Induced Fit and Mobility of Cycloalkanes within Nanometer-Sized Confinements at 5 K.

Host-guest architectures provide ideal systems for investigating site-specific physical and chemical effects. Condensation events in nanometer-sized confinements are particularly interesting for the investigation of intermolecular and molecule-surface interactions. They may be accompanied by conformational adjustments representing induced fit packing patterns. Here, we report that the symmetry of small clusters formed upon condensation, their registry with the substrate, their lateral packing, and their adsorption height are characteristically modified by the packing of cycloalkanes in confinements. While cyclopentane and cycloheptane display cooperativity upon filling of the hosting pores, cyclooctane and to a lesser degree cyclohexane diffusively redistribute to more favored adsorption sites. The dynamic behavior of cyclooctane is surprising at 5 K given the cycloalkane melting point of >0 °C. The site-specific modification of the interaction and behavior of adsorbates in confinements plays a crucial role in many applications of three-dimensional porous materials as gas storage agents or catalysts/biocatalysts.

Probing the binding mechanism of capecitabine to human serum albumin using spectrometric methods, molecular modeling, and chemometrics approach.

Capecitabine as a prodrug of 5-Fluorouracil plays an important role in the treatment of breast and gastrointestinal cancers. Herein, in view of the importance of this drug in chemotherapy, interaction mechanism between Capecitabine (CAP) and human serum albumin (HSA) as a major transport protein in the blood circulatory system has been investigated by using a combination of spectroscopic and molecular modeling methods. The fluorescence spectroscopic results revealed that capecitabine could effectively quench the intrinsic fluorescence of HSA through a static quenching mechanism. Evaluation of the thermodynamic parameters suggested that the binding process was spontaneous while hydrogen bonds and van der Waals forces played a major role in this interaction. The value of the binding constant (Kb = 1.820 × 104) suggested a moderate binding affinity between CAP and HSA which implies its easy diffusion from the circulatory system to the target tissue. The efficiency of energy transfer and the binding distance between the donor (HSA) and acceptor (CAP) were determined according to forster theory of nonradiation energy transfer as 0.410 and 4.135 nm, respectively. Furthermore, UV-Vis spectroscopic results confirmed that the interaction was occurred between HSA and CAP and caused conformational and micro-environmental changes of HSA during the interaction. Multivariate curve resolution-alternating least square (MCR-ALS) methodology as an efficient chemometric tool was used to separate the overlapped spectra of the species. The MCR-ALS result was exploited to estimate the stoichiometry of interaction and to provide concentration and structural information about HSA-CAP interactions. Molecular docking studies suggested that CAP binds mainly to the subdomain IIA of HSA, which were compatible with those obtained by experimental data. Finally, molecular dynamics simulation (MD) was performed on the best docked complex by considering the permanence and flexibility of HSA-CAP complex in the binding site. MD result showed that CAP could steadily bind to HSA in the site I based on the formation of hydrogen bond and π-π stacking interaction in addition to hydrophobic force.

Phase Transitions in Confinements: Controlling Solid to Fluid Transitions of Xenon Atoms in an On-Surface Network.

This study reports on "phase" transitions of Xe condensates in on-surface confinements induced by temperature changes and local probe excitation. The pores of a metal-organic network occupied with 1 up to 9 Xe atoms are investigated in their propensity to undergo "condensed solid" to "confined fluid" transitions. Different transition temperatures are identified, which depend on the number of Xe atoms in the condensate and relate to the stability of the Xe clustering in the condensed "phase." This work reveals the feature-rich behavior of transitions of confined planar condensates, which provide a showcase toward future "phase-transition" storage media patterned by self-assembly. This work is also of fundamental interest as it paves the way to real space investigations of reversible solid to fluid transitions of magic cluster condensates in an array of extremely well-defined quantum confinements.

The Different Faces of 4'-Pyrimidinyl-Functionalized 4,2':6',4''-Terpyridines: Metal-Organic Assemblies from Solution and on Au(111) and Cu(111) Surface Platforms.

A comparative investigation of crystal growth from solution and on-surface assembly in vacuo between copper and three 4'-(2-R-pyrimidin-5-yl)-4,2':6',4''-terpyridines, with R = H (1), Me (2), or Et (3), is presented. In solution, ligand 3 combines with copper(II) acetate or copper(I) triflate in MeOH solution to give [Cu2(OAc)4(3)]n or {[Cu(3)(OMe)(MeOH)][CF3SO3]·MeOH}n. In [Cu2(OAc)4(3)]n, paddle-wheel {Cu2(µ-OAc)4} nodes direct the assembly of one-dimensional (1D) zigzag chains which pack into two-dimensional (2D) sheets. In {[Cu(3)(OMe)(MeOH)][CF3SO3]·MeOH}n, the solvent is a ligand and also generates {Cu2(µ-OMe)2} units which function as planar 4-connecting nodes to generate a 2D (4,4) net with ligand 3. On Au(111) or Cu(111) surfaces in vacuo, no additional solvent or anions are involved in the assembly. The different substituents in 1, 2, or 3 allow precise molecular resolution imaging in scanning tunneling microscopy. On Au(111), 1 and 2 assemble into close-packed assemblies, while 3 forms a regular porous network. The deposition of Cu adatoms results in reorganization leading to ladder-shaped surface metal-organic motifs. These on-surface coordination assemblies are independent of the 4'-substituent in the 4,2':6',4''-tpy and are reproduced on Cu(111) where Cu adatoms are available during the deposition and relaxation process at room temperature. Upon annealing at elevated temperatures, the original surface assemblies of 1 and 3 are modified and a transition from ladders into rhomboid structures is observed; for 2, a further quasi-hexagonal nanoporous network is observed.

Adsorbate-Induced Modification of the Confining Barriers in a Quantum Box Array.

Quantum devices depend on addressable elements, which can be modified separately and in their mutual interaction. Self-assembly at surfaces, for example, formation of a porous (metal-) organic network, provides an ideal way to manufacture arrays of identical quantum boxes, arising in this case from the confinement of the electronic (Shockley) surface state within the pores. We show that the electronic quantum box state as well as the interbox coupling can be modified locally to a varying extent by a selective choice of adsorbates, here C60, interacting with the barrier. In view of the wealth of differently acting adsorbates, this approach allows for engineering quantum states in on-surface network architectures.

Molecular Chessboard Assemblies Sorted by Site-Specific Interactions of Out-of-Plane d-Orbitals with a Semimetal Template.

We show that highly ordered two-dimensional (2D) chessboard arrays consisting of a periodic arrangement of two different molecules can be obtained by self-assembly of unsubstituted metal-phthalocyanines (metal-Pcs) on a suitable substrate serving as the template. Specifically, CuPc + MnPc and CuPc + CoPc mixtures sort into highly ordered Cu/Mn and Cu/Co chessboard arrays on the square p(10 × 10) reconstruction of bismuth on Cu(100). Such created bimolecular chessboard assemblies emerge from the site-specific interactions between the central transition-metal ions and the periodically reconstructed substrate. This work provides a conceptually new approach to induce 2D chessboard patterns in that no functionalization of the molecules is needed.

Configuring Electronic States in an Atomically Precise Array of Quantum Boxes.

A 2D array of electronically coupled quantum boxes is fabricated by means of on-surface self-assembly assuring ultimate precision of each box. The quantum states embedded in the boxes are configured by adsorbates, whose occupancy is controlled with atomic precision. The electronic interbox coupling can be maintained or significantly reduced by proper arrangement of empty and filled boxes.