a loosely bound, conformationally flexible chromophore. In the trapped-twist model, the photoproduct chromophore is sterically constrained by hydrophobic amino acids, including the known Phe residues. Here, we have characterized chromophore structure in NpR6012g4 using solution nuclear magnetic resonance spectroscopy and a series of labeled chromophores. Four NH resonances are assigned for both the red-absorbing dark state and the green-absorbing photoproduct. Moreover, observed 13 C chemical shifts are in good agreement with those obtained for protonated rather than deprotonated bilins in ab initio calculations. Our results demonstrate that NpR6012g4 has a protonated, cationic bilin π system in both photostates, consistent with a photoproduct structure in which the chromophore is not extensively hydrated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A Mn Bipyrimidine Catalyst Predicted To Reduce CO 2 at Lower Overpotential

Experimentally, [(L)Mn(CO) 3 ] - (where L = bis-alkyl-substituted bipyridine) has been observed to catalyze the electrochemical reduction of CO 2 to CO in the presence of trifluoroethanol (TFEH). Here we report the atomistic level mechanism of complete catalytic cycles for this reaction, on the basis of DFT calculations (B3LYP-D3 with continuum solvation) of the free energies of reaction and activation, as well as reduction potentials for all catalytically relevant elementary steps. The highly exergonic homoconjugation and carbonation of TFE– play critical roles in reaction thermodynamics and kinetics, the overall half-reaction being 3CO 2 + 2TFEH + 2e – → CO + H 2 O + 2[F 3 CCH 2 OCO 2 ] - (calculated standard reduction potential: -1.49 V vs SCE). In the catalytic cycle for CO formation, CO 2 coordinates to [(L)Mn(CO) 3 ] - (1a, L = bpy), and the adduct is then protonated to form [(L)Mn(CO) 3 (CO 2 H)] (3a). 3a subsequently reacts to form [(L)Mn(CO) 4 ] 0 (5a) via one of two pathways: (a) TFEH-mediated dehydroxylation to [(L)Mn(CO) 4 ] + (4a), followed by one-electron reduction to 5a, or (b) under more reducing potentials, one-electron reduction to [(L)Mn(CO)3(CO2H)]- (3'a), followed by dehydroxylation to 5a. Pathway b has a lower activation energy by 2.2 kcal mol –1 . Consequently, the maximum catalytic turnover frequency (TOFmax) is achieved at ~-1.75 V vs SCE (~0.25 V overpotential). For the analogous bipyrimidine compound (not yet studied experimentally), reduction of 3b to 3'b occurs at a potential 0.5 V more positive than that of 3a, and the overpotential required to achieve TOF max is predicted to be lower by ~0.25 V. This improvement is, however, achieved at the price of a lower TOF max , and we predict that 1b has superior TOF at potentials above ~-1.6 V vs SCE. In addition, the various factors contributing to product selectivity (CO over H 2 ) are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations

The calculation of Hartree-Fock exchange (HFX) is computationally demanding for large systems described with high-quality basis sets. In this work, we show that excellent performance and good accuracy can nevertheless be obtained if an auxiliary density matrix is employed for the HFX calculation. Several schemes to derive an auxiliary density matrix from a high-quality density matrix are discussed. Key to the accuracy of the auxiliary density matrix methods (ADMM) is the use of a correction based on standard generalized gradient approximations for HFX. ADMM integrates seamlessly in existing HFX codes and, in particular, can be employed in linear scaling implementations. Demonstrating the performance of the method, the effect of HFX on the structure of liquid water is investigated in detail using Born-Oppenheimer molecular dynamics simulations (300 ps) of a system of 64 molecules. Representative for large systems are calculations on a solvated protein (Rubredoxin), for which ADMM outperforms the corresponding standard HFX implementation by approximately a factor 20.

Chemistry↗
DOE OSTI2010

Efficient Multistate Reactive Molecular Dynamics Approach Based on Short-Range Effective Potentials

Nonbonded interactions between molecules usually include the van der Waals forceand computationally expensive long-range electrostatic interactions. This article develops a moreefficient approach: the effective-interaction multistate empirical-valence-bond (EI-MS-EVB) model.The EI-MS-EVB method relies on a mapping of all interactions onto a short-range and thus,computationally efficient effective potential. The effective potential is tabulated by matching itsforce to known trajectories obtained from the full-potential empirical multistate empirical-valence-bond (MS-EVB) model. The effective pairwise interaction depends on and is uniquely determinedby the atomic configuration of the system, varying only with respect to the hydrogen-bondingtopology. By comparing the EI-MS-EVB and full MS-EVB calculations of several equilibriumand dynamic properties important to hydrated excess proton solvation and transport, we showthat the EI-MS-EVB model produces very accurate results for the specific system in which thetabulated potentials were generated. The EI-MS-EVB potential also transfers reasonably wellto similar systems with different temperatures and box sizes. The EI-MS-EVB method alsoreduces the computational cost of the nonbonded interactions by about 1 order of magnitude incomparison with the full algorithm.

Chen, Hanning↗
DOE OSTI2013

The Performance of Density Functionals for Sulfate-Water Clusters

The performance of 24 density functionals, Hartree-Fock, and MP2 is assessed with respect to the energetics of 49 sulfate-water clusters with between three and six water molecules. Included among the density functionals are GGA, meta-GGA, hybrid GGA, hybrid meta-GGA, and double hybrid density functionals, as well as the LDA. Three types of dispersion corrections (VV10, XDM, and -D) are tested in conjunction with these functionals. The functionals are compared using the relative and binding energies of the sulfatewater clusters as the main criteria. It is discovered that a majority of current density functionals are unable to simultaneously capture the physics necessary to describe both the relative and binding energies of the anionic solvation clusters. The only density functionals that perform acceptably with respect to both measures are XYG3 and XYGJOS, primarily due to their balanced treatment of exchange and correlation. On the other hand, density functionals with exact exchange that lack nonlocal correlation tend to perform well only for the relative energies. However, there is evidence that hybrid density functionals that provide a more comprehensive treatment of local correlation through their dependence on the kinetic energy density and their ability to treat the inhomogeneities in the present system can partially resolve this issue. While dispersion correction functionals cannot replace the accuracy provided by MP2 correlation, it is shown that the proper combination of a hybrid GGA functional with a dispersion correction functional can lead to drastic improvements in the binding energies of the parent functional, while preserving its performance with respect to the relative energies.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2013

Simulating One-Photon Absorption and Resonance Raman Scattering Spectra Using Analytical Excited State Energy Gradients within Time-Dependent Density Functional Theory

A parallel implementation of analytical time-dependent density functional theory gradients is presented for the quantum chemistry program NWChem. The implementation is based on the Lagrangian approach developed by Furche and Ahlrichs. To validate our implementation, we first calculate the Stokes shifts for a range of organic dye molecules using a diverse set of exchange-correlation functionals (traditional density functionals, global hybrids, and range-separated hybrids) followed by simulations of the one-photon absorption and resonance Raman scattering spectrum of the phenoxyl radical, the well-studied dye molecule rhodamine 6G, and a molecular host–guest complex (TTFcCBPQT 4+ ). The study of organic dye molecules illustrates that B3LYP and CAM-B3LYP generally give the best agreement with experimentally determined Stokes shifts unless the excited state is a charge transfer state. Absorption, resonance Raman, and fluorescence simulations for the phenoxyl radical indicate that explicit solvation may be required for accurate characterization. For the host–guest complex and rhodamine 6G, it is demonstrated that absorption spectra can be simulated in good agreement with experimental data for most exchange-correlation functionals. Finally, however, because one-photon absorption spectra generally lack well-resolved vibrational features, resonance Raman simulations are necessary to evaluate the accuracy of the exchange-correlation functional for describing a potential energy surface.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Ground and excited states of the [Fe(H2O)6]2+ and [Fe(H2O)6]3+ clusters: Insight into the electronic structure of the [Fe(H2O)6]2+ – [Fe(H2O)6]3+ complex

We report the ground and low lying electronically excited states of the [Fe(H2O)6]2+ and [Fe(H2O)6]3+ clusters using multi-configuration electronic structure theory. In particular, we have constructed the Potential Energy Curves (PECs) with respect to the iron-oxygen distance when removing all water ligands at the same time from the cluster minima and established their correlation to the long range dissociation channels. Due to the fact that both the second and third ionization potentials of iron are larger than the one for water, the ground state products asymptotically correlate with dissociation channels that are repulsive in nature at large separations as they contain at least one H2O+ fragment and a positive metal center. The most stable equilibrium structures emanate – via intersections and/or avoided crossings – from the channels consisting of the lowest electronic states of Fe2+(5D; 3d6) or Fe3+(6S; 3d5) and six neutral water molecules. Upon hydration, the ground state of Fe2+(H2O)6 is a triply (5Tg) degenerate one with the doubly (5Eg) degenerate state lying slightly higher in energy. Similarly, Fe3+(H2O)6 has a ground state of 6Ag symmetry under Th symmetry. We furthermore examine a multitude of electronically excited states of many possible spin multiplicities, and report the optimized geometries for several selected states. The PECs for those cases are characterized by a high density of states. Focusing on the ground and the first few excited states of the [Fe(H2O)6]2+ and [Fe(H2O)6]3+ clusters, we studied their mutual interaction in the gas phase. We obtained the optimal geometries of the Fe2+(H2O)6 – Fe3+(H2O)6 gas phase complex for different Fe–Fe distances. For distances shorter than 6.0 Å, the water molecules in the respective first solvation shells located between the two metal centers were found to interact via weak hydrogen bonds. We examined a total of ten electronic states for this complex, including those corresponding to the electron transfer (ET) from the ferrous to the ferric ion. The ET process is discussed and a possible path via a quasi-symmetric transition state is suggested. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Miliordos, Evangelos↗
DOE OSTI2010

Arsenic speciation in tissues of the hyperacumulator P. calomelanos var. austroamericana using x-ray absorption spectroscopy.

The fate and chemical speciation of arsenic (As) uptake, translocation and storage by the As hyperaccumulating fern Pityogramma calomelanos var. austroamericana (Pteridaceae) were examined using inductively coupled plasma-atomic emission spectrometry (ICP-AES) and synchrotron-based {mu}-X-ray absorption near edge structure ({mu}-XANES) and {mu}-X-ray fluorescence ({mu}-XRF) spectroscopies. Chemical analysis revealed total As concentration was ca. 6.5 times greater in young fronds (5845 mg kg {sup -1} dry weight) than in old frons (903 mg kg {sup -1} DW) pinnae, As concentration decreased from the base (6822 mg kg {sup -1} DW) to the apex (4301 mg kg {sup -1}DW) of the fronds. The results from {mu}-XANES and {mu}-XRF of living tissues suggested that more than 60% of arsenate (As{sup v}) absorbed was reduced to arsenite (As{sup III}) in roots, prior to transport through vascular tissues as As{sup v} and As{sup III}. In pinnules, As{sup III} was the predominate redox species (72-90%), presumably as solvated, oxygen coordinated compounds. The presence of putative As{sup III}-sulphide (S{sup -2}) coordinationthroughout the fern tissues (4-25%) suggests that S{sup 2-} functional groups may contribute in the biochemical reduction of As{sup v} to As{sup III} during uptake and transport at a whole plant level. Organic arsenicals and thiol-rich compounds were not detected in the species and are unlikely to play a role in As hyperaccumulation in this fern. The study provides important insights into homeostatic regulation of As following As uptake in P. calomelanos var. austroamericana.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Predicting Reduction Rates of Energetic Nitroaromatic Compounds Using Calculated One-Electron Reduction Potentials

The evaluation of new energetic nitroaromatic compounds (NACs) for use in green munitions formulations requires models that can predict their environmental fate. The susceptibility of energetic NACs to nitro reduction might be predicted from correlations between rate constants (k) for this reaction and one-electron reduction potentials (E1NAC) / 0.059 V, but the mechanistic implications of such correlations are inconsistent with evidence from other methods. To address this inconsistency, we have reevaluated existing kinetic data using a (non-linear) free-energy relationship (FER) based on the Marcus theory of outer-sphere electron transfer. For most reductants, the results are inconsistent with rate limitation by an initial, outer-sphere electron transfer, suggesting that the strong correlation between k and E1NAC is justified only as an empirical model. This empirical correlation was used to calibrate a new quantitative structure-activity relationship (QSAR) using previously reported values of k for non-energetic NAC reduction by Fe(II) porphyrin and newly reported values of E1NAC determined using density functional theory at the B3LYP/6-311++G(2d,2p) level with the COSMO solvation model. The QSAR was then validated for energetic NACs using newly measured kinetic data for 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), and 2,4-dinitroanisole (DNAN). The data show close agreement with the QSAR, supporting its applicability to energetic NACs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Impacts of Organic Ligands on Forsterite Reactivity in Supercritical CO 2 Fluids

Subsurface injection of CO 2 for enhanced hydrocarbon recovery, hydraulic fracturing of unconventional reservoirs, and geologic carbon sequestration produces a complex geochemical setting in which CO 2 -dominated fluids containing dissolved water and organic compounds interact with rocks and minerals. The details of these reactions are relatively unknown and benefit from additional experimentally derived data. In this study, we utilized an in situ X-ray diffraction technique to examine the carbonation reactions of forsterite (Mg 2 SiO 4 ) during exposure to supercritical CO 2 (scCO 2 ) that had been equilibrated with aqueous solutions of acetate, oxalate, malonate, or citrate at 50 °C and 90 bar. The organics affected the relative abundances of the crystalline reaction products, nesquehonite (MgCO 3 ·3H 2 O) and magnesite (MgCO 3 ), likely due to enhanced dehydration of the Mg 2+ cations by the organic ligands. These results also indicate that the scCO 2 solvated and transported the organic ligands to the forsterite surface. Lastly, this phenomenon has profound implications for mineral transformations and mass transfer in the upper crust.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Acid-Base Mechanism for Ruthenium-Based Water Oxidation Catalysts

We present a detailed theoretical study of the pathway for water oxidation in synthetic ruthenium-based catalysts. As a first step, we consider a recently discovered single center catalyst, where experimental observations suggest a purely single-center mechanism. We find low activation energies (<5 kcal/mol) for each rearrangement in the catalytic cycle. In the crucial step of O-O bond formation, a solvent water acts as a Lewis base and attacks a highly oxidized Ru{sup V} = O. Armed with the structures and energetics of the single-center catalyst, we proceed to consider a representative Ru-dimer which was designed to form O{sub 2} via coupling between the two centers. We discover a mechanism that proceeds in analogous fashion to the monomer case, with all the most significant steps occurring at a single catalytic center within the dimer. This acid-base mechanism suggests a new set of strategies for the rational design of multicenter catalysts: rather than coordinating the relative orientations of the subunits, one can focus on coordinating solvation-shell water molecules or tuning redox potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Theoretical Investigation of the Mechanism and Dynamics of Intramolecular Coherent Resonance Energy Transfer in Soft Molecules: A Case Study of Dithia-anthracenophane

A computational study is conducted on dithia-anthracenophane (DTA), for which there is experimental evidence for coherent resonance energy transfer dynamics, and on dimethylanthracene (DMA), a molecule representing the energy donor and the acceptor in DTA. Electronic excitation energies are calculated by configuration interaction singles (CIS) and time-dependent density functional theory (TDDFT) methods and are compared to experimental ones. Electronic coupling constants are calculated between two DMAs embedded into the ground-state structure of DTA employing methods based on transition densities. The resulting values of electronic coupling provide a more consistent interpretation of experiments than those based on one-half the level spacing of DTA excitation energies. Solvation effects are studied based on the polarizable continuum model (PCM). Solvent-induced polarization and screening effects are shown to make opposite contributions, and the net electronic coupling is little different from the value in a vacuum. The likelihood of coherent population transfer is assessed on the basis of a recently developed theory of coherent resonance energy transfer. The time scale of bath is shown to have an important role in sustaining the quantum coherence. The combination of quantum chemical and dynamical data suggests that the electronic coupling in DTA is in the range of 50-100 cm -1 . The presence of oscillatory excitation population dynamics can be understood from the picture of polaronic excitation moderately dressed with dispersive vibrational modes. The effect of torsional modulation on the excitation energies of DTA and electronic coupling is examined on the basis of optimized structures with the torsional angle constrained. The result suggests that inelastic effect due to torsional motion cannot be disregarded in DTA.

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

Charge-Dependent Dynamics of a Polyelectrolyte Dendrimer and Its Correlation with Invasive Water

Atomistic molecular dynamics (MD) simulations were carried out to investigate the local dynamics of polyelectrolyte dendrimers dissolved in deuterium oxide (D2O) and its dependence on molecular charge. Enhanced segmental dy-namics upon increase in molecular charge is observed, consistent with quasielastic neutron scattering (QENS) measurements. A strong coupling between the intra-dendrimer local hydration level and segmental dynamics is also revealed. Compelling evidence shows these findings originate from the electrostatic interaction between the hydrocarbon components of dendrimer and invasive water. This combined study provides fundamental insight into the dynamics of charged polyelectrolytes and the solvating water molecules.

Wu, Bin↗
DOE OSTI2014

Dynamics of soft Nanomaterials captured by transmission electron microscopy in liquid water

In this paper we present in situ transmission electron microscopy (TEM) of soft, synthetic nanoparticles with a comparative analysis using conventional TEM methods. This comparison is made with the simple aim of describing what is an unprecedented example of in situ imaging by TEM. However, we contend the technique will quickly become essential in the characterization of analogous systems, especially where dynamics are of interest in the solvated state. In this case, particles were studied which were obtained from the direct polymerization of an oxaliplatin analog, designed for an ongoing program in novel chemotherapeutic delivery systems. The resulting nanoparticles provided sufficient contrast for facile imaging in situ, and point toward key design parameters that enable this new characterization approach for organic nanomaterials. We describe the preparation of the synthetic micellar nanoparticles to- gether with their characterization in liquid water.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2013

Hydrogen-Bond Networks: Strengths of Different Types of Hydrogen Bonds and An Alternative to the Low Barrier Hydrogen-Bond Proposal

We report quantifying the strengths of different types of hydrogen bonds in hydrogen bond networks (HBNs) via measurement of the adiabatic electron detachment energy of the conjugate base of a small covalent polyol model compound (i.e., (HOCH2CH2CH(OH)CH2)2CHOH) in the gas phase and the pKa of the corresponding acid in DMSO. The latter result reveals that the hydrogen bonds to the charged center and those that are one solvation shell further away (i.e., primary and secondary) provide 5.3 and 2.5 pKa units of stabilization per hydrogen bond in DMSO. Computations indicate that these energies increase to 8.4 and 3.9 pKa units in benzene and that the total stabilizations are 16 (DMSO) and 25 (benzene) pKa units. Calculations on a larger linear heptaol (i.e., (HOCH2CH2CH(OH)CH2CH(OH)CH2)2CHOH) reveal that the terminal hydroxyl groups each contribute 0.6 pKa units of stabilization in DMSO and 1.1 pKa units in benzene. All of these results taken together indicate that the presence of a charged center can provide a powerful energetic driving force for enzyme catalysis and conformational changes such as in protein folding due to multiple hydrogen bonds in a HBN.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2014

First-principles Study of Phenol Hydrogenation on Pt and Ni Catalysts in Aqueous Phase

The effects of aqueous phase on the reactivity of phenol hydrogenation over Pt and Ni catalysts were investigated using density functional theory based ab initio molecular dynamics (AIMD) calculations. The adsorption of phenol and the first hydrogenation steps via three carbon positions (ortho, meta and para) with respect to the phenolic OH group were studied in both vacuum and liquid phase conditions. To gain insight into how the aqueous phase affects the metal catalyst surface, increasing water environments including singly adsorbed water molecule, mono- (9 water molecules), double layers (24 water molecules), and the bulk liquid water which (52 water molecules) on the Pt(111) and the Ni(111) surfaces were modeled. Compared to the vacuum/metal interfaces, AIMD simulation results suggest that the aqueous Pt(111) and Ni(111) interfaces have a lower metal work function in the order of 0.8 - 0.9 eV, thus, making the metals in aqueous phase stronger reducing agents and poorer oxidizing agents. Phenol adsorption from the aqueous phase is found to be slightly weaker that from the vapor phase. The first hydrogenation step of phenol at the ortho position of the phenolic ring is slightly favored over the other two positions. The polarization induced by the surrounding water molecules and the solvation effect play important roles in stabilizing the transition states associated with phenol hydrogenation by lowering the barriers of 0.1 - 0.4 eV. The detailed discussion on the basis of the interfacial electrostatics from the current study is very useful to understand the nature of a broader class of metal catalyzed reactions in liquid solution phase. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences and Office of Energy Efficiency and Renewable Energy. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.

aqueous phase↗