Philippe D'Arco

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.

Ab initio modeling of trititanate nanotubes

Nanotubes with H2Ti3O7 stoichiometry have been studied by ab initio methods in the diameter range of ∼20-60 Å. The distribution of the protons on the unit cell surface and its effect on the structure and electronic properties of the titanium dioxide backbone has been investigated. The preferred protonation pattern was found to be the function of the diameter of the nanotube and the convexity of the surface. Trititanate tubes have been found to be more stable than lepidocrocite nanotubes at all diameters. At diameters<50 Å the dissociation of water from the internal surface and the emergence of a new tube wall structure was observed. Band gaps were found to change only slightly with the curvature, the maximum difference from the flat slab values was ±0.5 eV.

Katoite under pressure: an ab initio investigation of its structural, elastic and vibrational properties sheds light on the phase transition

The evolution under pressures up to 65 GPa of structural, elastic and vibrational properties of the katoite hydrogarnet, Ca3Al2(OH)12, is investigated with an ab initio simulation performed at the B3LYP level of theory, by using all-electron basis sets with the Crystal periodic program. The high-symmetry Ia3d phase of katoite, stable under ambient conditions, is shown to be destabilized, as pressure increases, by interactions involving hydrogen atoms and their neighbors which weaken the hydrogen bonding network of the structure. The corresponding thermodynamical instability is revealed by anomalous deviations from regularity of its elastic constants and by numerous imaginary phonon frequencies, up to 50 GPa. Interestingly, as pressure is further increased above 50 GPa, the Ia3d structure is shown to become stable again (all positive phonon frequencies and regular elastic constants). However, present calculations suggest that, above about 15 GPa and up to at least 65 GPa, a phase of I4[combining macron]3d symmetry (a non-centrosymmetric subgroup of Ia3d) becomes more stable than the Ia3d one, being characterized by strengthened hydrogen bonds. At low-pressures (between about 5 GPa and 15 GPa), both phases show some instabilities (more so for I4[combining macron]3d than for Ia3d), thus suggesting either the existence of a third phase or a possible phase transition of second order.

Ionicity in silica

Coronavirus motif SIR I report the presence of a leucine zipper motif at the carboxyl end of the spike (S) glycoprotein, a transmembrane protein of coronaviruses. All the coronavirus S proteins whose sequences are known transmissible gastroenteritis virus (TGEV) FS772/70 (residues 1,3421,377), feline infectious peritonitis virus (FIPV) 79-1146 (1345-1380), mouse hepatitis virus (MHV) A59 (1217-1252), MHV JHM (1128-1163), human coronavirus (HCV) 229£ (1,067-1,102), bovine corona virus (BCV) Mebus ( 1,266--1,294) and infectious bronchitis virus (IBV) Beaudette (1,058-1,079) contain a