Element contents, sulfur and oxygen isotopes, and molecular biomarkers of phosphatic crust samples from the Chimbote Platform of the shelf off Peru

Authigenic phosphatic laminites enclosed in phosphorite crusts from the shelf off Peru (10°01' S and 10°24' S) consist of carbonate fluorapatite layers, which contain abundant sulfide minerals including pyrite (FeS2) and sphalerite (ZnS). Low d34Spyrite values (average -28.8 per mill) agree with bacterial sulfate reduction and subsequent pyrite formation. Stable sulfur isotopic compositions of sulfate bound in carbonate fluorapatite are lower than that of sulfate from ambient sea water, suggesting bacterial reoxidation of sulfide by sulfide-oxidizing bacteria. The release of phosphorus and subsequent formation of the autochthonous phosphatic laminites are apparently caused by the activity of sulfate-reducing bacteria and associated sulfide-oxidizing bacteria. Following an extraction-phosphorite dissolution-extraction procedure, molecular fossils of sulfate-reducing bacteria (mono-O-alkyl glycerol ethers, di-O-alkyl glycerol ethers, as well as the short-chain branched fatty acids i/ai-C15:0, i/ai-C17:0 and 10MeC16:0) are found to be among the most abundant compounds. The fact that these molecular fossils of sulfate-reducing bacteria are distinctly more abundant after dissolution of the phosphatic laminite reveals that the lipids are tightly bound to the mineral lattice of carbonate fluorapatite. Moreover, compared with the autochthonous laminite, molecular fossils of sulfate-reducing bacteria are: (1) significantly less abundant and (2) not as tightly bound to the mineral lattice in the other, allochthonous facies of the Peruvian crusts consisting of phosphatic coated grains. These observations confirm the importance of sulfate-reducing bacteria in the formation of the phosphatic laminite. Model calculations highlight that organic matter degradation by sulfate-reducing bacteria has the potential to liberate sufficient phosphorus for phosphogenesis.

A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Direct molecular level measurements of the electrostatic properties of a protein surface

In this work, we used direct measurements with the surface force apparatus to determine the pH-dependent electrostatic charge density of a single binding face of streptavidin. Mean field calculations have been used with considerable success to model electrostatic potential fields near protein surfaces, but these models and their inherent assumptions have not been tested directly at the molecular level. Using the force apparatus and immobilized, oriented monolayers of streptavidin, we measured a pI of 5–5.5 for the biotin-binding face of the protein. This differs from the pI of 6.3 for the soluble protein and confirms that we probed the local electrostatic features of the macromolecule. With finite difference solutions of the linearized Poisson–Boltzmann equation, we then calculated the pH-dependent charge densities adjacent to the same face of the protein. These calculated values agreed quantitatively with those obtained by direct force measurements. Although our study focuses on the pH-dependence of surface electrostatics, this direct approach to probing the electrostatic features of proteins is applicable to investigations of any perturbations that alter the charge distribution of the surfaces of immobilized molecules.

Femtosecond observation of benzyne intermediates in a molecular beam: Bergman rearrangement in the isolated molecule

In this communication, we report our femtosecond real-time observation of the dynamics for the three didehydrobenzene molecules (p-, m-, and o-benzyne) generated from 1,4-, 1,3-, and 1,2-dibromobenzene, respectively, in a molecular beam, by using femtosecond time-resolved mass spectrometry. The time required for the first and the second C-Br bond breakage is less than 100 fs; the benzyne molecules are produced within 100 fs and then decay with a lifetime of 400 ps or more. Density functional theory and high-level ab initio calculations are also reported herein to elucidate the energetics along the reaction path. We discuss the dynamics and possible reaction mechanisms for the disappearance of benzyne intermediates. Our effort focuses on the isolated molecule dynamics of the three isomers on the femtosecond time scale.

The importance of reactant positioning in enzyme catalysis: A hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

Hybrid quantum mechanics/molecular mechanics calculations using Austin Model 1 system-specific parameters were performed to study the SN2 displacement reaction of chloride from 1,2-dichloroethane (DCE) by nucleophilic attack of the carboxylate of acetate in the gas phase and by Asp-124 in the active site of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. The activation barrier for nucleophilic attack of acetate on DCE depends greatly on the reactants having a geometry resembling that in the enzyme or an optimized gas-phase structure. It was found in the gas-phase calculations that the activation barrier is 9 kcal/mol lower when dihedral constraints are used to restrict the carboxylate nucleophile geometry to that in the enzyme relative to the geometries for the reactants without dihedral constraints. The calculated quantum mechanics/molecular mechanics activation barriers for the enzymatic reaction are 16.2 and 19.4 kcal/mol when the geometry of the reactants is in a near attack conformer from molecular dynamics and in a conformer similar to the crystal structure (DCE is gauche), respectively. This haloalkane dehalogenase lowers the activation barrier for dehalogenation of DCE by 2–4 kcal/mol relative to the single point energies of the enzyme's quantum mechanics atoms in the gas phase. SN2 displacements of this sort in water are infinitely slower than in the gas phase. The modest lowering of the activation barrier by the enzyme relative to the reaction in the gas phase is consistent with mutation experiments.

Intermolecular and Intramolecular Charge Transfer in Functional Molecular Materials

This thesis is devoted to the investigation of inter and intramolecular charge transfer (CT) in molecular functional materials and specifically organic dyes and CT crystals. An integrated approach encompassing quantum-chemical calculations, semiempirical tools, theoretical models and spectroscopic measurements is applied to understand structure-property relationships governing the low-energy physics of these materials. Four main topics were addressed: 1) Spectral properties of organic dyes. Charge-transfer dyes are constituted by electron donor (D) and electron acceptor (A) units linked through bridge(s) to form molecules with different symmetry and dimensionality. Their low-energy physics is governed by the charge resonance between D and A groups and is effectively described by a family of parametric Hamiltonians known as essential-state models. These models account for few electronic states, corresponding to the main resonance structures of the relevant dye, leading to a simple picture that is completed introducing the coupling of the electronic system to molecular vibrations, treated in a non-adiabatic way, and an effective classical coordinate, describing polar solvation. In this work a specific essential-state model was proposed and parametrized for the dye Brilliant Green. The central issue in this work has been the definition of the diabatic states, a not trivial task for a multi-branched chromophore. In a second effort, we have used essential-state models for the description of the early-stage dynamics of excited states after ultrafast excitation. Crucial to this work is the fully non-adiabatic treatment of the coupled electronic and vibrational motion, allowing for a reliable description of the dynamics of systems showing a multistable, broken-symmetry excited state. 2) Mixed-stack CT salts. Mixed-stack (MS) CT crystals are an interesting class of multifunctional molecular materials, where D and A molecules arrange themselves to form stacks, leading to delocalized electrons in one dimension. The interplay between the intermolecular CT, electrostatic interactions, lattice phonons and molecular vibrations leads to intriguing physical properties that include (photoinduced) phase transitions, multistability, antiferromagnetism, ferroelectricity and potential multiferroicity. The standard microscopic model to describe this family of materials is the Modified Hubbard model accounting for electron-phonon coupling (Peierls coupling), electron-molecular vibrations coupling (Holstein coupling) and electrostatic interactions. We adopt and validate a method, based on DFT calculations on dimeric DA structures, to extract relevant model parameters. The approach offers a powerful tool to shed light on the complex physics of MS-CT salts. 3) Charge transfer in organic radical dipolar dyes. In collaboration with the group of Prof. Jaume Veciana (ICMAB- Barcellona), we have studied spectral properties of a special class of CT dyes with D-bridge-A structure where the acceptor group is a stable radical (of the perchlorotriphenylmethyl, PTM, family), leading to an open-shell CT dyes. These materials are of interest since they associate the electronic and optical properties of CT dyes with magnetic properties from the unpaired electron. The first effort was devoted to the parametrization of the relevant essential-state model. Two strategies were adopted, one based on the calculation of the low-energy spectral properties, the other based on the variation of ground state properties with an applied electric field. 4) The spectral properties of organic nanoparticles based on radical species are investigated in collaboration with Dr. I. Ratera (ICMAB- Barcellona). Intriguing spectroscopic behavior was observed pointing to the presence of excimer states. In an attempt to rationalize these findings, extensive calculations (TD-DFT and ZINDO) were performed. The results for the isolated dyes are validated against experimental spectra in solution. To address intermolecular interactions we studied dimeric structures in the gas phase, but the preliminary results obtained do not support excimer formation.

Dinâmica molecular de sistemas iônicos poliatômicos: modelos polarizável e não-polarizável

Simulações de sais de carbonato fundidos pelo método de Dinâmica Molecular (MD) foram efetuadas com o modelo polarizável de cargas flutuantes (FC). O modelo de cargas flutuantes implementa os efeitos de polarização pelo método de Lagrangiano estendido, onde as variáveis extras são as próprias cargas parciais do íon poliatômico. O modelo FC foi parametrizado por meio de cálculos ab inito, aplicado ao ânion carbonato. Cálculos de Química Quântica ab initio foram utilizados para corroborar o modelo proposto para o ânion carbonato. Os sistemas investigados consistem em misturas de carbonatos alcalinos fundidos, Li2CO3/K2CO3, os quais são utilizados como eletrólitos em células a combustível. As simulações MD foram utilizadas para verificar o efeito da polarização dos ânions sobre a estrutura e dinâmica do líquido. Estudamos o efeito da inclusão de polarização sobre a condutividade do eletrólito.

Modeling contact formation between atomic-sized gold tips via molecular dynamics

The formation and rupture of atomic-sized contacts is modelled by means of molecular dynamics simulations. Such nano-contacts are realized in scanning tunnelling microscope and mechanically controlled break junction experiments. These instruments routinely measure the conductance across the nano-sized electrodes as they are brought into contact and separated, permitting conductance traces to be recorded that are plots of conductance versus the distance between the electrodes. One interesting feature of the conductance traces is that for some metals and geometric configurations a jump in the value of the conductance is observed right before contact between the electrodes, a phenomenon known as jump-to-contact. This paper considers, from a computational point of view, the dynamics of contact between two gold nano-electrodes. Repeated indentation of the two surfaces on each other is performed in two crystallographic orientations of face-centred cubic gold, namely (001) and (111). Ultimately, the intention is to identify the structures at the atomic level at the moment of first contact between the surfaces, since the value of the conductance is related to the minimum cross-section in the contact region. Conductance values obtained in this way are determined using first principles electronic transport calculations, with atomic configurations taken from the molecular dynamics simulations serving as input structures.

Transport across two interacting quantum dots: Bulk Kondo, Kondo box, and molecular regimes

We analyze the transport properties of a double quantum dot device with both dots coupled to perfect conducting leads and to a finite chain of N noninteracting sites connecting both of them. The interdot chain strongly influences the transport across the system and the local density of states of the dots. We study the case of a small number of sites, so that Kondo box effects are present, varying the coupling between the dots and the chain. For odd N and small coupling between the interdot chain and the dots, a state with two coexisting Kondo regimes develops: the bulk Kondo due to the quantum dots connected to leads and the one produced by the screening of the quantum dot spins by the spin in the finite chain at the Fermi level. As the coupling to the interdot chain increases, there is a crossover to a molecular Kondo effect, due to the screening of the molecule (formed by the finite chain and the quantum dots) spin by the leads. For even N the two Kondo temperatures regime does not develop and the physics is dominated by the usual competition between Kondo and antiferromagnetism between the quantum dots. We finally study how the transport properties are affected as N is increased. For the study we used exact multiconfigurational Lanczos calculations and finite-U slave-boson mean-field theory at T=0. The results obtained with both methods describe qualitatively and also quantitatively the same physics.

Effect of Cyclic Topology on Charge-Transfer Properties of Organic Molecular Semiconductors: The Case of Cycloparaphenylene Molecules

We have studied the role played by cyclic topology on charge-transfer properties of recently synthesized π -conjugated molecules, namely the set of [n]cycloparaphenylene compounds, with n the number of phenylene rings forming the curved nanoring. We estimate the charge-transfer rates for holes and electrons migration within the array of molecules in their crystalline state. The theoretical calculations suggest that increasing the size of the system would help to obtain higher hole and electron charge-transfer rates and that these materials might show an ambipolar behavior in real samples, independently of the different mode of packing followed by the [6]cycloparaphenylene and [12]cycloparaphenylene cases studied.

Concentrations and isotopic compositions of low molecular weight hydrocarbons in hydrothermal fluids from ODP Field, Middle Valley, northern Juan de Fuca Ridge

The presence of sedimentary organic matter blanketing midocean ridge crests has a potentially strong impact on metal transport in hydrothermal vent fluids. To constrain the role of organic matter in metal mobility during hydrothermal sediment alteration, we reacted organic-rich diatomaceous ooze from Guaymas Basin, Gulf of California, and organic-poor hemipelagic mud from Middle Valley, northern Juan de Fuca Ridge, with seawater and a Na-Ca-K-Cl fluid of seawater chlorinity, at 275° to 400°C, 350 to 500 bars, and initial fluid: sediment mass ratios ranging from 1.6 to 9.8. Reaction of these fluids with both sediment types released CO2 and high concentrations of ore-forming metals (Fe, Mn, Zn, Pb) to solution. Relatively low concentrations of Cu were observed in solution and likely reflect the reducing conditions that resulted from the presence of sedimentary organic matter. Both the concentrations of CO2 and dissolved metals were lower in fluids reacted with Middle Valley sediment compared with aqueous concentrations in fluids reacted with Guaymas Basin sediment. During alteration of both sediment types, metal concentrations varied strongly as a function of temperature, increasing by up to an order of magnitude over the 75°C range of each experiment. Major element fluid chemistry and observed alteration assemblages suggest that during hydrothermal alteration of organic-lean sediment from Middle Valley a feldspar-quartz-illite mineral assemblage buffered in situ pH. In contrast, data from the experimental alteration of organic-rich Guaymas Basin sediment suggest that a calcite-plagioclase-quartz assemblage regulated in situ pH. Fluid speciation calculations suggest that in situ pH during Guaymas Basin sediment alteration was lower than during alteration of Middle Valley sediment and accounts for the substantially greater metal mobility at a given temperature and pressure during the former experiment. Comparison of our results with the results of basalt alteration experiments indicate that except for Cu, hydrothermal sediment alteration results in equal or greater concentrations of ore-forming metals at a given temperature and pressure. Accordingly, the presence of ore-forming metals in fluids currently venting from sediment-covered hydrothermal systems at concentrations substantially lower than in fluids from bare-rock systems may reflect chemical reequilibration during subsurface cooling within the sediment pile.

Dynamical properties of a strongly correlated model for quarter-filled layered organic molecular crystals

The dynamical properties of an extended Hubbard model, which is relevant to quarter-filled layered organic molecular crystals, are analyzed. We have computed the dynamical charge correlation function, spectral density, and optical conductivity using Lanczos diagonalization and large-N techniques. As the ratio of the nearest-neighbor Coulomb repulsion, V, to the hopping integral, t, increases there is a transition from a metallic phase to a charge-ordered phase. Dynamical properties close to the ordering transition are found to differ from the ones expected in a conventional metal. Large-N calculations display an enhancement of spectral weight at low frequencies as the system is driven closer to the charge-ordering transition in agreement with Lanczos calculations. As V is increased the charge correlation function displays a collective mode which, for wave vectors close to (pi,pi), increases in amplitude and softens as the charge-ordering transition is approached. We propose that inelastic x-ray scattering be used to detect this mode. Large-N calculations predict superconductivity with d(xy) symmetry close to the ordering transition. We find that this is consistent with Lanczos diagonalization calculations, on lattices of 20 sites, which find that the binding energy of two holes becomes negative close to the charge-ordering transition.

New insights into NO-carbon and N2O-carbon reactions from quantum mechanical calculations

Density functional theory calculations were used to investigate the mechanisms of NO-carbon and N2O-carbon reactions. It was the first time that the importance of surface nitrogen groups was addressed in the kinetic behaviors of the NO-carbon reaction. It was found that the off-plane nitrogen groups that are adjacent to the zigzag edge sites and in-plane nitrogen groups that are located on the armchair sites make the bond energy of oxygen desorption even ca. 20% lower than that of the off-plane epoxy group adjacent to zigzag edge sites and in-plane o-quinone oxygen atoms on armchair sites; this may explain the reason why the experimentally obtained activation energy of the NO-carbon reaction is ca. 20% lower than that of the O-2-carbon reaction over 923 K. A higher ratio of oxygen atoms can be formed in the N2O-carbon reaction, because of the lower dissociation energy of N2O, which results in a higher ratio of off-plane epoxy oxygen atoms. The desorption energy of semiquinone with double adjacent off-plane oxygen groups is ca. 20% less than that of semiquinone with only one adjacent off-plane oxygen group. This may be the reason why the activation energy of N2O is also ca. 20% less than that of the O-2-carbon reaction. The new mechanism can also provide a good qualitative comparison for the relative reaction rates of NO-, N2O-, and O-2-carbon reactions. The anisotropic characters of these gas-carbon reactions can also be well explained.

Characterization of carbon molecular sieves using methane and carbon dioxide as adsorptive probes

Nitrogen adsorption at 77 K is the current standard means for pore size determination of adsorbent materials. However, nitrogen adsorption reaches limitations when dealing with materials such as molecular sieving carbon with a high degree of ultramicroporosity. In this investigation, methane and carbon dioxide adsorption is explored as a possible alternative to the standard nitrogen probe. Methane and carbon dioxide adsorption equilibria and kinetics are measured in a commercially derived carbon molecular sieve over a range of temperatures. The pore size distribution is determined from the adsorption equilibrium, and the kinetics of adsorption is shown to be Fickian for carbon dioxide and non-Fickian for methane. The non-Fickian response is attributed to transport resistance at the pore mouth experienced by the methane molecules but not by the carbon dioxide molecules. Additionally, the change in the rate of adsorption with loading is characterized by the Darken relation in the case of carbon dioxide diffusion but is greater than that predicted by the Darken relation for methane transport. Furthermore, the proposition of inkbottle-shaped micropores in molecular sieving carbon is supported by the determination of the activation energy for the transport of methane and subsequent sizing of the pore-mouth barrier by molecular potential calculations.

Converged quantum calculations of HO2 bound states and resonances for J=6 and 10

Bound and resonance states of HO2 are calculated quantum mechanically using both the Lanczos homogeneous filter diagonalization method and the real Chebyshev filter diagonalization method for nonzero total angular momentum J=6 and 10, using a parallel computing strategy. For bound states, agreement between the two methods is quite satisfactory; for resonances, while the energies are in good agreement, the widths are in general agreement. The quantum nonzero-J specific unimolecular dissociation rates for HO2 are also calculated. (C) 2004 American Institute of Physics.