Showing papers by "Roberto Car published in 2006"

Functionalized Single Graphene Sheets Derived from Splitting Graphite Oxide

Abstract: A process is described to produce single sheets of functionalized graphene through thermal exfoliation of graphite oxide. The process yields a wrinkled sheet structure resulting from reaction sites involved in oxidation and reduction processes. The topological features of single sheets, as measured by atomic force microscopy, closely match predictions of first-principles atomistic modeling. Although graphite oxide is an insulator, functionalized graphene produced by this method is electrically conducting.

Oxygen-driven unzipping of graphitic materials.

Abstract: Optical microscope images of graphite oxide (GO) reveal the occurrence of fault lines resulting from the oxidative processes. The fault lines and cracks of GO are also responsible for their much smaller size compared with the starting graphite materials. We propose an unzipping mechanism to explain the formation of cracks on GO and cutting of carbon nanotubes in an oxidizing acid. GO unzipping is initiated by the strain generated by the cooperative alignment of epoxy groups on a carbon lattice. We employ two small GO platelets to show that through the binding of a new epoxy group or the hopping of a nearby existing epoxy group, the unzipping process can be continued during the oxidative process of graphite. The same epoxy group binding pattern is also likely to be present in an oxidized carbon nanotube and cause its breakup.

Electronic structure and reactivity of isomeric oxo-Mn(V) porphyrins: effects of spin-state crossing and pKa modulation.

Abstract: The reactivity of the isomeric oxo-Mn(V)-2-tetra-N-methylpyridyl (2-TMPyP) and oxo-Mn(V)-4-tetra-N-methylpyridyl (4-TMPyP) porphyrins has been investigated by a combined experimental and theoretical approach based on density functional theory. The unusual higher reactivity of the more electron-rich 4-TMPyP species appears to be related to both the higher basicity of its oxo ligand, compared to that of the 2-TMPyP isomer, and the smaller low-spin−high-spin promotion energy of 4-TMPyP, compared to that of 2-TMPyP, because of the stabilization of the A2u orbital in the latter isomer. Therefore, in a two-state energy profile involving crossing of the initial singlet and final quintet potential energy surfaces, the 4-TMPyP isomer should be kinetically favored. The calculated differences in the singlet−quintet gaps for the 2-TMPyP and 4-TMPyP systems compare well with the measured differences in the activation energies for two isomeric porphyrins. Both effects, proton affinity and electron-promotion energy, con...

Tuning the Photoinduced O2-Evolving Reactivity of Mn4O47+, Mn4O46+, and Mn4O3(OH)6+ Manganese−Oxo Cubane Complexes

Abstract: The manganese-oxo "cubane" core complex Mn(4)O(4)L(1)(6) (1, L(1) = Ph(2)PO(2-)), a partial model of the photosynthetic water oxidation site, was shown previously to undergo photodissociation in the gas phase by releasing one phosphinate anion, an O(2) molecule, and the intact butterfly core cation (Mn(4)O(2)L(1)(5+)). Herein, we investigate the photochemistry and electronic structure of a series of manganese-oxo cubane complexes: [Mn(4)O(4)L(2)(6)] (2), 1(+)(ClO(4-)), 2(+)(ClO(4-)), and Mn(4)O(3)(OH)L(1)(6) (1H). We report the atomic structure of [Mn(4)O(4)L(2)(6)](ClO(4)), 2(+)(ClO(4-)) [L(2) = (4-MeOPh)(2)PO(2-)]. UV photoexcitation of a charge-transfer band dissociates one phosphinate, two core oxygen atoms, and the Mn(4)O(2)L(5)(+) butterfly as the dominant (or exclusive) photoreaction of all cubane derivatives in the gas phase, with relative yields: 1H >> 2 > 1 > 2(+) > 1(+). The photodissociation yield increases upon (1) reducing the core oxidation state by hydrogenation of a corner oxo (1H), (2) increasing the electron donation from the phosphinate ligand (L(2)), and (3) reducing the net charge from +1 to 0. The experimental Mn-O bond lengths and Mn-O bond strengths and the calculated ligand binding energy explain these trends in terms of weaker binding of phosphinate L(2) versus L(1) by 14.7 kcal/mol and stronger Mn-(mu(3)-O)(core) bonds in the oxidized complexes 2(+) and 1(+) versus 2 and 1. The calculated electronic structure accounts for these trends in terms of the binding energy and antibonding Mn-O(core) and Mn-O'(ligand) character of the degenerate highest occupied molecular orbital (HOMO), including (1) energetic destabilization of the HOMO of 2 relative to 1 by 0.75 eV and (2) depopulation of the antibonding HOMO and increased ionic binding in 1(+) and 2(+) versus 1 and 2.

Testing the TPSS meta-generalized-gradient-approximation exchange-correlation functional in calculations of transition states and reaction barriers

Abstract: We have studied the performance of local and semilocal exchange-correlation functionals [meta-generalized-gradient-approximation (GGA)-TPSS, GGA–Perdew-Burke-Ernzerhof (PBE), and local density approximation (LDA)] in the calculation of transition states, reaction energies, and barriers for several molecular and one surface reaction, using the plane-wave pseudopotential approach. For molecular reactions, these results have been compared to all-electron Gaussian calculations using the B3LYP hybrid functional, as well as to experiment and high level quantum chemistry calculations, when available. We have found that the transition state structures are accurately identified irrespective of the level of the exchange-correlation functional, with the exception of a qualitatively incorrect LDA prediction for the H-transfer reaction in the hydrogen bonded complex between a water molecule and a OH radical. Both the meta-GGA-TPSS and the GGA-PBE functionals improve significantly the calculated LDA barrier heights. The meta-GGA-TPSS further improves systematically, albeit not always sufficiently, the GGA-PBE barriers. We have also found that, on the Si(001) surface, the meta-GGA-TPSS barriers for hydrogen adsorption agree significantly better than the corresponding GGA-PBE barriers with quantum Monte Carlo cluster results and experimental estimates.

Anisotropic Adsorption of Molecular Assemblies on Crystalline Surfaces

Abstract: Orientational order of surfactant micelles and proteins on crystalline templates has been observed but, given that the template unit cell is significantly smaller than the characteristic size of the adsorbate, this order cannot be attributed to lattice epitaxy. We interpret the template-directed orientation of rodlike molecular assemblies as arising from anisotropic van der Waals interactions between the assembly and crystalline surfaces where the anisotropic van der Waals interaction is calculated using the Lifshitz methodology. Provided the assembly is sufficiently large, substrate anisotropy provides a torque that overcomes rotational Brownian motion near the surface. The probability of a particular orientation is computed by solving a Smoluchowski equation that describes the balance between van der Waals and Brownian torques. Torque aligns both micelles and protein fibrils; the interaction energy is minimized when the assembly lies perpendicular to a symmetry axis of a crystalline substrate. Theoretical predictions agree with experiments for both hemi-cylindrical micelles and protein fibrils adsorbed on graphite.

Orientational order of molecular assemblies on inorganic crystals.

Abstract: Surfactant micelles form oriented arrays on crystalline substrates although registration is unexpected since the template unit cell is small compared to the size of a rodlike micelle. Interaction energy calculations based on molecular simulations reveal that orientational energy differences on a molecular scale are too small to explain matters. With atomic force microscopy, we show that orientational ordering is a dynamic, multimolecule process. Treating the cooperative processes as a balance between van der Waals torque on a large, rodlike micellar assembly and Brownian motion shows that orientation is favored.

Resolving the CO/CN ligand arrangement in CO-inactivated [FeFe] hydrogenase by first principles density functional theory calculations

Abstract: The currently presumed assignment of CO/CN ligands in the structure of the active cluster in CO-inactivated [FeFe] hydrogenase is shown to be inconsistent with the available IR data in the enzyme from Clostridium pasteurianum I. A different arrangement has the correct qualitative and quantitative features, reproducing the observed line spacing and intensities and the observed line shift consequent to inactivation with labeled 13CO instead of 12CO. The new assignment is also consistent with the observed change from rhombic to axial symmetry of the electron paramagnetic resonance g tensor upon inactivation.

Theoretical studies of [FeFe]-hydrogenase: structure and infrared spectra of synthetic models.

Abstract: First-principles density functional theory calculations of synthetic models of [FeFe]-hydrogenase are used to show that the theoretical methods reproduce observed structures and infrared spectra to high accuracy. The accuracy is demonstrated for synthetic Fe(I)Fe(I) models ([(μ-PDT)Fe 2 (CO) 6 ] and [(CN)(CO) 2 (μ-PDT)Fe 2 -(CO) 2 (CN)] 2- ), for which we show that their infrared spectra are sensitive to the geometric arrangement of their CO/CN ligands and can be used in conjunction with quantum-mechanical total energies to predict the correct ligand geometry. We then analyze and predict the structure of mixed-valence Fe(II)Fe(I) models ([(μ-MeSCH 2 C(Me)(CH 2 S) 2 )Fe 2 (CO) 4 (CN) 2 ] x- ). These capabilities promise to distinguish among the various structural isomers of the enzyme's active site which are consistent with the limited accuracy of the X-ray observations.

Kohn-Sham Master Equation Approach to Transport Through Single Molecules

Abstract: In recent years it has become possible to study experimentally charge transport through single molecules [Nitzan 2003]. Typically, the devices in which such experiments can be realized consist of metal-molecule-metal junctions, where two metallic leads are connected by some molecule. Such junctions are expected to be at the basis of future molecular-based electronic devices. But apart from technological applications, these experiments can also be taken as a basis for understanding electron tunneling in general. The theoretical modeling of molecular transport, however, is a very challenging task: On one hand, it is intuitively clear that the conduction properties of a molecular junction will crucially depend on details of the chemical bonding, particularly at the interface between the metal electrodes and the molecule. Such properties are routinely studied using methods based on density-functional theory (DFT) [Hohenberg 1964]. On the other hand, ground-state theories like DFT cannot be directly applied to systems with a finite current, because such devices are out of equilibrium. A standard methodology that allows to calculate transport properties from first principles is based on non-equilibrium Green’s functions (NEGF) [Keldysh 1965]. In this framework, which is today adopted for almost all calculations in this field, the current is obtained by solving an elastic scattering problem with open boundaries through which electrons are injected from the leads. The NEGF formalism is often used together with DFT in order to achieve chemical accuracy also in systems containing several tens to hundreds of atoms. The NEGF method is explained in detail in Chap. 32 of this book. Here we present an alternative formulation that can be seen as a generalization of the Boltzmann transport equation (BTE) [Ashcroft 1976] to the fully quantum mechanical case. The BTE is a very successful approach to study transport in non-equilibrium systems. In contrast to NEGF formalisms, where energy-dependent scattering problems are solved, the BTE is formulated in the time-domain: Electrons are accelerated by an external driving force (an electric field, for instance), and the energy which is injected in this way into the system is dissipated by inelastic scattering events. The interplay between acceleration and dissipation leads to a steady state in which

Chapter 3 Ab initio Molecular Dynamics: Dynamics and Thermodynamic Properties

Abstract: Publisher Summary Molecular dynamics is a powerful technique to simulate classical many-body systems. It amounts to solving numerically the equations of motion. Molecular dynamics simulations have become possible with the advent of high-speed digital computers, and, from the early pioneering papers, molecular dynamics simulations have gained vast popularity and are now common in physics, chemistry, materials science, and biochemistry/biophysics. Molecular dynamics assumes that the atoms behave like classical particles. Given the value of the atomic masses, this is usually a good approximation in materials and molecules when the temperature is not too low. With presently available computational resources, it is possible to generate ab initio molecular dynamics trajectories spanning tens of picoseconds. These times are longer than molecular vibration periods and are also longer than typical relaxation times in a liquid. Significantly longer times, the order of hundreds of nanoseconds, are ordinarily accessible in simulations based on empirical potentials. Yet, all these times are very short on a macroscopic scale. Many physical phenomena involve collective molecular motions that occur on time scales inaccessible to direct molecular dynamics simulation.