Oxygen Activation in Aromatic Ring Cleaving Salicylate Dioxygenase: Detection of Reaction Intermediates with a Nitro-substituted Substrate Analog.

Cupin dioxygenases such as salicylate 1,2-dioxygense (SDO) perform aromatic C-C bond scission via a 3-His motif tethered iron cofactor. Here, transient kinetics measurements are used to monitor the catalytic cycle of SDO by using a nitro-substituted substrate analog, 3-nitrogentisate. Compared to the natural substrate, the nitro group reduces the enzymatic kcat by 500-fold, thereby facilitating the detection and kinetic characterization of reaction intermediates. Sums and products of reciprocal relaxation times derived from kinetic measurements were found to be linearly dependent on O2 concentration, suggesting reversible formation of two distinct intermediates. Dioxygen binding to the metal cofactor takes place with a forward rate of 5.9×103 M-1 s-1: two orders of magnitude slower than other comparable ring-cleaving dioxygenses. Optical chromophore of the first intermediate is distinct from the in situ generated SDO Fe(III)-O2⋅- complex but closer to the enzyme-substrate precursor.

Calculation of Mode Grüneisen Parameters Made Simple.

A novel method to calculate mode Grüneisen parameters of a material from first principles is presented. This method overcomes the difficulties and limitations of existing approaches, based on the calculation of either third-order force constants or phonon frequencies at different volumes. Our method requires the calculation of phonon frequencies of a material at only the volume of interest, it is based on the second-order differentiation of a corrected stress tensor with respect to normal mode coordinates, and it yields simultaneously all the components of the mode Grüneisen parameters tensor. In this work, after discussing conceptual and technical aspects, the method is applied to silicon, aluminum, scandium fluoride, and a metallic alloy. These calculations show that our method is straightforward and it is suited to be applied to the broad class of materials prone to exhibit structural instabilities, or presenting anisotropy, or chemical and/or structural disorder.

First-Principles Calculation of Third-Order Elastic Constants via Numerical Differentiation of the Second Piola-Kirchhoff Stress Tensor.

A general method is presented to calculate from first principles the full set of third-order elastic constants of a material of arbitrary symmetry. The method here illustrated relies on a plane-wave density functional theory scheme to calculate the Cauchy stress and the numerical differentiation of the second Piola-Kirchhoff stress tensor to evaluate the elastic constants. It is shown that finite difference formulas lead to a cancellation of the finite basis set errors, whereas simple solutions are proposed to eliminate numerical errors arising from the use of Fourier interpolation techniques. Applications to diamond, silicon, aluminum, magnesium, graphene, and a graphane conformer give results in excellent agreement with both experiments and previous calculations based on fitting energy density curves, demonstrating both the accuracy and generality of our new methodology to investigate nonlinear elastic behaviors of materials.

Elastic coupling between layers in two-dimensional materials.

Two-dimensional materials, such as graphene and MoS2, are films of a few atomic layers in thickness with strong in-plane bonds and weak interactions between the layers. The in-plane elasticity has been widely studied in bending experiments where a suspended film is deformed substantially; however, little is known about the films' elastic modulus perpendicular to the planes, as the measurement of the out-of-plane elasticity of supported 2D films requires indentation depths smaller than the films' interlayer distance. Here, we report on sub-ångström-resolution indentation measurements of the perpendicular-to-the-plane elasticity of 2D materials. Our indentation data, combined with semi-analytical models and density functional theory, are then used to study the perpendicular elasticity of few-layer-thick graphene and graphene oxide films. We find that the perpendicular Young's modulus of graphene oxide films reaches a maximum when one complete water layer is intercalated between the graphitic planes. This non-destructive methodology can map interlayer coupling and intercalation in 2D films.

Density functional theory modeling of multilayer "epitaxial" graphene oxide.

CONSPECTUS: Graphene oxide (GO) is a complex material of both fundamental and applied interest. Elucidating the structure of GO is crucial to achieve control over its properties and technological applications. GO is a nonstoichiometric and hygroscopic material with a lamellar structure, and its physical chemical properties depend critically on synthesis procedures and postsynthesis treatments. Numerous efforts are in place to both understand and exploit this versatile layered carbon material. This Account reports on recent density functional theory (DFT) studies of "epitaxial" graphene oxide (hereafter EGO), a type of GO obtained by oxidation of graphene films grown epitaxially on silicon carbide. Here, we rely on selected X-ray photoelectron spectroscopy (XPS), infrared spectroscopy (IR), and X-ray diffraction (XRD) measurements of EGO, and we discuss in great detail how we utilized DFT-based techniques to project out from the experimental data basic atomistic information about the chemistry and structure of these films. This Account provides an example as to how DFT modeling can be used to elucidate complex materials such as GO from a limited set of experimental information. EGO exhibits a uniform layered structure, consisting of a stack of graphene planes hosting predominantly epoxide and hydroxyl groups, and water molecules intercalated between the oxidized carbon layers. Here, we first focus on XPS measurements of EGO, and we use DFT to generate realistic model structures, calculate core-level chemical shifts, and through the comparison with experiment, gain insight on the chemical composition and metastability characteristics of EGO. DFT calculations are then used to devise a simplistic but accurate simulation scheme to study thermodynamic and kinetic stability and to predict the intralayer structure of EGO films aged at room temperature. Our simulations show that aged EGO encompasses layers with nanosized oxidized domains presenting a high concentration of oxygen functionalities and local structural order, surrounded by regions of pristine graphene. Through the analysis of XRD and IR measurements, our DFT calculations finally show that in EGO, the oxidized domains of stacked layers overlap and locally confine about a monolayer of water molecules. The overall water content in EGO remains below 10%, and intralayer and interlayer spatial ditribution of oxygen species in EGO lead to a layered porous film with an interlayer spacing of about 10 Å. The basic insight gained from our DFT studies, from chemical composition to a nanoscale characterization of the film structure, will be used to fine-tune synthesis methods and EGO properties.

Calcium mediated static and dynamic allostery in S100A12: Implications for target recognition by S100 proteins.

Structure and functions of S100 proteins are regulated by two distinct calcium binding EF hand motifs. In this work, we used solution-state NMR spectroscopy to investigate the cooperativity between the two calcium binding sites and map the allosteric changes at the target binding site. To parse the contribution of the individual calcium binding events, variants of S100A12 were designed to selectively bind calcium to either the EF-I (N63A) or EF-II (E31A) loop, respectively. Detailed analysis of the backbone chemical shifts for wildtype protein and its mutants indicates that calcium binding to the canonical EF-II loop is the principal trigger for the conformational switch between 'closed' apo to the 'open' Ca2+ -bound conformation of the protein. Elimination of binding in S100-specific EF-I loop has limited impact on the calcium binding affinity of the EF-II loop and the concomitant structural rearrangement. In contrast, deletion of binding in the EF-II loop significantly attenuates calcium affinity in the EF-I loop and the structure adopts a 'closed' apo-like conformation. Analysis of experimental amide nitrogen (15 N) relaxation rates (R1 , R2 , and 15 N-{1 H} NOE) and molecular dynamics (MD) simulations demonstrate that the calcium bound state is relatively floppy with pico-nanosecond motions induced in functionally relevant domains responsible for target recognition such as the hinge domain and the C-terminal residues. Experimental relaxation studies combined with MD simulations show that while calcium binding in the EF-I loop alone does not induce significant motions in the polypeptide chain, EF-I regulates fluctuations in the polypeptide in the presence of bound calcium in the EF-II loop. These results offer novel insights into the dynamic regulation of target recognition by calcium binding and unravels the role of cooperativity between the two calcium binding events in S100A12.

Room-temperature metastability of multilayer graphene oxide films.

Graphene oxide potentially has multiple applications. The chemistry of graphene oxide and its response to external stimuli such as temperature and light are not well understood and only approximately controlled. This understanding is crucial to enable future applications of this material. Here, a combined experimental and density functional theory study shows that multilayer graphene oxide produced by oxidizing epitaxial graphene through the Hummers method is a metastable material whose structure and chemistry evolve at room temperature with a characteristic relaxation time of about one month. At the quasi-equilibrium, graphene oxide reaches a nearly stable reduced O/C ratio, and exhibits a structure deprived of epoxide groups and enriched in hydroxyl groups. Our calculations show that the structural and chemical changes are driven by the availability of hydrogen in the oxidized graphitic sheets, which favours the reduction of epoxide groups and the formation of water molecules.

Protons crossing triple phase boundaries based on a metal catalyst, Pd or Ni, and barium zirconate.

Density functional theory calculations are used to investigate the energetics of protons crossing triple phase boundaries based on a metal catalyst, Pd or Ni, and barium zirconate. Our calculations show that the proton transfer reaction at these interfaces is controlled by the terminal layer of the electrolyte in contact with the metallic and gas phases. The hydrogen spilling process onto the electrolyte surface is energetically favored at peripheral sites of the metal-electrolyte interface, and proton incorporation into the sub-surface region of the electrolyte involves energies of the order of 1 eV. At the triple phase boundary, the energy cost associated with the proton transfer reaction is controlled by both the nature of chemical contact and the Schottky barrier at the metal-electrolyte interface.

Anomalous pseudocapacitive behavior of a nanostructured, mixed-valent manganese oxide film for electrical energy storage.

While pseudocapacitors represent a promising option for electrical energy storage, the performance of the existing ones must be dramatically enhanced to meet today's ever-increasing demands for many emerging applications. Here we report a nanostructured, mixed-valent manganese oxide film that exhibits anomalously high specific capacitance (∼2530 F/g of manganese oxide, measured at 0.61 A/g in a two-electrode configuration with loading of active materials ∼0.16 mg/cm(2)) while maintaining excellent power density and cycling life. The dramatic performance enhancement is attributed to its unique mixed-valence state with porous nanoarchitecture, which may facilitate rapid mass transport and enhance surface double-layer capacitance, while promoting facile redox reactions associated with charge storage by both Mn and O sites, as suggested by in situ X-ray absorption spectroscopy (XAS) and density functional theory calculations. The new charge storage mechanisms (in addition to redox reactions of cations) may offer critical insights to rational design of a new-generation energy storage devices.

Pressure-Induced Formation and Mechanical Properties of 2D Diamond Boron Nitride.

Understanding phase transformations in 2D materials can unlock unprecedented developments in nanotechnology, since their unique properties can be dramatically modified by external fields that control the phase change. Here, experiments and simulations are used to investigate the mechanical properties of a 2D diamond boron nitride (BN) phase induced by applying local pressure on atomically thin h-BN on a SiO2 substrate, at room temperature, and without chemical functionalization. Molecular dynamics (MD) simulations show a metastable local rearrangement of the h-BN atoms into diamond crystal clusters when increasing the indentation pressure. Raman spectroscopy experiments confirm the presence of a pressure-induced cubic BN phase, and its metastability upon release of pressure. Å-indentation experiments and simulations show that at pressures of 2-4 GPa, the indentation stiffness of monolayer h-BN on SiO2 is the same of bare SiO2, whereas for two- and three-layer-thick h-BN on SiO2 the stiffness increases of up to 50% compared to bare SiO2, and then it decreases when increasing the number of layers. Up to 4 GPa, the reduced strain in the layers closer to the substrate decreases the probability of the sp2-to-sp3 phase transition, explaining the lower stiffness observed in thicker h-BN.

Thermodynamic stability limits of simple monoatomic materials.

This computational study addresses the thermodynamical stability of superheated crystals. Molecular dynamics simulations are employed to derive the caloric curves of the solid and liquid phases of a material. Caloric curves are used to derive thermodynamic state functions, the parameters of the equilibrium melting phase transition, and the regions of thermodynamical stability of the liquid and solid phases. Molecular dynamics trajectories are also analyzed to gain insight on the mechanisms leading to the instability of the homogeneous superheated solid phase. This study shows that in simple and homogeneous solids the configurational entropy is not zero and that its excitations can occur without disrupting the crystallinity of the lattice. The superheating and supercooling limits of the solid and liquid phases are found to correspond to states of equal entropy and enthalpy.

Oligonucleotide-stabilized Ag nanocluster fluorophores.

Single-stranded oligonucleotides stabilize highly fluorescent Ag nanoclusters, with emission colors tunable via DNA sequence. We utilized DNA microarrays to optimize these scaffold sequences for creating nearly spectrally pure Ag nanocluster fluorophores that are highly photostable and exhibit great buffer stability. Five different nanocluster emitters have been created with tunable emission from the blue to the near-IR and excellent photophysical properties. Ensemble and single molecule fluorescence studies show that oligonucleotide encapsulated Ag nanoclusters exhibit significantly greater photostability and higher emission rates than commonly used cyanine dyes.

Energy landscape of an electron hole in hydrated DNA.

First-principles/molecular mechanics, force-field, and 1-D lattice model schemes are used to address the energy landscape of an electron hole in hydrated DNA. Force-field calculations are used to derive a statistical description of the electrostatic fluctuations in DNA yielded by the polar environment, and a periodic first-principles/molecular mechanics scheme is employed to calculate the hole energy at uniform DNA segments embedded in hydrated DNA double helices. The results are then mapped onto 1-D lattice models to address issues relevant to charge transfer in hydrated DNA. It is shown that the polar environment generates an intense dynamical energy disorder along the DNA strands, exhibiting exponential spatio-temporal correlations. The fluctuations of the polar environment lead to hole states localized over a few DNA bases and compete evenly with the DNA sequence to define the hole energy landscape. The spatial correlations of the environment-induced fluctuations are also shown to influence strongly the hole transfer dynamics in DNA.

Ultrahard carbon film from epitaxial two-layer graphene.

Atomically thin graphene exhibits fascinating mechanical properties, although its hardness and transverse stiffness are inferior to those of diamond. So far, there has been no practical demonstration of the transformation of multilayer graphene into diamond-like ultrahard structures. Here we show that at room temperature and after nano-indentation, two-layer graphene on SiC(0001) exhibits a transverse stiffness and hardness comparable to diamond, is resistant to perforation with a diamond indenter and shows a reversible drop in electrical conductivity upon indentation. Density functional theory calculations suggest that, upon compression, the two-layer graphene film transforms into a diamond-like film, producing both elastic deformations and sp 2 to sp 3 chemical changes. Experiments and calculations show that this reversible phase change is not observed for a single buffer layer on SiC or graphene films thicker than three to five layers. Indeed, calculations show that whereas in two-layer graphene layer-stacking configuration controls the conformation of the diamond-like film, in a multilayer film it hinders the phase transformation.

Author Correction: Ultrahard carbon film from epitaxial two-layer graphene.

In the version of this Article originally published, the second affiliation for Walter A. de Heer had not been included; it should be 'TICNN, Tianjin University, Tianjin, China'. This has now been added and the numbering of subsequent affiliations amended accordingly in all versions of the Article.

Atomistic Corrective Scheme for Supercell Density Functional Theory Calculations of Charged Defects.

A new method to correct formation energies of charged defects obtained by supercell density-functional calculations is presented and applied to bulk, surface, and low-dimensional systems. The method relies on atomistic models and a polarizable force field to describe a material system and its dielectric properties. The polarizable force field is based on a minimal set of fitting parameters, it accounts for the dielectric screening arising from ions and electrons separately, and it can be easily implemented in any software for atomistic molecular dynamics simulations. This work illustrates both technical aspects and applications of the new corrective scheme. The method is tested on systems in vacuo to validate the energy scheme. It is applied to charged defects in the bulk and at the surface of realistic materials to achieve comparison with published results obtained by using available corrective schemes based on continuum electrostatics treatments. Moreover, to demonstrate its generality, the method is used to correct the formation energy obtained by DFT of a singly negatively charged S vacancy in monolayer, bilayer, trilayer and bulk MoS2.

RNA intrusions change DNA elastic properties and structure.

The units of RNA, termed ribonucleoside monophosphates (rNMPs), have been recently found as the most abundant defects present in DNA. Despite the relevance, it is largely unknown if and how rNMPs embedded in DNA can change the DNA structure and mechanical properties. Here, we report that rNMPs incorporated in DNA can change the elastic properties of DNA. Atomic force microscopy (AFM)-based single molecule elasticity measurements show that rNMP intrusions in short DNA duplexes can decrease--by 32%--or slightly increase the stretch modulus of DNA molecules for two sequences reported in this study. Molecular dynamics simulations and nuclear magnetic resonance spectroscopy identify a series of significant local structural alterations of DNA containing embedded rNMPs, especially at the rNMPs and nucleotide 3' to the rNMP sites. The demonstrated ability of rNMPs to locally alter DNA mechanical properties and structure may help in understanding how such intrusions impact DNA biological functions and find applications in structural DNA and RNA nanotechnology.

Origin of the chemical and kinetic stability of graphene oxide.

At moderate temperatures (≤ 70°C), thermal reduction of graphene oxide is inefficient and after its synthesis the material enters in a metastable state. Here, first-principles and statistical calculations are used to investigate both the low-temperature processes leading to decomposition of graphene oxide and the role of ageing on the structure and stability of this material. Our study shows that the key factor underlying the stability of graphene oxide is the tendency of the oxygen functionalities to agglomerate and form highly oxidized domains surrounded by areas of pristine graphene. Within the agglomerates of functional groups, the primary decomposition reactions are hindered by both geometrical and energetic factors. The number of reacting sites is reduced by the occurrence of local order in the oxidized domains, and due to the close packing of the oxygen functionalities, the decomposition reactions become - on average - endothermic by more than 0.6 eV.

Bonding trends and dimensionality crossover of gold nanoclusters on metal-supported MgO thin films.

Bonding of gold clusters, , 16, and 20, on MgO(100) and on thin MgO films supported on Mo(100) is investigated using first-principles density-functional theory. Enhanced adhesive bonding is found for clusters deposited on metal-supported MgO films of thickness up to about 1 nm, or 4 to 5 MgO layers, originating from electrostatic interaction between the underlying metal and metal-induced excess electronic charge accumulated at the cluster interface with the oxide film. The increased wetting propensity is accompanied by a dimensionality crossover from three-dimensional optimal cluster geometries on MgO(100) to energetically favored two-dimensional structures on the metal-supported films.

Oxidative damage to DNA: counterion-assisted addition of water to ionized DNA.

Oxidative damage to DNA, implicated in mutagenesis, aging, and cancer, follows electron loss that generates a radical cation that migrates to a guanine, where it may react with water to form 8-oxo-7,8-dihydroguanine (8-OxoG). Molecular dynamics and ab initio quantum simulations on a B-DNA tetradecamer reveal activated reaction pathways that depend on the local counterion arrangement. The lowest activation barrier, 0.73 eV, is found for a reaction that starts from a configuration where a Na(+) resides in the major groove near the N7 atoms of adjacent guanines, and evolves through a transition state where a bond between a water oxygen atom and a carbon atom forms concurrently with displacement of a proton toward a neighboring water molecule. Subsequently, a bonded complex of a hydronium ion and the nearest backbone phosphate group forms. This counterion-assisted proton shuttle mechanism is supported by experiments exploiting selective substitution of backbone phosphates by methylphosphonates.