Electrostatic potentials of atomic nanostructures at metal surfaces quantified by scanning quantum dot microscopy.

The discrete and charge-separated nature of matter - electrons and nuclei - results in local electrostatic fields that are ubiquitous in nanoscale structures and relevant in catalysis, nanoelectronics and quantum nanoscience. Surface-averaging techniques provide only limited experimental access to these potentials, which are determined by the shape, material, and environment of the nanostructure. Here, we image the potential over adatoms, chains, and clusters of Ag and Au atoms assembled on Ag(111) and quantify their surface dipole moments. By focusing on the total charge density, these data establish a benchmark for theory. Our density functional theory calculations show a very good agreement with experiment and allow a deeper analysis of the dipole formation mechanisms, their dependence on fundamental atomic properties and on the shape of the nanostructures. We formulate an intuitive picture of the basic mechanisms behind dipole formation, allowing better design choices for future nanoscale systems such as single-atom catalysts.

Accurate quantification of the stability of the perylene-tetracarboxylic dianhydride on Au(111) molecule-surface interface.

Studying inorganic/organic hybrid systems is a stepping stone towards the design of increasingly complex interfaces. A predictive understanding requires robust experimental and theoretical tools to foster trust in the obtained results. The adsorption energy is particularly challenging in this respect, since experimental methods are scarce and the results have large uncertainties even for the most widely studied systems. Here we combine temperature-programmed desorption (TPD), single-molecule atomic force microscopy (AFM), and nonlocal density-functional theory (DFT) calculations, to accurately characterize the stability of a widely studied interface consisting of perylene-tetracarboxylic dianhydride (PTCDA) molecules on Au(111). This network of methods lets us firmly establish the adsorption energy of PTCDA/Au(111) via TPD (1.74 ± 0.10 eV) and single-molecule AFM (2.00 ± 0.25 eV) experiments which agree within error bars, exemplifying how implicit replicability in a research design can benefit the investigation of complex materials properties.

Design Principles for Metastable Standing Molecules.

Molecular nanofabrication with a scanning probe microscope (SPM) is a promising route toward the prototyping of metastable functional molecular structures and devices which do not form spontaneously. The aspect of mechanical stability is crucial for such structures, especially if they extend into the third dimension vertical to the surface. A prominent example is freestanding molecules fabricated on a metal which can function as field emitters or electric field sensors. Improving the stability of such molecular configurations is an optimization task involving many degrees of freedom and therefore best tackled by computational nanostructure design. Here, we use density functional theory to study 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA) standing on the Ag(111) surface as well as on the tip of a scanning probe microscope. We cast our results into a simple set of design principles for such metastable structures, the validity of which we subsequently demonstrate in two computational case studies. Our work proves the capabilities of computational nanostructure design in the field of metastable molecular structures and offers the intuition needed to fabricate new devices without tedious trial and error.

The stabilization potential of a standing molecule.

The part-by-part assembly of functional nanoscale machinery is a central goal of nanotechnology. With the recent fabrication of an isolated standing molecule with a scanning probe microscope, the third dimension perpendicular to the surface will soon become accessible to molecule-based construction. Beyond the flatlands of the surface, a wealth of structures and functionalities is waiting for exploration, but issues of stability are becoming more critical. Here, we combine scanning probe experiments with ab initio potential energy calculations to investigate the thermal stability of a prototypical standing molecule. We reveal its generic stabilization mechanism, a fine balance between covalent and van der Waals interactions including the latter's long-range screening by many-body effects, and find a remarkable agreement between measured and calculated stabilizing potentials. Beyond their relevance for the design and construction of three-dimensional molecular devices at surfaces, our results also indicate that standing molecules may serve as tunable mechanical gigahertz oscillators.

Design, synthesis, and biological evaluation of new 1,4-diarylazetidin-2-one derivatives (ß-lactams) as selective cyclooxygenase-2 inhibitors.

A new series of 1,4-diarylazetidin-2-one derivatives (ß-lactams) were designed and synthesized to evaluate their biological activities as selective cyclooxygenase-2 (COX-2) inhibitors. In vitro COX-1 and COX-2 inhibition studies showed that all compounds were selective inhibitors of the COX-2 isozyme with IC50 values in the 0.05-0.11 µM range, and COX-2 selectivity indexes in the range of 170-703.7. Among the synthesized ß-lactams, 3-methoxy-4-(4-(methylsulfonyl)phenyl)-1-(3,4,5-trimethoxyphenyl)azetidin-2-one (4j) possessing trimethoxy groups at the N-1 phenyl ring exhibited the highest COX-2 inhibitory selectivity and potency, even more potent than the reference drug celecoxib. The analgesic activity of the synthesized compounds was also determined using the formalin test. Compound 4f displayed the best analgesic activity among the synthesized molecules. Molecular modeling studies indicated that the methylsulfonyl pharmacophore group can be inserted into the secondary pocket of the COX-2 active site for interactions with Arg513 . The structure-activity data acquired indicate that the ß-lactam ring moiety constitutes a suitable scaffold to design new 1,4-diarylazetidin-2-ones with selective COX-2 inhibitory activity.

Novel Colchicine Analogues Target Mitochondrial PT Pores Using Free Tubulins and Induce ROS-Mediated Apoptosis in Cancerous Lymphocytes.

B-acute lymphoblastic leukemia (B-ALL) is the frequent pediatric malignity. Chemotherapy is the most practical approaches to deal with such malignancies. Microtubule-targeted agents are one of the most strategic drugs which formerly used in chemotherapy. Although colchicine-binding anti-tubulin agents exhibited promising effects in clinical trials, their exact mechanism of action is not fully understood. In this study, the effects of two newly synthesized of colchicine derivatives were investigated on cell viability of cancerous and normal lymphocytes. The viability test was carried out by MTT assay. Apoptosis vs. necrosis was measured by double staining with annexin V/PI, and caspase-3 as the ultimate mediator of apoptotic measured through the colorimetric assay. Parameters of mitochondrial damage (ROS formation, MMP (Mitochondrial Membrane Potential) decline, mitochondrial swelling, and cytochrome c release following treatment by colchicine derivatives. By focusing on mitochondrial parameters, we showed that following treatment by two newly synthesized colchicine derivatives, apoptosis is triggered in cancerous B-lymphocytes. We demonstrated these compounds could activate apoptosis in cancerous lymphocytes by augmentation of reactive oxygen species (ROS), a decline in mitochondrial membrane potential (MMP), mitochondrial swelling, release of cytochrome c, and also caspase-3 activation. Considering the obtained evidence, these inhibitors could be the new therapeutic strategies in ALL treatment.

Self-Assembly of Nanocubic Molecular Capsules via Solvent-Guided Formation of Rectangular Blocks.

We investigate the mechanism underlying the self-assembly of gear-shaped amphiphilic molecules into a highly ordered nanocubic capsule ("nanocube") in aqueous methanol. Simulation results show that the solvent molecules play a significant role in the assembly process by directing the primitive intermediates to orthogonal/rectangular shapes, thus creating appropriate building blocks for cubic assembly while avoiding off-pathway stacked aggregates. Free-energy analyses reveal that the interplay of the direct intermonomer interaction and the solvent-mediated repulsion between large aromatic cores (via preferential solvation of methanol on hydrophobic surfaces) leads to the strong trend for perpendicular binding of monomers and hence the solvent-guided formation of rectangular blocks. Furthermore, we report the self-assembly simulation of the nanocube using replica exchange with solute tempering and demonstrate that the simulation can predict a highly ordered nanocapsule structure, assembly intermediates, and encapsulated molecules, which helps promote computer-aided design of functional molecular self-assemblies in explicit solvent.

Design, Synthesis and Biological Evaluation of New 1,3-diphenyl-3- (phenylamino)propan-1-ones as Selective Cyclooxygenase (COX-2) Inhibitors.

BACKGROUND: Prostaglandins are a family of eicosanoids biosynthesized from arachidonic acid through cyclooxygenase (COX) pathway. Two isoforms of COX are well established: COX-1, COX-2. Evidence supports the notion that cyclooxygenase-2, plays a crucial role in some pathological conditions such as inflammation and cancer. OBJECTIVE: A new group of 1,3-diphenyl-3-(phenylamino)propan-1-ones was designed and synthesized to investigate for their COX-2 inhibitory activity and inhibition of platelet aggregation. METHOD: Docking study was performed using AutoDock vina software. In vitro COX-1 and COX- 2 isozyme inhibition studies were accomplished to obtain structure activity relationship data. The in vitro antiplatelet aggregation activity was determined by turbidimetric procedure. RESULTS: In vitro COX inhibition assay showed that except compound 8c, all derivatives were selective COX-2 inhibitors with IC50 values in the potent 0.20-0.35 µM range with high COX-2 selectivity indexes (SI). Molecular modeling and docking studies indicated that synthesized compounds had a binding similar to that of the known inhibitor SC-558 and the SO2Me group was inserted into the COX-2 secondary pocket (Val523, Phe518, Ile517, Arg513 and His90) and C=O of the central α, ß-unsaturated-carbonyl moiety was oriented toward the entrance to the COX-2 binding site (Tyr355 and Arg120). CONCLUSION: The 1,3-diphenyl-3-(phenylamino)propan-1-ones are novel COX-2 inhibitors with good COX-2 inhibitory and low affinity for COX-1 isoenzyme. Also our results demonstrated that majority of these compounds inhibited AA-induced platelet aggregation.

Communication: Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering.

Conventional molecular-dynamics (cMD) simulation has a well-known limitation in accessible time and length scales, and thus various enhanced sampling techniques have been proposed to alleviate the problem. In this paper, we explore the utility of replica exchange with solute tempering (REST) (i.e., a variant of Hamiltonian replica exchange methods) to simulate the self-assembly of a supramolecular polymer in explicit solvent and compare the performance with temperature-based replica exchange MD (T-REMD) as well as cMD. As a test system, we consider a relatively simple all-atom model of supramolecular polymerization (namely, benzene-1,3,5-tricarboxamides in methylcyclohexane solvent). Our results show that both REST and T-REMD are able to predict highly ordered polymer structures with helical H-bonding patterns, in contrast to cMD which completely fails to obtain such a structure for the present model. At the same time, we have also experienced some technical challenge (i.e., aggregation-dispersion transition and the resulting bottleneck for replica traversal), which is illustrated numerically. Since the computational cost of REST scales more moderately than T-REMD, we expect that REST will be useful for studying the self-assembly of larger systems in solution with enhanced rearrangement of monomers.

ß-lactam Structured, 4-(4-(Methylsulfonyl)phenyl)-1-pentyl-3-phenoxyazetidin-2-one: Selectively Targets Cancerous B Lymphocyte Mitochondria.

BACKGROUND: ß lactam-structured Cox-2 inhibitors, possesses anti-proliferative and anti-inflammatory effects. OBJECTIVE: In this research, the actions of a synthetic ß lactam-structured Cox-2 inhibitor with 4-(4- (Methylsulfonyl) phenyl)-1-pentyl-3-phenoxyazetidin-2-one on cellular viability of cancerous lymphoblast obtained from patients with acute lymphocytic leukemia (ALL) and normal lymphocytes obtained from healthy donors were compared. METHODS: % the cell viability of cancerouslymphoblasts and normal lymphocytes treated with ß lactam derivatives were assayed with MTT test. Early apoptosis and necrosis were detected by double staining of annexin V/ propidium iodide and activity of caspase 3 as the final mediator in apoptotic mode of cell death was evaluated by colorimetric assay. RESULTS: Our results showed that ß lactam derivatives inhibited the proliferation of cancerous lymphoblast but not normal lymphocytes in a concentration-dependent mode by inducing apoptosis. Treatment with ß lactam derivatives resulted in a rapid loss of mitochondrial trans-membrane potential and induction of reactive oxygen species (ROS) formation, and cytochrome c release in cytosol of mitochondria resulted in activation of procaspase-9 and formation of active apoptosome. CONCLUSION: These findings suggest that 4-(4-(Methylsulfonyl)phenyl)-1-pentyl-3-phenoxyazetidin-2-one as a ß lactam could induce ROS-mediated death signaling throughmitochondrial pathway that results in apoptosis in only cancerous lymphoblast cells. The stimulationof apoptosis by ß lactams may provide a pivotal mechanismfor their anticancer effect in acute lymphocytic leukemia cells.

Binary functionalization of H:Si(111) surfaces by alkyl monolayers with different linker atoms enhances monolayer stability and packing.

Alkyl monolayer modified Si forms a class of inorganic-organic hybrid materials with applications across many technologies such as thin-films, fuel/solar-cells and biosensors. Previous studies have shown that the linker atom, through which the monolayer binds to the Si substrate, and any tail group in the alkyl chain, can tune the monolayer stability and electronic properties. In this paper we study the H:Si(111) surface functionalized with binary SAMs: these are composed of alkyl chains that are linked to the surface by two different linker groups. Aiming to enhance SAM stability and increase coverage over singly functionalized Si, we examine with density functional theory simulations that incorporate vdW interactions, a range of linker groups which we denote as -X-(alkyl) with X = CH2, O(H), S(H) or NH(2) (alkyl = C6 and C12 chains). We show how the stability of the SAM can be enhanced by adsorbing alkyl chains with two different linkers, e.g. Si-[C, NH]-alkyl, through which the adsorption energy is increased compared to functionalization with the individual -X-alkyl chains. Our results show that it is possible to improve stability and optimum coverage of alkyl functionalized SAMs linked through a direct Si-C bond by incorporating alkyl chains linked to Si through a different linker group, while preserving the interface electronic structure that determines key electronic properties. This is important since any enhancement in stability and coverage to give more densely packed monolayers will result in fewer defects. We also show that the work function can be tuned within the interval of 3.65-4.94 eV (4.55 eV for bare H:Si(111)).

Design, Synthesis and Biological Evaluation of New 1, 4-Dihydropyridine (DHP) Derivatives as Selective Cyclooxygenase-2 Inhibitors.

As a continuous research for discovery of new COX-2 inhibitors, chemical synthesis, in vitro biological activity and molecular docking study of a new group of 1, 4-dihydropyridine (DHP) derivatives were presented. Novel synthesized compounds possessing a COX-2 SO2Me pharmacophore at the para position of C-4 phenyl ring, different hydrophobic groups (R1) at C-2 position and alkoxycarbonyl groups (COOR2) at C-3 position of 1, 4-dihydropyridine, displayed selective inhibitory activity against COX-2 isozyme. Among them, compound 5e was identified as the most potent and selective COX-2 inhibitor with IC50 value of 0.30 µM and COX-2 selectivity index of 92. Molecular docking study was performed to determine probable binding models of compound 5e. The study showed that the p-SO2Me-phenyl fragment of 5e inserted inside secondary COX-2 binding site (Arg(513), Phe(518), Gly(519), and His(90)). The structure-activity relationships acquired reveal that compound 5e with methyl and ethoxycarbonyl as R1 and COOR2 substitutions has the necessary geometry to provide selective inhibition of the COX-2 isozyme and it can be a good basis for the development of new hits.

Density functional theory with van der waals corrections study of the adsorption of alkyl, alkylthiol, alkoxyl, and amino-alkyl chains on the H:Si(111) surface.

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future miniaturized electronic and sensor devices. Understanding the roles played by the nature of the linking group and the chain length on the adsorption structures and stabilities of these assemblies is vital to advance this technology. This paper presents a density functional theory (DFT) study of the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si-(CH2)n-CH2 and H:Si-X-(CH2)n-CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)-hexane and (X)-dodecane functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0-3, n = 5-7, and n = 9-11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length.