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The vibrational spectrum of [alpha]-AlOOH diaspore calculated at the B3LYP level of theory with a double-(symbol) quality Gaussian-type basis set by using the periodic ab initio CRYSTAL code is reported.

The ground state electronic structure in various magnetic phases of two Ge garnets (80 atoms in the primitive cell; cubic symmetry), Ca3Fe2Ge3O12 and Ca3Cr2Ge3O12, has been investigated with the periodic ab initio CRYSTAL code by adopting an all-electron Gaussian-type basis set and two hybrid functionals, namely B3LYP and PBE0, which contain a fraction of exact Hartree–Fock exchange. The evaluation of the exchange coupling constants among first (J1a, and J1b: there are two different kinds of neighbors at the same distance), second (J2), and third (J3) neighbors, separated by about 5.3, 6.1, and 8.7 Å, respectively, requires calculations involving the 160 atoms conventional cell. The Ji values turn out to be in qualitative agreement with experimental data. As a consequence of the different J1a to J1b ratios, and of the opposite sign of J2, two different magnetic ground states are found for the Cr and Fe compounds, in agreement with experimental observations. The mechanism for the stabilization of the magnetic states is discussed in the context of the Anderson theory of superexchange by evaluating the kinetic energy gain in the magnetic states and examining spin density maps and profiles. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

The lack of experimental data on the dynamics of aspartic acid species in water for its range of protonation states and the details of their atomic-level interaction with aqueous calcium carbonate species is a driver for accurate force field development. A classical model that is consistent with the few pieces of experimental data available and with first principles calculations has been developed. The complex dynamics of the aspartate anions relevant to biomineralization and calcium carbonate crystal growth has been explored in water, providing a quantitative description of solvation structure and free energies, including conformational free energy profiles and pairing free energies. The model has been used to probe the structure and dynamics of aqueous calcium aspartate homo- and hetero-chiral clusters, confirming their unlikelihood due to weak and water-mediated interactions. This supports the hypothesis that the formation of such clusters, observed while growing vaterite in the presence of acidic chiral amino acids, is favoured by the presence of the crystal surface.

Crystallization of alkaline earth metal carbonates from water is important for biomineralization and environmental geochemistry. Here, large-scale computer simulations are a useful approach to complement experimental studies by providing atomistic insights and even by quantitatively determining the thermodynamics of individual steps. However, this is dependent on the existence of force field models that are sufficiently accurate while being computationally efficient enough to sample complex systems. Here, we introduce a revised force field for aqueous alkaline earth metal carbonates that reproduces both the solubilities of the crystalline anhydrous minerals, as well as the hydration free energies of the ions. The model is also designed to run efficiently on graphical processing units thereby reducing the cost of such simulations. The performance of the revised force field is compared against previous results for important properties relevant to crystallization, including ion-pairing and mineral-water interfacial structure and dynamics. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Biomineralized structures are complex functional hierarchical assemblies composed of biomineral building blocks joined together by an organic phase. The formation of individual mineral units is governed by the cellular tissue component that orchestrates the process of biomineral nucleation, growth, and morphogenesis. These processes are imprinted in the structural, compositional, and crystallographic properties of the emerging biominerals on all scales. Measurement of these properties can provide crucial information on the mechanisms that are employed by the organism to form these complex 3D architectures and to unravel principles of their functionality. Nevertheless, so far, this has only been possible at the macroscopic scale, by averaging the properties of the entire composite assembly, or at the mesoscale, by looking at extremely small parts of the entire picture. In this study, the newly developed synchrotron-based dark-field X-ray microscopy method is employed to study the link between 3D crystallographic properties of relatively large calcitic prisms in the shell of the mollusc Pinna nobilis and their local lattice properties with extremely high angular resolution down to 0.001°. Mechanistic links between variations in local lattice parameters and spacing, crystal orientation, chemical composition, and the deposition process of the entire mineral unit are unraveled., (© 2022 The Authors. Advanced Materials published by Wiley-VCH GmbH.)

The interaction of organic molecules with mineral systems is relevant to a wide variety of scientific problems both in the environment and minerals processing. In this study, the coordination of small organics that contain the two most relevant functional groups for biomineralisation of calcium carbonate, namely carboxylate and ammonium, with the corresponding mineral ions are examined in aqueous solution. Specifically, two force fields have been examined based on rigid-ion or polarisable models, with the latter being within the AMOEBA formalism. Here the parameters for the rigid-ion model are determined to target the accurate reproduction of the hydration structure and solvation thermodynamics, while both force fields are designed to be compatible with the corresponding recently published models for aqueous calcium carbonate. The application of these force fields to ion pairing in aqueous solution is studied in order to quantitatively determine the extent of association.

Breast implant-associated anaplastic large cell lymphoma (ALCL) is a distinctive type of T-cell lymphoma that arises around textured-surface breast implants. In a subset of patients, this disease can involve surrounding tissues, spread to regional lymph nodes, and rarely metastasize to distant sites. The aim of this study was to assess sequential pathologic specimens from patients with breast implant-associated ALCL to better understand the natural history of early-stage disease. To achieve this goal, we searched our files for patients who had breast implant-associated ALCL and who had undergone earlier surgical intervention with assessment of biopsy or cytologic specimens. We then focused on the patient subset in whom a definitive diagnosis was not established, and patients did not receive current standard-of-care therapy at that time. We identified a study group of ten patients with breast implant-associated ALCL in whom pathologic specimens were collected 0.5 to 4 years before a definitive diagnosis was established. A comparison of these serial biopsy specimens showed persistent disease without change in pathologic stage in three patients, progression in five patients, and persistence versus progression in two patients. Eventually, six patients underwent implant removal with complete capsulectomy and four underwent partial capsulectomy. Seven patients also received chemotherapy because of invasive disease, three of whom also received radiation therapy, two brentuximab vedotin after chemotherapy failure, and one allogeneic stem cell transplant. Eight patients achieved complete remission and two had partial remission after definitive therapy. At time of last follow-up, six patients were alive without disease, one had evidence of disease, one died of disease, and two patients died of unrelated cancers. In summary, this analysis of sequential specimens from patients with breast implant-associated ALCL suggests these neoplasms persist or progress over time if not treated with standard-of-care therapy., (© 2021. The Author(s), under exclusive licence to United States & Canadian Academy of Pathology.)

Classical molecular and lattice dynamics were applied to explore the structure and dynamics of water on different surfaces of vaterite, the least abundant calcium carbonate polymorph. Surfaces were generated starting from the three possible structural models for vaterite (monoclinic, hexagonal/trigonal, and triclinic) and pre-screened using their surface energies in an implicit solvent. Surfaces with energies lower than 0.55 J/m 2 were then run in explicit water. The majority of these surfaces dissolve in less than 100 ns, highlighting the low stability of this phase in abiotic environments. Three stable surfaces were identified; they exhibited only minor structural changes when in contact with explicit water and did not show any tendency to dissolve during 1 µs molecular dynamics simulations. The computed water density profiles show that all these surfaces have two distinct hydration layers. The water residence time at the various calcium sites was computed to be within 0.7 and 20.5 ns, which suggests that specific Ca ions will be more readily available to bind with organic molecules present in solution. This analysis is a step forward in understanding the structure of this complex mineral and its role in biomineralization, as it provides a solid theoretical background to explore its surface chemistry. In particular, this study provides realistic surface models and predicts the effect of water exchange at the surface active sites on the adsorption of other molecules.

Background: The present retrospective study reviewed acute promyelocytic leukemia (APL) cases recorded in Mexico between January 2007 and January 2017. The primary objective of the study was to evaluate overall survival (OS) in Mexican patients with APL. Secondary objective was to evaluate the impact of induction treatment with different anthracyclines on OS, event-free survival (EFS) and complications in this patient population., Methods: The medical charts of patients referred to medical institutions in Mexico from January 2007 through January 2017 for the treatment of suspected APL were reviewed retrospectively. Patients aged 15 - 75 years, in whom the diagnosis of APL was confirmed, who had an Eastern Cooperative Group performance status of 0 - 2, and who were eligible for combined treatment with intensive chemotherapy and all-trans retinoic acid (ATRA), were included in the study. Study participants received induction and consolidation treatment with ATRA plus either daunorubicin or idarubicin, followed by 2 years of single-agent ATRA as maintenance therapy. Patients who were unable to pay for ATRA treatment received anthracycline-based induction and consolidation, with methotrexate plus mercaptopurine as maintenance therapy., Results: A total of 360 patients from 21 public and private hospitals were included in the study. The median age of the population was 37 years, and 51% were male. Of the 360 patients, 205 (57%) vs. 155 (43%) received daunorubicin vs. idarubicin as induction treatment for APL. ATRA was administered to 201 (98%) patients in the daunorubicin group vs. 138 (89%) in the idarubicin group (P = 0.001), and was initiated at diagnosis in 92% vs. 73% of recipients, respectively (P = 0.0001). At 150 months, OS and EFS for the entire population were 84% and 79%, respectively. Both OS (90% vs. 76%, P = 0.003) and EFS (85% vs. 72%, P = 0.001) were significantly prolonged in daunorubicin vs. idarubicin recipients. Rates of complications were similar in the two groups., Conclusions: As arsenic trioxide (ATO) is not currently available in Mexico, anthracycline plus ATRA is the mainstay of treatment for APL here. Our results confirm the efficacy of this strategy, with high OS and EFS rates being observed 12.5 years after diagnosis., Competing Interests: The authors have no potential conflict of interest to disclose., (Copyright 2021, Zapata-Canto et al.)

CRYSTAL is a periodic ab initio code that uses a Gaussian-type basis set to express crystalline orbitals (i.e., Bloch functions). The use of atom-centered basis functions allows treating 3D (crystals), 2D (slabs), 1D (polymers), and 0D (molecules) systems on the same grounds. In turn, all-electron calculations are inherently permitted along with pseudopotential strategies. A variety of density functionals are implemented, including global and range-separated hybrids of various natures and, as an extreme case, Hartree-Fock (HF). The cost for HF or hybrids is only about 3-5 times higher than when using the local density approximation or the generalized gradient approximation. Symmetry is fully exploited at all steps of the calculation. Many tools are available to modify the structure as given in input and simplify the construction of complicated objects, such as slabs, nanotubes, molecules, and clusters. Many tensorial properties can be evaluated by using a single input keyword: elastic, piezoelectric, photoelastic, dielectric, first and second hyperpolarizabilities, etc. The calculation of infrared and Raman spectra is available, and the intensities are computed analytically. Automated tools are available for the generation of the relevant configurations of solid solutions and/or disordered systems. Three versions of the code exist: serial, parallel, and massive-parallel. In the second one, the most relevant matrices are duplicated on each core, whereas in the third one, the Fock matrix is distributed for diagonalization. All the relevant vectors are dynamically allocated and deallocated after use, making the code very agile. CRYSTAL can be used efficiently on high performance computing machines up to thousands of cores.

Classical molecular dynamics simulations and free energy methods have been used to obtain a better understanding of the molecular processes occurring prior to the first nucleation event for calcium phosphate biominerals. The association constants for the formation of negatively charged complexes containing calcium and phosphate ions in aqueous solution have been computed, and these results suggest that the previously proposed calcium phosphate building unit, [Ca(HPO 4 ) 3 ] 4- , should only be present in small amounts under normal experimental conditions. However, the presence of an activation barrier for the removal of an HPO 4 2- ion from this complex indicates that this species could be kinetically trapped. Aggregation pathways involving CaHPO 4 , [Ca(HPO 4 ) 2 ] 2- , and [Ca(HPO 4 ) 3 ] 4- complexes have been explored with the finding that dimerization is favorable up to a Ca/HPO 4 ratio of 1:2., Competing Interests: The authors declare no competing financial interest., (Copyright © 2019 American Chemical Society.)

Since Pasteur first successfully separated right-handed and left-handed tartrate crystals in 1848, the understanding of how homochirality is achieved from enantiomeric mixtures has long been incomplete. Here, we report on a chirality dominance effect where organized, three-dimensional homochiral suprastructures of the biomineral calcium carbonate (vaterite) can be induced from a mixed nonracemic amino acid system. Right-handed (counterclockwise) homochiral vaterite helicoids are induced when the amino acid L-Asp is in the majority, whereas left-handed (clockwise) homochiral morphology is induced when D-Asp is in the majority. Unexpectedly, the Asp that incorporates into the homochiral vaterite helicoids maintains the same enantiomer ratio as that of the initial growth solution, thus showing chirality transfer without chirality amplification. Changes in the degree of chirality of the vaterite helicoids are postulated to result from the extent of majority enantiomer assembly on the mineral surface. These mechanistic insights potentially have major implications for high-level advanced materials synthesis.

A new force field has been derived for the aqueous calcium phosphate system that aims to reproduce the key thermodynamic properties of the system, including free energies of hydration of the ions and the solubility of the solid mineral phases. Interactions of three phosphate anions (PO 4 3- , HPO 4 2- , and H 2 PO 4 - ) with water were calibrated through comparison with the results obtained from ab initio molecular dynamics using both GGA and hybrid density functional theory with dispersion corrections. In the solid state, the force field has been evaluated by benchmarking against experiment and other existing models and is shown to reproduce the structural and mechanical properties well, despite the primary focus being on thermodynamics. To validate the force field, the thermodynamics of ion pairing for calcium phosphate species in water has been computed and shown to be in excellent agreement with experimental data.