Maximally valent orbitals in systems with non-ideal bond-angles: atomic Wannier orbitals guided by the Mayer bond order.

In pursuit of a directed minimal set of basis for systems with non-ideal bond angles, in this work we find the exact orientation of the major overlapping orbitals along the nearest neighbouring coordination segments in a given system such that they maximally represent the covalent interactions throughout the system. We compute Mayer's bond order, akin to Wiberg's bond index, on the basis of atomic Wannier orbitals with customizable non-degenerate hybridization leading to variable orientations, constructed from first principles, in a representative variety of molecules and layered systems. We put such orbitals in perspective with unbiased maximally localized descriptions of bonding and non-bonding orbitals, and energetics to tunneling of electrons through them between nearest neighbours, to describe the different physical aspects of covalent interactions, which are not necessarily represented using a single unique set of atomic or bonding orbitals.

Reservoir bathymetry and riparian corridor assessment in two dammed sections of the Teesta River in Eastern Himalaya.

As of mid-2021, four hydroelectric dams are operational on the main channel of the Teesta River in the mountainous and tectonically active Sikkim-Darjeeling-Kalimpong region of India. Riparian ecological and fluvial morphological changes after damming have not been documented. This paper describes an early study of a section of the middle Teesta River, at two of the dam-created reservoirs, just before the river enters the plains. High-resolution, multi-beam, geo-located sonar was used to map the bathymetry of the reservoirs. This resulted in the creation of 30cm-resolution bathymetric maps of the two reservoirs showing valley bottom morphology within them. The bathymetric maps were compared with pre-dam digital elevation models of the valley to create topographic change-maps. The change-maps indicate significant differences in valley morphology due to erosion and deposition processes. Land cover changes due to inundation were quantified from analysis of satellite imagery time series data of the reservoir riparian zones. Land cover change analysis showed a loss of ~ 74,000 trees in ~ 225 ha of flooded riparian corridors due to long-term inundation. The study shows that the dams have caused 7.4% of the river length to become quasi-lentic, and drastically altered sediment dynamics and hydrologic flow. Sediment deposition calculations indicate the reservoirs losing almost three-quarters of their surface areas to sediment deposition features within 15 years. This study will serve as an important baseline for future studies, and influence design and policy regarding riparian and fluvial ecosystem management, monitoring, and evaluation in the Teesta and similar mountainous river basins in the Eastern Himalaya.

Hybrid Atomic Orbital Basis from First Principles: Bottom-Up Mapping of Self-Energy Correction to Large Covalent Systems.

Construction of hybrid atomic orbitals is proposed as the approximate common eigenstates of finite first moment matrices. Their hybridization and orientation can be a priori tuned as per their anticipated neighborhood. Their Wannier function counterparts constructed from the Kohn-Sham (KS) single particle states constitute an orthonormal multiorbital tight binding (TB) basis resembling hybrid atomic orbitals locked to their immediate atomic neighborhood, while spanning the subspace of KS states. The proposed basis thus renders predominantly single TB parameters from first principles for each nearest neighbor bond involving no more than two orbitals irrespective of their orientation and also facilitates an easy route for the transfer of such TB parameters across isostructural systems exclusively through mapping of neighborhoods and projection of orbital charge centers. With hybridized 2s, 2p and 3s, 3p valence electrons, the spatial extent of the self-energy correction (SEC) to TB parameters in the proposed basis is found to be localized mostly within the third nearest neighborhood, thus allowing effective transfer of self-energy-corrected TB parameters from smaller reference systems to much larger target systems, with nominal additional computational cost beyond that required for explicit computation of SEC in the reference systems. The proposed approach promises inexpensive estimation of the quasi-particle structures of large covalent systems with workable accuracy.

Transferability of self-energy correction in tight-binding basis constructed from first principles.

We demonstrate in this work the transferability of self-energy (SE) correction (SEC) of Kohn-Sham (KS) single particle states from smaller to larger systems, when mapped through localized orbitals constructed from the KS states. The approach results in a SE corrected TB framework within which the mapping of SEC of TB parameters is found to be transferable from smaller to larger systems of similar morphology, leading to a computationally inexpensive approach for the estimation of SEC in large systems with reasonably high accuracy. The scheme has been demonstrated in insulating, semiconducting, and magnetic nanoribbons of graphene and hexagonal boron nitride, where the SEC tends to strengthen the individual π bonds, leading to transfer of charges from the edge to bulk. Additionally, in magnetic bipartite systems, the SEC tends to enhance inter-sublattice spin separation. The proposed scheme thus promises to enable the estimation of SEC of bandgaps of large systems without the need to explicitly calculate the SEC of KS single particle levels, which can be computationally prohibitively expensive.

In vivo studies of a peptidomimetic that targets EGFR dimerization in NSCLC.

Studies related to lung cancer have shown a link between human epidermal growth factor receptor-2 (HER2) expression and poor prognosis in patients with non-small cell lung cancer (NSCLC). HER2 overexpression has been observed in 3-38% of NSCLC, while strong HER2 protein overexpression is found in 2.5% of NSCLC. However, HER2 dimerization is important in lung cancer, including EGFR mutated NSCLC. Since HER2 dimerization leads to cell proliferation, targeting the dimerization of HER2 will have a significant impact on cancer therapies. A peptidomimetic has been designed that can be used as a therapeutic agent for a subset of NSCLC patients overexpressing HER2 or possessing HER2 as well as EGFR mutation. A cyclic peptidomimetic (18) has been designed to inhibit protein-protein interactions of HER2 with its dimerization partners EGFR and HER3. Compound 18 exhibited antiproliferative activity in HER2-positive NSCLC cell lines at nanomolar concentrations. Western blot analysis showed that 18 inhibited phosphorylation of HER2 and Akt in vitro and in vivo. Stability studies of 18 at various temperature and pH (pH 1 and pH 7.6), and in the presence of liver microsomes indicated that 18 was stable against thermal and chemical degradation. Pharmacokinetic parameters were evaluated in nude mice by administrating single doses of 4 mg/kg and 6 mg/kg of 18 via IV. The anticancer activity of 18 was evaluated using an experimental metastasis lung cancer model in mice. Compound 18 suppressed the tumor growth in mice when compared to control. A proximity ligation assay further proved that 18 inhibits HER2:HER3 and EGFR: HER2 dimerization. Overall, these results suggest that 18 can be a potential treatment for HER2-dimerization related NSCLC.

Bias induced ferromagnetism and half-metallicity in graphene nano-ribbons.

Towards spin selective electronics made of three coordinated carbon atoms, here we computationally propose robust and reversibly bias driven evolution of pristine undoped graphene nano-ribbons(GNR) into ferromagnetic-semiconductor, metal or a half metal, irrespective of their edge configurations. The evolution is a result of a rare ferromagnetic(FM) order emerging among nearest neighbouring(n-n) sites, in positively biased regions in their in-homogeneous bias unit-cells, in attempt to cooperatively minimise on-site Coulomb repulsion and kinetic energy, while maximising localization of electrons at the positively biased sites. The phenomenon appears to be a general property of in-homogeneously biased Coulomb correlated bipartite systems. Consequences are particularly rich in zigzag edged graphene nano-ribbons(ZGNR) due to the contest of bias driven n-n FM order and the inter-edge antiferromagnetic order inherent to ZGNRs, leading to systematic closing of gap for one of the spins, amounting to bias controlled unmissable opening of window for FM-semiconducting and half-metallic transport.

Norstictic Acid Inhibits Breast Cancer Cell Proliferation, Migration, Invasion, and In Vivo Invasive Growth Through Targeting C-Met.

Breast cancer is a major health problem affecting the female population worldwide. The triple-negative breast cancers (TNBCs) are characterized by malignant phenotypes, worse patient outcomes, poorest prognosis, and highest mortality rates. The proto-oncogenic receptor tyrosine kinase c-Met is usually dysregulated in TNBCs, contributing to their oncogenesis, tumor progression, and aggressive cellular invasiveness that is strongly linked to tumor metastasis. Therefore, c-Met is proposed as a promising candidate target for the control of TNBCs. Lichens-derived metabolites are characterized by their structural diversity, complexity, and novelty. The chemical space of lichen-derived metabolites has been extensively investigated, albeit their biological space is still not fully explored. The anticancer-guided fractionation of Usnea strigosa (Ach.) lichen extract led to the identification of the depsidone-derived norstictic acid as a novel bioactive hit against breast cancer cell lines. Norstictic acid significantly suppressed the TNBC MDA-MB-231 cell proliferation, migration, and invasion, with minimal toxicity to non-tumorigenic MCF-10A mammary epithelial cells. Molecular modeling, Z'-LYTE biochemical kinase assay and Western blot analysis identified c-Met as a potential macromolecular target. Norstictic acid treatment significantly suppressed MDA-MB-231/GFP tumor growth of a breast cancer xenograft model in athymic nude mice. Lichen-derived natural products are promising resources to discover novel c-Met inhibitors useful to control TNBCs.

Activation of Graphenic Carbon Due to Substitutional Doping by Nitrogen: Mechanistic Understanding from First Principles.

Nitrogen-doped graphene and carbon nanotubes are popularly in focus as metal-free electrocatalysts for oxygen reduction reactions (ORR) central to fuel cells. N-doped CNTs have been also reported to chemisorb mutually, promising a route to their robust predetermined assembly into devices and mechanical reinforcements. We propose from first principles a common mechanistic understanding of these two aspects pointing further to a generic chemical activation of carbon atoms due to substitution by nitrogen in experimentally observed configurations. Wannier-function based orbital resolved study of mechanisms suggests increase in C-N bond-orders in attempt to retain π-conjugation among carbon atoms, causing mechanical stress and loss of charge neutrality of nitrogen and carbon atoms, which remedially facilitate chemical activation of N-coordinated C atoms, enhancing sharply with increasing coordination to N and proximity to zigzag edges. Activated C atoms facilitate covalent adsorption of radicals in general, diradicals like O2 relevant to ORR, and also other similarly activated C atoms, leading to self-assembly of graphenic nanostructures while remaining inert to ordinary graphenic C atoms.

Immunocompetence of breeding females is sensitive to cortisol levels but not to communal rearing in the degu (Octodon degus).

One hypothesis largely examined in social insects is that cooperation in the context of breeding benefits individuals through decreasing the burden of immunocompetence and provide passive immunity through social contact. Similarly, communal rearing in social mammals may benefit adult female members of social groups by reducing the cost of immunocompetence, and through the transfer of immunological compounds during allonursing. Yet, these benefits may come at a cost to breeders in terms of a need to increase investment in individual immunocompetence. We examined how these potential immunocompetence costs and benefits relate to reproductive success and survival in a natural population of the communally rearing rodent, Octodon degus. We related immunocompetence (based on ratios of white blood cell counts, total and specific immunoglobulins of G isotype titers) and fecal glucocorticoid metabolite (FGC) levels of adults immunized with hemocyanin from the mollusk Concholepas concholepas to measures of sociality (group size) and communal rearing (number of breeding females). Offspring immunocompetence was quantified based on circulating levels of the same immune parameters. Neither female nor offspring immunocompetence was influenced by communal rearing or sociality. These findings did not support that communal rearing and sociality enhance the ability of females to respond to immunological challenges during lactation, or contribute to enhance offspring condition (based on immunocompetence) or early survival (i.e., to 3months of age). Instead, levels of humoral and cellular components of immunocompetence were associated with variation in glucorcorticoid levels of females. We hypothesize that this covariation is driven by physiological (life-history) adjustments needed to sustain breeding.

Half-metallicity in graphene nanoribbons with topological defects at edge.

We report first principles studies of zigzag edged graphene nanoribbons (ZGNR) with one edge partially covered by topological defects. With increasing coverage of an edge by pentagons and heptagons, which are two of the simplest topological defects possible in a graphenic lattice, ZGNRs evolve from a magnetic semiconductor to a ferromagnetic metal. This evolution can be intermediated by a narrow bandgap half-metallic phase, upon suitable concentration and conformation of defects at the edge. Spin-frustration induced by topological defects lead to substantial lowering of magnetic ordering and localization of defect-states in the vicinity of the defects. Dispersion of bands constituted by the defect-states within the bandgap of the corresponding unmodified ZGNR, leads to availability of energy windows for spin-polarized electron transport. Driven primarily by exchange interactions, the energy window for transport of electrons near Fermi energy, is consistently wider and more prevalent for the minority spin, in the entire class of ZGNRs with discontinuous patches of topological defects at an edge. Such defects have been widely predicted and observed to be naturally present at the interfaces in polycrystalline graphene, and can even be formed through chemical and physical processes. Our approach thus may lead to a feasible strategy to manifest workable half-metallicity in ZGNRs without involving non-carbon dopants or functional groups.

Wannier orbital overlap population (WOOP), Wannier orbital position population (WOPP) and the origin of anomalous dynamical charges.

Most d(0) transition metal (TM) oxides exhibit anomalously large Born dynamical charges associated with off-centering or motion of atoms along the TM-O chains. To understand their chemical origin, we introduce "Wannier orbital overlap population" (WOOP) and "Wannier orbital position population" (WOPP) in terms of the Wannier function based description of electronic structure obtained within first-principles density functional theory. We apply these concepts in a precise analysis of anomalous dynamical charges in PbTiO(3), BaTiO(3) and BaZrO(3) in the cubic perovskite structure. Determining contributions of different atomic orbitals to the dynamical charge and their break-up into local polarizability, charge transfer and covalency, we find that p orbitals of oxygen perpendicular to the -TM-O- chain contribute most prominently to the anomalous charge, by facilitating a transfer of tiny electronic charge through one unit cell from one TM atom to the next. Our results explain why the corner-shared linkage of TMO(6) octahedra, as in the perovskite structure, is ideal for large dynamical charges and hence for ferroelectricity.

Molecular-scale quantum dots from carbon nanotube heterojunctions.

Carbon nanotube heterojunctions (HJs), which seamlessly connect nanotubes of different chiral structure using a small number of atomic-scale defects, represent the ultimate scaling of electronic interfaces. Here we report the first electrical transport measurements on a HJ formed between semiconducting and metallic nanotubes of known chiralities. These measurements reveal asymmetric IV-characteristics and the presence of a quantum dot (QD) with approximately 60 meV charging energy and approximately 75 meV level spacing. A detailed atomistic and electronic model of the HJ enables the identification of specific defect arrangements that lead to the QD behavior consistent with the experiment.

Synthesis, characterization, and theory of [9]-, [12]-, and [18]cycloparaphenylene: carbon nanohoop structures.

The first synthesis and characterization of [9]-, [12]-, and [18]cycloparaphenylene was demonstrated utilizing a novel aromatization reaction. We refer to these fascinating structures as "carbon nanohoops" due to their structural similarity to carbon nanotubes. Additionally, we have utilized computational methods to understand the unique properties of these fully conjugated macrocycles.

Closed-cage clusters in the gaseous and condensed phases derived from sonochemically synthesized MoS2 nanoflakes.

The Mo(13) clusters we previously reported were derived from MoS(2) flakes prepared from bulk MoS(2), although the nature of the precursor species was not fully understood. The existence of the clusters in the condensed phase was a question. Here we report the preparation of MoS(2) nanoflakes from elemental precursors using the sonochemical method and study the gas-phase clusters derived from them using mass spectrometry. Ultraviolet-visible (UV-vis) spectrum of the precursor is comparable to nano MoS(2) derived from bulk MoS(2). High-resolution transmission electron microscopy (HRTEM) revealed the formation of nanoflakes of MoS(2) with 10- to 30-nm length and 3- to 5-nm thickness. Laser desorption ionization mass spectrometry (LDI-MS) confirmed the formation of Mo(13) clusters from this nanomaterial. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) points to the existence of Mo(13) clusters in the condensed phase. The clusters appear to be stable because they do not fragment in the mass spectrometer even at the highest laser intensity. Computational analysis based on generalized Wannier orbitals is used to understand bonding and stability of the clusters. These clusters are highly stable with a rich variety in terms of centricity and multiplicity of Mo-Mo, S-Mo, and S-S bonds.

Structure of incommensurate gold sulfide monolayer on Au(111).

We develop an atomic-scale model for an ordered incommensurate gold sulfide (AuS) adlayer which has previously been demonstrated to exist on the Au(111) surface, following sulfur deposition and annealing to 450 K. Our model reproduces experimental scanning tunneling microscopy images. Using state-of-the-art Wannier-function-based techniques, we analyze the nature of bonding in this structure and provide an interpretation of the unusual stoichiometry of the gold sulfide layer. The proposed structure and its chemistry have implications for related S-Au interfaces, as in those involved in self-assembled monolayers of thiols on Au substrates.

Structural studies of TcO2 by neutron powder diffraction and first-principles calculations.

Crystalline technetium dioxide was prepared and for the first time its crystal structure determined by neutron powder diffraction. In addition, electronic structure calculations using density functional theory were performed to further elucidate the bonding mechanisms in TcO2. The crystal structure determined by Rietveld analysis with the NPD data is of a distorted rutile type, similar to that of MoO2; space group P21/c, a = 5.6891(1), b = 4.7546(1), c = 5.5195(1) A, and beta = 121.453(1) degrees . The NPD analysis also establishes a new neutron scattering length of 6.00(3) fm for 99Tc. Our results clearly show metal-metal bonding between Tc pairs along the edge-sharing chains of TcO6 octahedra. The Tc-Tc bond was found to be 2.622(1) A from NPD profile analysis and 2.59 A from first-principles DFT calculations. The bond is somewhat longer than expected from earlier predictions, suggesting that the nature of the Tc-Tc interaction is weaker than anticipated for the Tc(IV) cation with three outer electrons. The NPD results supported by the DFT calculations suggest that the filling of antibonding orbitals and the influence of the crystal field stabilization of the d3 Tc cations lead to more regular TcO6 octahedra and diminish the metal-metal bond strength compared with closely related oxides such MoO2 and WO2.

Rich coordination chemistry of Au adatoms in gold sulfide monolayer on Au(111).

The rich chemistry of Au nanoparticles and ions has attracted tremendous interest, in part because the surfaces of bulk Au have traditionally been considered to be chemically inert. On the other hand, large-scale mass transport and the formation of vacancy islands have been observed on the Au(111) surface following the deposition of adsorbates, such as sulfur and thiols, that can interact strongly with the Au surface. In this work, we revisit the structure and chemistry of an ordered incommensurate AuS adlayer that forms on Au(111) following the deposition of sulfur and annealing to 450 K. A structural model of this AuS surface phase has not yet been determined experimentally due to the complexity of the system. Here, we use state-of-the-art density functional theory to develop an atomic-scale model that is consistent with the previously reported Au-S stoichiometry. In particular, we introduce theoretical techniques to take into account the charge transfer in an incommensurate system. Our model reproduces convincingly STM images and is remarkably robust. Bonding analysis based on Wannier functions shows that the model exhibits rich coordination chemistry corresponding to different Au oxidation states. The extraordinary stability and rich chemistry of this structure have implications for related S-Au interfaces and previously reported surface features of this system.

Novel cage clusters of MoS2 in the gas phase.

Laser evaporation of MoS(2) nanoflakes gives negatively charged magic number clusters of compositions Mo(13)S(25) and Mo(13)S(28), which are shown to have closed-cage structures. The clusters are stable and do not show fragmentation in the post-source decay analysis even at the highest laser powers. Computations suggest that Mo(13)S(25) has a central cavity with a diameter of 4.5 A. The nanosheets of MoS(2) could curl upon laser irradiation, explaining the cluster formation.