Model Hessian for accelerating first-principles structure optimizations

We present two methods to accelerate first-principles structural relaxations, both based on the dynamical matrix obtained from a universal model of springs for bond stretching and bending. Despite its simplicity, the normal modes of this model Hessian represent excellent internal coordinates for molecules and solids irrespective of coordination, capturing not only the long-wavelength acoustic modes of large systems, but also the short-wavelength low-frequency modes that appear in complex systems. In the first method, the model Hessian is used to precondition a conjugate gradients minimization, thereby drastically reducing the effective spectral width and thus obtaining a substantial improvement of convergence. The same Hessian is used in the second method as a starting point of a quasi-Newton algorithm (Broyden's method and modifications thereof), reducing the number of steps needed to find the correct Hessian. Results for both methods are presented for geometry optimizations of clusters, slabs, and biomolecules, with speed-up factors between 2 and 8.Comment: 5 pages, 3 figures submites to Phys. Rev.

Structural and dielectric properties of Sr2_{2}TiO4_{4} from first principles

We have investigated the structural and dielectric properties of Sr$_{2}$TiO$_{4}$,the first member of the Sr$_{n+1}$Ti$_{n}$O$_{3n+1}$ Ruddlesden-Popper series, within density functional theory. Motivated by recent work in which thin films of Sr$_{2}$TiO$_{4}$ were grown by molecular beam epitaxy (MBE) on SrTiO$_{3}$ substrates, the in-plane lattice parameter was fixed to the theoretically optimized lattice constant of cubic SrTiO$_{3}$ (n=$\infty$), while the out-of-plane lattice parameter and the internal structural parameters were relaxed. The fully relaxed structure was also investigated. Density functional perturbation theory was used to calculate the zone-center phonon frequencies, Born effective charges, and the electronic dielectric permittivity tensor. A detailed study of the contribution of individual infrared-active modes to the static dielectric permittivity tensor was performed. The calculated Raman and infrared phonon frequencies were found to be in agreement with experiment where available. Comparisons of the calculated static dielectric permittivity with experiments on both ceramic powders and epitaxial thin films are discussed.Comment: 11 pages, 1 figure, 8 tables, submitted to Phys. Rev.

Characterization of Low Energy Charge Transfer Transitions in (terpyridine)(bipyridine)Ruthenium(II) Complexes and their Cyanide-Bridged Bi- and Tri-Metallic Analogues

The lowest energy metal-to-ligand charge transfer (MLCT) absorption bands found in ambient solutions of a series of [Ru(tpy)(bpy)X](m+) complexes (tpy = 2,2':3',2 ''-terpyridine; bpy = 2,2'-bipyridine; and X = a monodentate ancillary ligand) feature one or two partly resolved weak absorptions (bands I and/or II) on the low energy side of their absorption envelopes. Similar features are found for the related cyanide-bridged bi- and trimetallic complexes. However, the weak absorption band I of [(bpy)(2)Ru{CNRu(tpy)(bpy)}(2)](4+) is missing in its [(bpy)(2)Ru{NCRu(tpy)(bpy)}(2)](4+) linkage isomer demonstrating that this feature arises from a Ru(II)/tpy MLCT absorption. The energies of the MLCT band I components of the [Ru(tpy)(bpy)X](m+) complexes are proportional to the differences between the potentials for the first oxidation and the first reduction waves of the complexes. Time-dependent density functional theory (TD-DFT) computational modeling indicates that these band I components correspond to the highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) transition, with the HOMO being largely ruthenium-centered and the LUMO largely tpy-centered. The most intense contribution to a lowest energy MLCT absorption envelope (band III) of these complexes corresponds to the convolution of several orbitally different components, and its absorption maximum has an energy that is about 5000 cm(-1) higher than that of band L The multimetallic complexes that contain Ru(II) centers linked by cyanide have mixed valence excited states in which more than 10% of electronic density is delocalized between the nearest neighbor ruthenium centers, and the corresponding stabilization energy contributions in the excited states are indistinguishable from those of the corresponding ground states. Single crystal X-ray structures and computational modeling indicate that the Ru-(C N)-Ru linkage is quite flexible and that there is not an appreciable variation in electronic structure or energy among the conformational isomers

Reduced-intensity conditioning and HLA-matched haemopoietic stem-cell transplantation in patients with chronic granulomatous disease: a prospective multicentre study

BACKGROUND: In chronic granulomatous disease allogeneic haemopoietic stem-cell transplantation (HSCT) in adolescents and young adults and patients with high-risk disease is complicated by graft-failure, graft-versus-host disease (GVHD), and transplant-related mortality. We examined the effect of a reduced-intensity conditioning regimen designed to enhance myeloid engraftment and reduce organ toxicity in these patients. METHODS: This prospective study was done at 16 centres in ten countries worldwide. Patients aged 0-40 years with chronic granulomatous disease were assessed and enrolled at the discretion of individual centres. Reduced-intensity conditioning consisted of high-dose fludarabine (30 mg/m2 [infants <9 kg 1•2 mg/kg]; one dose per day on days -8 to -3), serotherapy (anti-thymocyte globulin [10 mg/kg, one dose per day on days -4 to -1; or thymoglobuline 2•5 mg/kg, one dose per day on days -5 to -3]; or low-dose alemtuzumab [<1 mg/kg on days -8 to -6]), and low-dose (50-72% of myeloablative dose) or targeted busulfan administration (recommended cumulative area under the curve: 45-65 mg/L × h). Busulfan was administered mainly intravenously and exceptionally orally from days -5 to -3. Intravenous busulfan was dosed according to weight-based recommendations and was administered in most centres (ten) twice daily over 4 h. Unmanipulated bone marrow or peripheral blood stem cells from HLA-matched related-donors or HLA-9/10 or HLA-10/10 matched unrelated-donors were infused. The primary endpoints were overall survival and event-free survival (EFS), probabilities of overall survival and EFS at 2 years, incidence of acute and chronic GVHD, achievement of at least 90% myeloid donor chimerism, and incidence of graft failure after at least 6 months of follow-up. RESULTS: 56 patients (median age 12•7 years; IQR 6•8-17•3) with chronic granulomatous disease were enrolled from June 15, 2003, to Dec 15, 2012. 42 patients (75%) had high-risk features (ie, intractable infections and autoinflammation), 25 (45%) were adolescents and young adults (age 14-39 years). 21 HLA-matched related-donor and 35 HLA-matched unrelated-donor transplants were done. Median time to engraftment was 19 days (IQR 16-22) for neutrophils and 21 days (IQR 16-25) for platelets. At median follow-up of 21 months (IQR 13-35) overall survival was 93% (52 of 56) and EFS was 89% (50 of 56). The 2-year probability of overall survival was 96% (95% CI 86•46-99•09) and of EFS was 91% (79•78-96•17). Graft-failure occurred in 5% (three of 56) of patients. The cumulative incidence of acute GVHD of grade III-IV was 4% (two of 56) and of chronic graft-versus-host disease was 7% (four of 56). Stable (≥90%) myeloid donor chimerism was documented in 52 (93%) surviving patients. INTERPRETATION: This reduced-intensity conditioning regimen is safe and efficacious in high-risk patients with chronic granulomatous disease