Raffaella Demichelis

Stable prenucleation mineral clusters are liquid-like ionic polymers

Calcium carbonate is an abundant substance that can be created in several mineral forms by the reaction of dissolved carbon dioxide in water with calcium ions. Through biomineralization, organisms can harness and control this process to form various functional materials that can act as anything from shells through to lenses. The early stages of calcium carbonate formation have recently attracted attention as stable prenucleation clusters have been observed, contrary to classical models. Here we show, using computer simulations combined with the analysis of experimental data, that these mineral clusters are made of an ionic polymer, composed of alternating calcium and carbonate ions, with a dynamic topology consisting of chains, branches and rings. The existence of a disordered, flexible and strongly hydrated precursor provides a basis for explaining the formation of other liquid-like amorphous states of calcium carbonate, in addition to the non-classical behaviour during growth of amorphous calcium carbonate.

A new structural model for disorder in vaterite from first-principles calculations

Both of the previously proposed Pbnm and P6522 ordered structures for vaterite are found to be unstable transition states using first-principles methods. Five stable structures are located, the lowest energy one being of P3221 symmetry. Since interconversion between these structures requires only thermal energy, this provides an additional source of disorder within the vaterite structure.

On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two‐dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono‐ and bi‐electronic integrals that enter into the Fock (Kohn‐Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M × 2M matrix. The efficiency and accuracy of the computational scheme is documented.

Structure and energetics of imogolite: a quantum mechanical ab initio study with B3LYP hybrid functional

Imogolite (Al2(OH)3SiO3OH) single-walled nanotubes are simulated at the ab initio level by using an all electron Gaussian type basis set and the hybrid B3LYP functional. Full exploitation of the roto-translational symmetry drastically reduces the computational cost. Two kinds of tubes, (n, 0) and (n, n), are considered, resulting from rolling up a hypothetical structure containing a gibbsite-like hexagonal layer linked to a silanolic SiOH unit. In both cases a minimum is observed, corresponding to n = 10 for (n, 0) (the radius, taken as the distance between the tube axis and one of the basal SiO4 oxygen atoms, is 7.26 A) and n = 8 for (n, n) (10.3 A). Hydrogen bonds and orientation of the silanolic group inside the tube play an important role in stabilising the structures. The (10, 0) structure is 10.6 kJ mol−1 per formula unit more stable than the (8, 8) tube, the difference being due, at least partially, to the formation of hydrogen bonds in the inner wall of the tube (the shortest H⋯O distances are 2.14 and 3.01 A, respectively). Two curves are observed in the (n, 0) case, whose minima, both at n = 10, are separated by 2.0 kJ mol−1 per formula unit. These two structures are extremely similar, the main difference being the orientation of the OH unit pointing inside the tube.

Oxygen Spectroscopy and Polarization-Dependent Imaging Contrast (PIC)-Mapping of Calcium Carbonate Minerals and Biominerals

X-ray absorption near-edge structure (XANES) spectroscopy and spectromicroscopy have been extensively used to characterize biominerals. Using either Ca or C spectra, unique information has been obtained regarding amorphous biominerals and nanocrystal orientations. Building on these results, we demonstrate that recording XANES spectra of calcium carbonate at the oxygen K-edge enables polarization-dependent imaging contrast (PIC) mapping with unprecedented contrast, signal-to-noise ratio, and magnification. O and Ca spectra are presented for six calcium carbonate minerals: aragonite, calcite, vaterite, monohydrocalcite, and both hydrated and anhydrous amorphous calcium carbonate. The crystalline minerals reveal excellent agreement of the extent and direction of polarization dependences in simulated and experimental XANES spectra due to X-ray linear dichroism. This effect is particularly strong for aragonite, calcite, and vaterite. In natural biominerals, oxygen PIC-mapping generated high-magnification maps of unprecedented clarity from nacre and prismatic structures and their interface in Mytilus californianus shells. These maps revealed blocky aragonite crystals at the nacre-prismatic boundary and the narrowest calcite needle-prisms. In the tunic spicules of Herdmania momus, O PIC-mapping revealed the size and arrangement of some of the largest vaterite single crystals known. O spectroscopy therefore enables the simultaneous measurement of chemical and orientational information in CaCO3 biominerals and is thus a powerful means for analyzing these and other complex materials. As described here, PIC-mapping and spectroscopy at the O K-edge are methods for gathering valuable data that can be carried out using spectromicroscopy beamlines at most synchrotrons without the expense of additional equipment.

Assessing thermochemical properties of materials through ab initio quantum-mechanical methods: the case of α-Al2O3

The thermochemical behavior of α-Al2O3 corundum in the whole temperature range 0-2317 K (melting point) and under pressures up to 12 GPa is predicted by applying ab initio methods based on the density functional theory (DFT), the use of a local basis set and periodic-boundary conditions. Thermodynamic properties are treated both within and beyond the harmonic approximation to the lattice potential. In particular, a recent implementation of the quasi-harmonic approximation, in the Crystal program, is here shown to provide a reliable description of the thermal expansion coefficient, entropy, constant-volume and constant-pressure specific heats, and temperature dependence of the bulk modulus, nearly up to the corundum melting temperature. This is a remarkable outcome suggesting α-Al2O3 to be an almost perfect quasi-harmonic crystal. The effect of using different computational parameters and DFT functionals belonging to different levels of approximations on the accuracy of the thermal properties is tested, providing a reference for further studies involving alumina polymorphs and, more generally, quasi-ionic minerals.

Ab-initio quantum mechanical study of akdalaite (5Al2O3· H2O): structure and vibrational spectrum

The structure and the vibrational spectrum of akdalaite (5Al2O3·H2O, also known as tohdite) have been investigated at the periodic ab-initio quantum-mechanical level by using a high quality Gaussian type basis set and the hybrid B3LYP Hamiltonian with the CRYSTAL06 code. Three space groups proposed in the literature, namely P63mc and its two P31c and Cmc21 subgroups, have been considered, obtaining essentially the same energy (the largest total energy difference is 0.2 kJ/mol per cell) and geometry. The harmonic frequencies at the τ point have been computed. Isotopic substitution and graphical representation permit a complete classification of normal modes in terms of simple models (octahedra and tetrahedra modes, hydrogen stretching and bending). The Al-O octahedra and tetrahedra modes appear below 880 cm−1, Al-OH bending modes are located in the range 870-900 cm−1, and OH stretching modes are at 3330-3400 cm-1.

Dye functionalized carbon nanotubes for photoelectrochemical water splitting – role of inner tubes

Dye sensitized water splitting photoelectrochemical (PEC) cells generally require the attachment of photosensitizer to a semiconductor and a water oxidation catalyst (WOC). Here we report for the first time that dye, including zinc phthalocyanine (ZnPc), cobalt phthalocyanine (CoPc) and tris(bipyridine)ruthenium(II) (Rubpy), sensitized or functionalized pristine carbon nanotubes (dye/CNTs) without the presence of semiconducting oxides and conventional WOCs have unusually high activity for PEC water splitting in alkaline solutions under ultraviolet (UV) and visible light. The PEC activities of dye/CNTs show distinctive volcano curves as a function of number of walls with the highest activity observed on double- and triple-walled CNTs (DWNTs and TWNTs). For example, the photocurrent of the ZnPc functionalized TWNTs at 1.2 V vs. RHE is 0.32 mA cm−2, which is ∼4 times of 0.09 mA cm−2 obtained on the ZnPc functionalized single-walled CNTs (SWNTs) and one order of magnitude higher than 0.02 mA cm−2 on ZnPc functionalized multi-walled CNTs (MWNTs). On the other hand, the photocurrents are negligible on pristine CNTs, less than 0.005 mA cm−2 under identical experimental conditions. This remarkable feature is due to the unique charge separation ability of the dye/CNTs, where the photoexcited electrons are transferred to the inner tubes via the electron tunneling under the dc bias voltage, and the significant electrocatalytic activities of DWNTs and TWNTs for the water oxidation reaction. The results provide new opportunities for the development of artificial photosynthetic systems via the manipulation of the quantum properties of CNTs.

Ab Initio Modelling of the Structure and Properties of Crystalline Calcium Carbonate

Many biominerals occur as crystalline materials, and their formation often involves steps where metastable crystalline phases appear. The latter can correspond either to intermediate species that then transform into more stable phases or to the final mineral crystal. Because of their instability and rare occurrence, the structure and properties of such intermediate metastable phases may not always be fully understood from experiment alone. Vaterite (CaCO3) is one such phase, and recent advances in understanding its complex structure were achieved through ab initio modelling techniques. This chapter will highlight the importance of achieving a comprehensive understanding of the atomic details of the crystalline phases involved in biomineralisation. Examples will be focused on calcium carbonate, and especially on vaterite, and ab initio methods based on density functional theory (DFT) will be proposed as the main tool to undertake this kind of investigation, together with more traditional techniques such as spectroscopic methods, microscopies and X-ray and neutron diffraction.

Serpentine polymorphism: a quantitative insight from first-principles calculations

Single-walled chrysotile nanotubes [Mg3Si2O5(OH)4] of increasing size (up to 5004 atoms per unit cell, corresponding to a radius of 205 A) have been modelled at the Density Functional level of theory. For the first time, it is demonstrated that the (n, −n) and (n, n) series present a minimum energy structure at a specific radius (88.7 and 89.6 A, respectively, referring to the neutral surface), corresponding to a rolling vector of (60, −60) and (105, 105), respectively. The minima are nearly overlapped and are lower in energy than the corresponding slab of lizardite (the flat-layered polymorph of chrysotile) by about 3.5 kJ mol−1 per formula unit. In both cases, the energy profile presents a shallow minimum, where radii in the range of 63 to 139 A differ in energy by less than 0.5 kJ mol−1 per formula unit. The energy of larger nanotubes has a trend that slowly converges to the limit of the flat lizardite slab. Structural quantities such as bond distances and angles of nanotubes with increasing size asymptotically converge to the flat slab limit, with no discontinuities in the surrounding of the minimum energy structures. However, analysis of the elongation of a rectangular pseudo-unit cell along the nanotube circumference indicates that the main factor that leads lizardite to curl in tubes is the elastic strain caused by the mismatch between the lattice parameters of the two adjacent tetrahedral and octahedral sheets. It is also shown in this study that the curvature of the layers in one of the lately proposed models of antigorite, the “wavy-layered” polymorph of chrysotile, falls within the range of radii of minimum energy for the nanotubes. These findings provide quantitative insights into the peculiar polymorphism of these three phyllosilicates. They show also that chrysotile belongs to those families of inorganic nanotubes that present a minimum in their strain energy profile at a specific range of radii, which is lower in energy with respect to their flat equivalent.