Nanoparticles with cubic symmetry: classification of polyhedral shapes.

Structural studies of polyhedral bodies can help to analyze geometric details of observed crystalline nanoparticles (NP) where we consider compact polyhedra of cubic point symmetry as simple models. Their surfaces are described by facets with normal vectors along selected Cartesian directions (a, b, c) together with their symmetry equivalents forming a direction family {abc}. Here we focus on polyhedra with facets of families {100}, {110}, and {111}, suggested for metal and oxide NPs with cubic lattices. Resulting generic polyhedra, cubic, rhombohedral, octahedral, and tetrahexahedral, have been observed as NP shapes by electron microscopy. They can serve for a complete description of non-generic polyhedra as intersections of corresponding generic species, not studied by experiment so far. Their structural properties are shown to be fully determined by only three parameters, facet distancesR100,R110, andR111of the three facet types. This provides a novel phase diagram to systematically classify all corresponding polyhedra. Their structural properties, such as shape, size, and facet geometry, are discussed in analytical and numerical detail with visualization of typical examples. The results may be used for respective NP simulations but also as a repository stimulating the structural interpretation of new NP shapes to be observed by experiment.

Fragment motion in motor molecules: basic concepts and application to intra-molecular rotations.

The complex motion of atoms inside large molecules can be analyzed by considering translation, rotation, and flexibility of corresponding molecular fragments and by applying classical mechanics based on Pulay forces on the atoms, as in molecular dynamics. We propose a fragment motion analysis that provides a basic qualitative understanding of the motion of the different molecular components. Further, it can help to describe or design simplified fragment motions, e.g. the rotation of a rotator with respect to its stator counterpart in a rotor molecule, despite the higher actual complexity due to flexibility of rotator and stator or due to a variable rotation axis. The formal aspects of the fragment motion analysis are discussed in detail. Its application is illustrated by the rotational motion inside the BTP-BCO molecule and by rotational transitions between cis- and trans-stilbene isomers.

Interlocking Molecular Gear Chains Built on Surfaces.

Periodic chains of molecular gears in which molecules couple with each other and rotate on surfaces have been previously explored by us theoretically using ab initio simulation tools. On the basis of the knowledge and experience gained about the interactions between neighboring molecular gears, we here explore the transmission of rotational motion and energy over larger distances, namely, through a longer chain of gear-like passive "slave" molecules. Such microscopic gears exhibit quite different behaviors compared to rigid cogwheels in the macroscopic world due to their structural flexibility affecting intermolecular interaction. Here, we investigate the capabilities of such gear chains and reveal the mechanisms of the transmission process in terms of both quantum-level density functional theory (DFT) and simple classical mechanics. We find that the transmission of rotation along gear chains depends strongly on the gear-gear distance: short distances can cause tilting of gears and even irregular "creep-then-jump" (or "stick-slip") motion or expulsion of gears; long gear-gear distances cause weak coupling between gears, slipping and skipping. More importantly, for transmission of rotation at intermediate gear-gear distances, our modeling clearly exhibits the relative roles of several important factors: flexibility of gear arms, axles, and supports, as well as resulting rotational delays, slippages, and thermal and other effects. These studies therefore allow better informed design of future molecular machine components involving motors, gears, axles, etc.

Interlocking Mechanism between Molecular Gears Attached to Surfaces.

While molecular machines play an increasingly significant role in nanoscience research and applications, there remains a shortage of investigations and understanding of the molecular gear (cogwheel), which is an indispensable and fundamental component to drive a larger correlated molecular machine system. Employing ab initio calculations, we investigate model systems consisting of molecules adsorbed on metal or graphene surfaces, ranging from very simple triple-arm gears such as PF3 and NH3 to larger multiarm gears based on carbon rings. We explore in detail the transmission of slow rotational motion from one gear to the next by these relatively simple molecules, so as to isolate and reveal the mechanisms of the relevant intermolecular interactions. Several characteristics of molecular gears are discussed, in particular the flexibility of the arms and the slipping and skipping between interlocking arms of adjacent gears, which differ from familiar macroscopic rigid gears. The underlying theoretical concepts suggest strongly that other analogous structures may also exhibit similar behavior which may inspire future exploration in designing large correlated molecular machines.

Intramolecular torque, an indicator of the internal rotation direction of rotor molecules and similar systems.

Rotation-inducing torque is ubiquitous in many molecular systems. We present a straightforward theoretical method based on forces acting on atoms and obtained from atomistic quantum mechanics calculations to quickly and qualitatively determine whether a molecule or sub-unit thereof has a tendency to rotate and, if so, around which axis and in which sense: clockwise or counterclockwise. The method also indicates which atoms, if any, are predominant in causing the rotation. Our computational approach can in general efficiently provide insights into the internal rotational degrees of freedom of all molecules and help to theoretically screen or modify them in advance of experiments or to efficiently guide a detailed analysis of their rotational behavior with more extensive computations. As an example, we demonstrate the effectiveness of the approach using a specific light-driven molecular rotary motor which was successfully synthesized and analyzed in prior experiments and simulations.

Computational prediction of optimal metal ions to induce coordinated polymerization of muscle-like [c2]daisy chains.

Recently, a muscle-like organometallic polymer has been successfully synthesized using Fe(2+) as a linker atom. The polymer exhibits acid-base controllable muscle-like expansion and contraction on the micrometer scale. Further development could be facilitated by revealing the polymerization mechanism and by searching for optimal linker atoms. In this work, we have examined possible equilibrium and intermediate polymer structures, which consist of [c2]daisy chains linked by divalent transition metal ions (Sc(2+), Ti(2+), Fe(2+), Co(2+), Ni(2+) or Zn(2+)) with various hexa-coordination arrangements, based on calculations using density functional theory. We find that the metal linkers in polymers are weaker in acid than in base due to excess positive charges on the polymer, leading to their thermodynamical instability or even decomposition. This can explain the experimental difficulty in improving the degree of polymerization for metal-linked polymers. We also find that the polymers with either Fe(2+) or Co(2+) are the most favorable, with the latter extending 1.4% longer than with the former. Since Fe(2+) has been confirmed experimentally to be a successful linker, Co(2+) would function equally well and thus could be used as an alternative choice for polymerization.

Revealing highly unbalanced energy barriers in the extension and contraction of the muscle-like motion of a [c2]daisy chain.

Nanoscale muscle-like materials have aroused great interest as they may provide controllable mechanical operations by artificial actuations. Molecular designs to achieve the desired motion at the macroscopic scale in experiments require atomic level understanding. By systematic quantum chemical and molecular dynamics calculations we reveal that the length change is not only due to the linear telescoping from the dibenzo[24]crown-8 recognition at two docking stations but also the folding/unfolding of two bulky stoppers. The extension and contraction processes of a [c2]daisy chain under acidic vs. basic conditions are exothermic but need to cross very different energy barriers, being at least double the height under acidic compared to basic conditions, hindering balanced cyclic motions at moderate excitation. Our result suggests that to realize the desired muscle-like motion one should adopt sufficiently high external excitation, using for example reasonably high temperature and further optimizing the solution used.

Analysis of the near-edge X-ray-absorption fine-structure of anthracene: a combined theoretical and experimental study.

The near-edge fine structure of the carbon K-edge absorption spectrum of anthracene was measured and theoretically analyzed by density functional theory calculations implemented in the StoBe code. It is demonstrated that the consideration of electronic relaxation of excited states around localized core holes yields a significant improvement of the calculated excitation energies and reproduces the experimentally observed fine structure well. The detailed analysis of excitation spectra calculated for each symmetry inequivalent excitation center allows in particular to examine the influence of chemical shifts and core hole effects on the excitation energies. Moreover, the visualization of final states explains the large variations in the oscillator strength of various transitions as well as the nature of Rydberg-states that exhibit a notable density of states below the ionization potentials.

How strain affects the reactivity of surface metal oxide catalysts.

Highly dispersed molybdenum oxide supported on mesoporous silica SBA-15 has been prepared by anion exchange resulting in a series of catalysts with changing Mo densities (0.2-2.5 Mo atoms nm(-2) ). X-ray absorption, UV/Vis, Raman, and IR spectroscopy indicate that doubly anchored tetrahedral dioxo MoO4 units are the major surface species at all loadings. Higher reducibility at loadings close to the monolayer measured by temperature-programmed reduction and a steep increase in the catalytic activity observed in metathesis of propene and oxidative dehydrogenation of propane at 8 % of Mo loading are attributed to frustration of Mo oxide surface species and lateral interactions. Based on DFT calculations, NEXAFS spectra at the O-K-edge at high Mo loadings are explained by distorted MoO4 complexes. Limited availability of anchor silanol groups at high loadings forces the MoO4 groups to form more strained configurations. The occurrence of strain is linked to the increase in reactivity.

Reduced skin reactivity to vasoconstrictor and vasodilator substances in atopic eczema.

UNLABELLED: Atopic eczema is a common chronic inflammatory disease with itchy skin and altered skin reactions to acetylcholine and nicotinic acid compared to healthy non-atopic individuals. AIM: The aim of this study was to evaluate skin reactivity to 11 vasoactive substances and peptides by skin prick and intradermal tests in 20 patients with atopic eczema and 20 healthy controls. METHODS: Skin reactions, blanching, wheal and flare areas were measured by planimetry, 15 minutes after provocation. RESULTS: Patients with atopic eczema had significantly smaller reactions at certain concentrations of the vasodilators acetylcholine, bradykinin, calcitonin gene-related peptide, substance P and vasoactive intestinal peptide for flare, and of substance P and vasoactive intestinal peptide for wheals, in intradermal testing and/or in skin prick testing. Testing of the vasoconstrictors angiotensin-II, arginine-vasopressin, endothelin-1 and noradrenaline in atopic eczema resulted in significantly smaller reactions at certain concentrations for blanching in intradermal testing and/or skin prick testing. Significantly smaller reactions were seen with arginine-vasopressin for wheals and with arginine-vasopressin and noradrenaline for flares in intradermal testing and/or skin prick testing at certain concentrations. Significantly larger wheals were seen with angiotensin-II and endothelin-1 in intradermal testing and/or skin prick testing at certain concentrations. No significant differences were found for prostaglandin E2. CONCLUSION: These results demonstrate not only a reduced responsiveness to vasodilators but also to vasoconstrictor substances and peptides in patients with atopic eczema, which may be considered a general feature of atopic eczema skin.

Periodic overlayers and moiré patterns: theoretical studies of geometric properties.

Single crystal surfaces with periodic overlayers, such as graphene on hexagonal metal substrates, are found to exhibit, apart from their intrinsic periodicity, additional long-range order expressed by approximate surface lattices with large lattice constants. This phenomenon can be described as geometrically analogous to lateral interference effects resulting in periodic moiré patterns which are characterized by two-dimensional moiré lattices. Here we discuss in detail the mathematical formalism determining such moiré patterns based on concepts of two-dimensional Fourier transformation including coincidence lattices. The formalism provides simple relations that allow one to calculate possible moiré lattice vectors in their dependence on rotation angles α and scaling factors p1,p2 for periodic (p1 × p2)Rα overlayers on substrate surfaces described by general Bravais lattices. Specific emphasis will be given to hexagonal lattices where experimental data are available.

Identification of the human/mouse syntenic common fragile site FRA7K/Fra12C1--relation of FRA7K and other human common fragile sites on chromosome 7 to evolutionary breakpoints.

Common fragile sites (CFSs) are expressed as chromosome gaps in cells of different species including human and mouse as a result of the inhibition of DNA replication. They may serve as hot spots for DNA breakage in processes such as tumorigenesis and chromosome evolution. Using multicolor fluorescence in situ hybridization mapping, the authors describe here human CFS FRA7K on chromosome band 7q31.1 and its murine homolog Fra12C1. Within the syntenic FRA7K/Fra12C1 region lies the IMMP2L/Immp2l gene with a size of 899/983 kb. The authors further mapped 2 amplification breakpoints of the breast cancer cell line SKBR3 to the CFSs FRA7G and FRA7H. The 5 molecularly defined CFSs on chromosome 7 do not preferentially colocalize with synteny breaks between the human and mouse genomes and with intragenomic duplications that have occurred during chromosome evolution. In addition, in contrast to all currently reported data, CFSs in chromosome band 7q31 do not show increased DNA helix flexibility in comparison with control regions without CFS expression.

Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes.

Common fragile sites (CFSs) are seen as chromosomal gaps and breaks brought about by inhibition of replication, and it is thought that they cluster with tumor breakpoints. This study presents a comprehensive analysis using conventional and molecular cytogenetic mapping of CFSs and their expression frequencies in two mouse strains, BALB/c and C57BL/6, and in human probands. Here we show that induced mouse CFSs relate to sites of spontaneous gaps and breaks and that CFS expression levels in chromosome bands are conserved between the two mouse strains and between syntenic mouse and human DNA segments. Furthermore, four additional mouse CFSs were found to be homologous to human CFSs on the molecular cytogenetic level (Fra2D-FRA2G, Fra4C2-FRA9E, Fra6A3.1-FRA7G, and Fra6B1-FRA7H), increasing the number of such CFSs already described in the literature to eight. Contrary to previous reports, DNA helix flexibility is not increased in the 15 human and eight mouse CFSs molecularly defined so far, compared to large nonfragile control regions. Our findings suggest that the mechanisms that provoke instability at CFSs are evolutionarily conserved. The role that large transcriptionally active genes may play in CFS expression is discussed.

Molecular profiling of laser-microdissected matched tumor and normal breast tissue identifies karyopherin alpha2 as a potential novel prognostic marker in breast cancer.

PURPOSE: The aim of the present study was to identify human genes that might prove useful in the diagnosis and therapy of primary breast cancer. EXPERIMENTAL DESIGN: Twenty-four matched pairs of invasive ductal breast cancer and corresponding benign breast tissue were investigated by a combination of laser microdissection and gene expression profiling. Differential expression of candidate genes was validated by dot blot analysis of cDNA in 50 pairs of matching benign and malignant breast tissue. Cellular expression of candidate genes was further validated by RNA in situ hybridization, quantitative reverse transcription-PCR, and immunohistochemistry using tissue microarray analysis of 272 nonselected breast cancers. Multivariate analysis of factors on overall survival and recurrence-free survival was done. RESULTS: Fifty-four genes were found to be up-regulated and 78 genes were found to be down-regulated. Dot blot analysis reduced the number of up-regulated genes to 15 candidate genes that showed at least a 2-fold overexpression in >15 of 50 (30%) tumor/normal pairs. We selected phosphatidic acid phosphatase type 2 domain containing 1A (PPAPDC1A) and karyopherin alpha2 (KPNA2) for further validation. PPAPDC1A and KPNA2 RNA was up-regulated (fold change >2) in 84% and 32% of analyzed tumor/normal pairs, respectively. Nuclear protein expression of KPNA2 was significantly associated with shorter overall survival and recurrence-free survival. Testing various multivariate Cox regression models, KPNA2 expression remained a highly significant, independent and adverse risk factor for overall survival. CONCLUSIONS: Gene expression profiling of laser-microdissected breast cancer tissue revealed novel genes that may represent potential molecular targets for breast cancer therapy and prediction of outcome.

Transcriptional census of 36 microdissected colorectal cancers yields a gene signature to distinguish UICC II and III.

UICC stage II and III colorectal cancers (CRC) differ fundamentally in prognosis and therapeutic concepts. To analyze differential gene expression between both stages and to establish a relationship between molecular background and clinical presentation, tumor material from 36 unselected consecutive patients presenting with sporadic CRC, 18 UICC stage II and 18 UICC stage III, were laser microdissected to separate epithelial tumor cells. Gene expression levels were measured using U133A Affymetrix gene arrays. Twelve CRC associated signal transduction pathways as well as all 22,000 probe sets were screened for differential gene expression. We identified a signature consisting of 45 probe sets that allowed discrimination between UICC stage II and stage III with a rate of correct classification of about 80%. The most distinctive elements in this signature were the gene GSTP-binding elongation factor (GSPT2) and the transcription factor HOXA9. Differential expression of these genes was confirmed by quantitative real-time polymerase chain reaction (p(HOXA9) = 0.04, p(GSTP2) = 0.02). Despite the reliability of the presented data, there was no substantial differential expression of genes in cancer-related pathways. However, the comparison with recently published data corroborates the 45 gene signature showing structural agreement in the direction of fold changes of gene expression levels for our set of genes chosen to discriminate between both stages.

Critical influence of adsorption geometry in the heterogeneous epoxidation of "allylic" alkenes: structure and reactivity of three phenylpropene isomers on Cu(111).

It has long been conjectured that the difficulty of heterogeneously epoxidizing higher alkenes such as propene is due to the presence in the molecule of "allylic" H atoms that are readily stripped off by the oxygenated surface of the metal catalyst resulting in combustion. Here, taking advantage of the intrinsically higher epoxidation selectivity of Cu over Ag under vacuum conditions, we have used three phenylpropene structural isomers to examine the correlation between adsorption geometry and oxidation chemistry. It is found that under comparable conditions alpha-methylstyrene, trans-methylstyrene, and allylbenzene behave very differently on the oxygenated Cu(111) surface: the first undergoes extensive epoxidation accompanied by relatively little decomposition of the alkene; the second leads to some epoxide formation and extensive alkene decomposition; and the third is almost inert with respect to both reaction pathways. This reactive behavior is understandable in terms of the corresponding molecular conformations determined by near-edge X-ray absorption fine structure spectroscopy and density functional theory calculations. The proximity to the surface of the C=C function and of the allylic H atoms is critically important in determining reaction selectivity. This demonstrates the importance of adsorption geometry and confirms that allylic H stripping is indeed a key process that limits epoxidation selectivity in such cases.

The interaction of C6H6 and C6H12 with noble metal surfaces: electronic level alignment and the origin of the interface dipole.

The electronic interaction of two molecules, the aromatic benzene (C6H6) and the saturated hydrocarbon cyclohexane (C6H12) with a Cu(111) surface, have been determined using precise, ab initio electronic structure calculations. For the interaction of these adsorbates with the substrate, we present a detailed analysis and decomposition of various individual chemical mechanisms that contribute. A novel aspect of this analysis is the use of charge-density difference contour plots to graphically display the chemistry. A wave-function-based approach was used in order to avoid problems when the presently most commonly employed approach, density-functional theory, is applied to weakly chemisorbed molecules, where the interaction is dominated by van der Waals forces. The present information are not only relevant with regard to understanding the chemistry going on when molecules are adsorbed on a Cu surface but also have important consequences with regard to charge injection in molecular electronic devices, e.g., organic field-effect transistors and organic light-emitting diodes.

Loss of SFRP1 is associated with breast cancer progression and poor prognosis in early stage tumors.

Aberrant activation of the Wnt signaling pathway plays an important role in the development of solid tumors such as breast and colon cancer. Secreted Frizzled-related protein 1 (SFRP1) is a negative regulator of the Wnt pathway. It has been described that SFRP1 mRNA is strongly down-regulated in breast cancer and a putative tumor suppressor function has been postulated. We have generated and characterized an SFRP1 specific antibody to analyze its expression on protein level and to investigate the association of SFRP1 expression with clinicopathological parameters and patient survival. Analysis of >2000 invasive breast tumors and 56 carcinoma in situ revealed similar frequencies of SFRP1 loss in these tumors (46% and 43% respectively). Therefore, we propose that loss of SFRP1 expression is an early event in breast tumorigenesis. SFRP1 expression was inversely correlated with tumor stage (p<0.001) but not with tumor grade (p=0.14) or lymph node status (p=0.84). Performing a multivariate analysis we could confirm the association between tumor stage and SFRP1 expression (p=0.029). In particular, loss of SFRP1 expression in early stage breast tumors (pT1) was associated with poor prognosis (p=0.04). In conclusion, expression of SFRP1 is commonly lost in breast cancer. SFRP1 expression might be useful as a novel prognostic marker in early stage breast cancer.

Soft copy versus hard copy reading in digital mammography.

The objective of this study was to compare soft copy reading at a mammography work station with hard copy reading of full-field digital mammographic images. Mammograms of 60 patients ( n = 29 malignant, n = 31 benign) performed with full-field digital mammography (Senographe 2000D, GE, Buc, France) were evaluated. Reading was performed based on hard copy prints (Scopix, Agfa, Leverkusen, Germany) and on 2 k x 2.5 k high-resolution monitors (Sun Ultra 60, Sun Microsystems, Palo Alto, California, USA). Four readers with different levels of experience in mammography categorized the mammograms according to the BI-RADS classification. The comparative study was performed by four readers, and at least 2 months elapsed between the reading sessions. Postprocessing, of course, was available only at the work station (windowing and leveling, zooming, inversion). Sensitivity, specificity, and positive predictive value were evaluated. Diagnostic accuracy of the evaluation was determined. Sensitivity for malignant lesions in hard copy versus soft copy reading was 97% vs 90%, 97% vs 97%, 93% vs 97%, and 76% vs 76% for the four readers, respectively. Specificity was 52% vs 68%, 58% vs 74%, 65% vs 48%, and 61% vs 68%. Accuracy for the classification of malignant lesions according to the BI-RADS categories showed no difference between hard copy and soft copy reading. Soft copy reading is possible with the available system and enables radiologists to use the advantages of a digital system.

Changes in Angiotensin Peptides in Plasma and Urine in Patients with Anaphylaxis.

Angiotensins (ANG) I and II were measured in the plasma of patients with hymenoptera venom allergy and found to be significantly decreased as compared to controls. An inverse correlation between the plasma levels of ANG I and ANG II and the intensity of clinical symptoms of anaphylaxis was observed. In a separate study, ANG I and ANG II were measured in urine from healthy volunteers and from patients with anaphylactic reactions to drugs, food, and additives. An increase in both peptides was observed in patients with anaphylactic reactions during oral provocation. These findings suggest a possible involvement of ANG peptides in anaphylactic reactions.