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ABSTRACT: Certain bacterial enzymes, the diiron hydrogenases, have turnover numbers for hydrogen production from water as large as 10(4)/s. Their much smaller common active site, composed of earth-abundant materials, has a structure that is an attractive starting point for the design of a practical catalyst for electrocatalytic or solar photocatalytic hydrogen production from water. In earlier work, our group has reported the computational design of [FeFe](P)/FeS(2), a hydrogenase-inspired catalyst/electrode complex, which is efficient and stable throughout the production cycle. However, the diiron hydrogenases are highly sensitive to ambient oxygen by a mechanism not yet understood in detail. An issue critical for practical use of [FeFe](P)/FeS(2) is whether this catalyst/electrode complex is tolerant to the ambient oxygen. We report demonstration by ab initio simulations that the complex is indeed tolerant to dissolved oxygen over timescales long enough for practical application, reducing it efficiently. This promising hydrogen-producing catalyst, composed of earth-abundant materials and with a diffusion-limited rate in acidified water, is efficient as well as oxygen tolerant.
Proceedings of the National Academy of Sciences 01/2013; · 9.68 Impact Factor
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ABSTRACT: The burning rate of the monopropellant nitromethane (NM) has been observed to increase by adding and dispersing small amounts of functionalized graphene sheets (FGSs) in liquid NM. Until now no plausible mechanisms for FGSs acting as combustion catalysts have been presented. Here, we report ab-initio molecular dynamics simulations showing that carbon vacancy defects within the plane of the FGSs, functionalized with oxygen-containing groups, greatly accelerate the thermal decomposition of NM and its derivatives. This occurs through reaction pathways involving the exchange of protons or oxygens between the oxygen-containing functional groups and NM and its derivatives. FGS initiates and promotes the decomposition of the monopropellant and its derivatives, ultimately forming H2O, CO2, and N2. Concomitantly, oxygen-containing functional groups on the FGSs are consumed and regenerated without significantly changing the FGSs, in accord with experiments indicating that the FGSs are not consumed during combustion.
Journal of the American Chemical Society 10/2012; · 9.91 Impact Factor
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ABSTRACT: We study the quantum nature of the protons participating in hydrogen bonds in several ice structures by analyzing the one
particle density matrix. We find that in all cases, including ice Ih, the most common form of ice, and the high pressure phases,
ice VIII, VII, and X, the system is ground-state dominated. However, while the dynamics is uncorrelated in the structures
with standard asymmetric hydrogen bonds, such as ice Ih and VIII, local correlations among the protons characterize ice VII
and, to a lesser extent, ice X in the so-called low barrier hydrogen bond regime. The correlations appear along the path to
hydrogen bond symmetrization, when quantum fluctuations delocalize the proton on the two bond sides. The correlations derive
from a strong requirement for local charge neutrality that favors concerted motion along the bonds. The resulting behavior
deviates substantially from mean field theory, which would predict in ice VII coherent tunneling of the proton between the
two bond sides, thereby causing an ionization catastrophe. Due to the correlations, the quantum state of the proton is entangled.
KeywordsHydrogen bonding–Proton tunneling–High pressure ice phases
Journal of Statistical Physics 04/2012; 145(2):365-384. · 1.40 Impact Factor
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ABSTRACT: We calculate the x-ray absorption spectra of liquid water at ambient
conditions and of hexagonal ice close to melting, using a static GW approach
that includes approximately local field effects. Quantum dynamics of the nuclei
is taken into account by averaging the absorption cross section over molecular
configurations generated by path integral simulations. We find that inclusion
of quantum disorder is essential to bring the calculated spectra in close
agreement with experiment. In particular, the intensity of the pre-edge
feature, a spectral signature of broken and distorted hydrogen bonds, is
accurately reproduced, in water and ice, only when quantum nuclei are
considered. The effect of the local fields is less important but non
negligible, particularly in ice.
04/2012;
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ABSTRACT: We introduce a novel theoretical approach for determining oxidation states (OS) from quantum-mechanical calculations. For a transition-metal ion, for example, the metal-ligand orbital mixing contribution to the charge allocated to the ion is separated from that due to the actual occupation of the d-orbitals from which OS can then be inferred. We report the application of this approach to different transition-metal systems: molecular complexes, ruthenium-dye molecules, ruthenium complexes with noninnocent ligands, and bulk semiconductors. The computations were carried out using density-functional theory with a Hubbard U correction. The oxidation states were determined without ambiguity.
Inorganic Chemistry 09/2011; 50(20):10259-67. · 4.60 Impact Factor
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ABSTRACT: In catalysis by metalloenzymes and in electrocatalysis by clusters related in structure and composition to the active components of such enzymes transition-metal atoms can play a central role in the catalyzed redox reactions. Changes to their oxidation states (OSs) are critical for understanding the reactions. The OS is a local property and we introduce a new, generally useful local method for determining OSs, their changes, and the associated bonding changes and electron flow. The method is based on computing optimally localized orbitals (OLOs). With this method, we analyze two cases, superoxide reductase (SOR) and a proposed hydrogen-producing model electrocatalyst [FeS(2)]/[FeFe](P), a modification of the active site of the diiron hydrogenase enzymes. Both utilize an under-coordinated Fe site where a one-electron reduction (for SOR) or a two-electron reduction (for [FeFe](P)) of the substrate occurs. We obtain the oxidation states of the Fe atoms and of their critical ligands, the changes of the bonds to those ligands, and the electron flow during the catalytic cycle, thereby demonstrating that OLOs constitute a powerful interpretive tool for unraveling reaction mechanisms by first-principles computations.
Chemistry 09/2011; 17(43):12136-43. · 5.93 Impact Factor
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ABSTRACT: By analyzing the momentum distribution obtained from path integral and phonon
calculations we find that the protons in hexagonal ice experience an
anisotropic quasi-harmonic effective potential with three distinct principal
frequencies that reflect molecular orientation. Due to the importance of
anisotropy, anharmonic features of the environment cannot be extracted from
existing experimental distributions that involve the spherical average. The
full directional distribution is required, and we give a theoretical prediction
for this quantity that could be verified in future experiments. Within the
quasi-harmonic context, anharmonicity in the ground state dynamics of the
proton is substantial and has quantal origin, a finding that impacts the
interpretation of several spectroscopies.
02/2011;
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ABSTRACT: Bacterial di-iron hydrogenases produce hydrogen efficiently from water. Accordingly, we have studied by first-principles molecular-dynamics simulations (FPMD) electrocatalytic hydrogen production from acidified water by their common active site, the [FeFe]H cluster, extracted from the enzyme and linked directly to the (100) surface of a pyrite electrode. We found that the cluster could not be attached stably to the surface via a thiol link analogous to that which attaches it to the rest of the enzyme, despite the similarity of the (100) pyrite surface to the Fe4S4 cubane to which it is linked in the enzyme. We report here a systematic sequence of modifications of the structure and composition of the cluster devised to maintain the structural stability of the pyrite/cluster complex in water throughout its hydrogen production cycle, an example of the molecular design of a complex system by FPMD.
09/2010;
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ABSTRACT: The proton momentum distribution, accessible by deep inelastic neutron scattering, is a very sensitive probe of the potential of mean force experienced by the protons in hydrogen-bonded systems. In this work we introduce a novel estimator for the end-to-end distribution of the Feynman paths, i.e., the Fourier transform of the momentum distribution. In this formulation, free particle and environmental contributions factorize. Moreover, the environmental contribution has a natural analogy to a free energy surface in statistical mechanics, facilitating the interpretation of experiments. The new formulation is not only conceptually but also computationally advantageous. We illustrate the method with applications to an empirical water model, ab initio ice, and one dimensional model systems.
Physical Review Letters 09/2010; 105(11):110602. · 7.37 Impact Factor
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ABSTRACT: The x-ray absorption spectra of water and ice are calculated with a many-body approach for electron-hole excitations. The experimental features, including the effects of temperature change in the liquid, are reproduced from configurations generated by ab initio molecular dynamics. The spectral difference between the solid and the liquid is due to two major short-range order effects. One, due to breaking of hydrogen bonds, enhances the pre-edge intensity in the liquid. The other, due to a nonbonded molecular fraction in the first coordination shell, affects the main spectral edge in the conversion of ice to water. This effect may not involve hydrogen bond breaking as shown by experiment in high-density amorphous ice.
Physical Review Letters 07/2010; 105(1):017802. · 7.37 Impact Factor
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ABSTRACT: The possibility of using the active site, the [FeFe](H) cluster, of the bacterial di-iron hydrogenases as a catalyst for hydrogen production from water by electro- or photocatalysis is of current scientific and technological interest. We present here a theoretical study of hydrogen production by a modified [FeFe](H) cluster stably linked to a pyrite electrode immersed in acidified water. We employed state-of-the-art electronic-structure and first-principles molecular-dynamics methods. We found that a stable sulfur link of the cluster to the surface analogous to that linking the cluster to its enzyme environment cannot be made. However, we have discovered a modification of the cluster which does form a stable, tridentate link to the surface. The pyrite electrode readily produces hydrogen from acidified water when functionalized with the modified cluster, which remains stable throughout the hydrogen production cycle.
Journal of the American Chemical Society 06/2010; 132(25):8593-601. · 9.91 Impact Factor
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ABSTRACT: We investigate the quantum-mechanical localization of protonated and deterated isotopes in the symmetric low-barrier hydrogen-bonds of potassium dihydrogen phosphate (KDP) crystals in the paraelectric phase. The spatial density distributions of these hydrogen atoms are suspected to be responsible for the surprisingly large isotope effect observed for the ferroelectric phase transition in KDP. We employ ab initio path integral molecular dynamics simulations to obtain the nuclear real-space and momentum-space densities n(R) and n(k) of protons and deuterons, which are compared to experimental Neutron Compton Scattering data. Our results suggest a qualitative difference in the nature of the paraelectic phase in KDP between the two isotopes. We are able to discriminate between real quantum delocalization and vibration-assisted hopping and thus provide evidence for two distinct mechanisms of the ferroelectric phase transition in this class of materials. Comment: 5 pages, 4 figures
02/2010;
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ABSTRACT: We explored the reactivity of the active center of the [FeFe]-hydrogenases detached from the enzyme and immersed in acidified water by first-principles Car-Parrinello molecular-dynamics simulations. We focused on the identification of the structures that are stable and metastable in acidified water and on their activity for hydrogen production. Our calculations revealed that the naked active center could be an efficient catalyst provided that electrons are transferred to the cluster. We found that both bridging and terminal isomers are present at equilibrium and that the bridging configuration is essential for efficient hydrogen production. The formation of the hydrogen molecule occurs via sequential protonations of the distal iron and of the N-atom of the S-CH(2)-NH-CH(2)-S chelating group. H(2) desorption does not involve a significant energy barrier, making the process very efficient at room temperature. We established that the bottleneck in the reaction is the direct proton transfer from water to the vacant site of the distal iron. Moreover, we found that even if the terminal isomer is present at the equilibrium, its strong local hydrophobicity prevents poisoning of the cluster.
The Journal of Physical Chemistry B 10/2009; 113(39):13096-106. · 3.70 Impact Factor
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ABSTRACT: Recent theoretical work has provided evidence that hybrid functionals, which include a fraction of exact (Hartree-Fock) exchange in the density functional theory exchange and correlation terms, significantly improve the description of band gaps of semiconductors compared with local and semilocal approximations. Based on a recently developed order-N method for calculating the exact exchange in extended insulating systems, we have implemented an efficient scheme to determine the hybrid functional band gap. We use this scheme to study the band gap and other electronic properties of the ternary compound In1−xGaxN using a 64-atom supercell model.
Phys. Rev. B. 09/2009; 80(11).
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Paolo Giannozzi,
Stefano Baroni,
Nicola Bonini,
Matteo Calandra, Roberto Car,
Carlo Cavazzoni,
Davide Ceresoli,
Guido L Chiarotti,
Matteo Cococcioni,
Ismaila Dabo, [......],
Stefano Paolini,
Alfredo Pasquarello,
Lorenzo Paulatto,
Carlo Sbraccia,
Sandro Scandolo,
Gabriele Sclauzero,
Ari P Seitsonen,
Alexander Smogunov,
Paolo Umari,
Renata M Wentzcovitch
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ABSTRACT: QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.
Journal of Physics Condensed Matter 08/2009; 21(39):395502. · 2.55 Impact Factor
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ABSTRACT: Recent theoretical work has provided evidence that hybrid functionals, which include a fraction of exact (Hartree Fock) exchange in the density functional theory (DFT) exchange and correlation terms, significantly improve the description of band gaps of semiconductors compared with local and semilocal approximations. Based on a recently developed order-$N$ method for calculating the exact exchange in extended insulating systems, we have implemented an efficient scheme to determine the hybrid functional band gap. We use this scheme to study the band gap and other electronic properties of the ternary compound In$_{1-x}$Ga$_{x}$N using a 64-atom supercell model. Comment: 3 figures, 2 tables
07/2009;
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ABSTRACT: Novel experimental and computational studies have uncovered the proton momentum distribution in hydrogen bonded systems. In this work, we utilize recently developed open path integral Car-Parrinello molecular dynamics methodology in order to study the momentum distribution in phases of high pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum tunneling. We find that the symmetric hydrogen bonded phase possesses a narrowed momentum distribution as compared with a covalently bonded phase, in agreement with recent experimental findings. The signatures of tunneling that we observe are a narrowed distribution in the low-to-intermediate momentum region, with a tail that extends to match the result of the covalently bonded state. The transition to tunneling behavior shows similarity to features observed in recent experiments performed on confined water. We corroborate our ice simulations with a study of a particle in a model one-dimensional double well potential that mimics some of the effects observed in bulk simulations. The temperature dependence of the momentum distribution in the one-dimensional model allows for the differentiation between ground state and mixed state tunneling effects.
The Journal of chemical physics 06/2009; 130(20):204511. · 3.09 Impact Factor
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ABSTRACT: We present an extended discussion of a recently proposed theoretical approach for off-resonance tunneling transport. The proofs and the arguments are explained at length and simple analogies and illustrations are used where possible. The result is an analytic formula for the asymptotic tunneling conductance which involves the overlap of three well defined physical quantities. We argue that the formula can be used to gain fresh insight into the tunneling transport characteristics of various systems. The formalism is applied here to molecular devices consisting of planar phenyl chains connected to gold electrodes via amine linkers.
04/2009;
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ABSTRACT: The recently proposed partition theory (PT) (J. Phys. Chem. A2007, 111, 2229.) is illustrated on a simple one-dimensional model of a heteronuclear diatomic molecule, 1DAB. It is shown that a sharp definition for the charge of molecular fragments emerges from PT and that the ensuing population analysis can be used to study how charge redistributes during dissociation and the implications of that redistribution for the dipole moment. Interpreting small differences between the isolated parts' ionization potentials as due to environmental inhomogeneities, we gain insight into how electron localization takes place in H2(+) as the molecule dissociates. Furthermore, by studying the preservation of the shapes of the parts as different parameters of the model are varied, we address the issue of transferability of the parts. We find good transferability within the chemically meaningful parameter regime, raising hopes that PT will prove useful in chemical applications.
The Journal of Physical Chemistry A 03/2009; 113(10):2183-92. · 2.95 Impact Factor
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ABSTRACT: We probe the bending characteristics of functionalized graphene sheets with the tip of an atomic force microscope. Individual sheets are transformed from a flat into a folded configuration. Sheets can be reversibly folded and unfolded multiple times, and the folding always occurs at the same location. This observation suggests that the folding and bending behavior of the sheets is dominated by pre-existing kink (or even fault) lines consisting of defects and/or functional groups.
ACS Nano 01/2009; 2(12):2577-84. · 10.77 Impact Factor
