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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.

The characteristics of interaction between six transition-metal porphyrines and the Ag(111) surface are detailed here as resulted from DFT calculations. Van der Waals interactions as well as the strong correlation in 3d orbitals of transition metals were taken into account in all calculations, including the structural relaxation. For each system we investigate four relative positions of the metallic atom on top the surface. We show that the interaction between the transition metal and silver is the result of a combination between the dispersion interaction, charge transfer and weak chemical interaction. The detailed analysis of the physical properties, such as dipolar and magnetic moments and the molecule–surface charge transfer, analyzed for different geometric configurations allows us to propose qualitative models, relevant for the understanding of the self-assembly processes and related phenomena.

Acenes and azaacenes lie at the core of molecular materials' applications due to their important optical and electronic features. A critical aspect is provided by their heteroatom multiplicity, which can strongly affect their properties. Here we report pyrazinacenes containing the dihydro-decaazapentacene and dihydro-octaazatetracene chromophores and compare their properties/functions as a model case at an oxidizing metal substrate. We find a distinguished, oxidation-state-dependent conformational adaptation and self-assembly behaviour and discuss the analogies and differences of planar benzo-substituted decaazapentacene and octaazatetracene forms. Our broad experimental and theoretical study reveals that decaazapentacene is stable against oxidation but unstable against reduction, which is in contrast to pentacene, its C-H only analogue. Decaazapentacenes studied here combine a planar molecular backbone with conformationally flexible substituents. They provide a rich model case to understand the properties of a redox-switchable pi-electronic system in solution and at interfaces. Pyrazinacenes represent an unusual class of redox-active chromophores. Acenes are a promising class of organic materials with distinctive electronic and optical properties. Here decaazapentacene and octaazatetracenes are prepared and their self-assembly behaviour at different oxidation states is analysed. Práce se zabývá studiem pyrazinacenů obsahujících dihydro-dekaazapentacenové a dihydro-oktaazatetracenové chromofory a porovnáním jejich vlastností při modelovém chování na oxidačním kovovém substrátu. Byla nalezena odlišná, na oxidačním stavu závislá konformační adaptace a samouspořádající se chování. Byly připraveny dekaazapentaceny a oktaazatetraceny a analyzováno jejich samoorganizující se chování v různých oxidačních stavech.

Using first-principles calculations, we investigate the binding energy for six transition metal - phthalocyanine molecules adsorbed on Au(111). We focus on the effect of translation on molecule - surface physical properties; van der Waals interactions as well as the strong correlation in d orbitals of transition metals are taken into account in all calculations. We found that dispersion interaction and charge transfer have the dominant role in the molecule-surface interaction, while the interaction between the transition metal and gold has a rather indirect influence over the physics of the molecule-surface system. A detailed analysis of the physical properties of the adsorbates at different geometric configurations allows us to propose qualitative models to account for all values of interface dipole charge transfer and magnetic moment of metal-phthalocyanines adsorbed on Au(111).

We present a theoretical investigation that addresses the most important aspects of the interaction between α-glycero-phosphatidyl-choline and Au(111) surface. For the density functional calculations we employed both traditional exchange-correlation functionals and newly developed vdW-D2 corrected one. The comparison between these functionals allows us to spot the role of van der Waals effects into the molecule– surface interaction. The effect of an external field applied to the molecule–surface system was also explicitly investigated. Our results reveal a complex picture where the molecular adsorption is dominated by the interplay between a weak molecule–surface interaction and a rather important deformation energy of the adsorbed molecule. In the presence of an external electric field, the choline moiety provided the strongest response in terms of binding energy as well as geometric configuration of the adsorbate.

Complexation in solution between meclofenamate sodium (MCF) and β-cyclodextrin was studied using one- and two-dimensional 1H NMR spectroscopy and molecular docking coupled with ab initio calculations. The large variation of chemical shifts from protons located inside the hydrophobic cavity of β-cyclodextrin, provided clear evidence of inclusion complexation. The stoichiometry of the inclusion complex was determined to be 1:1, using the method of continuous variation. To ascertain the solution geometry of the host–guest complex a ROESY experiment was carried out. The results suggested a preferential binding of the dichlorophenyl moiety of the guest molecule within the β-cyclodextrin cavity, conformation which also sustained by the theoretical computational investigations. The association constant of the inclusion complex was determined using 1H NMR titration method in solution followed by a non-linear least-square regression implemented in CONSTEQ, a software developed in our group. After a preliminary molecular docking investigation, the most probable conformation was subjected to ab initio calculations using SIESTA software package, to characterize more precisely the stabilization energy of the 1:1 inclusion complex.

We investigate the weak interactions taking place in the tetraphenylporphyrin dimers by using Wannier orbitals and DFT. The Van der Waals interaction energies for various geometric configurations of the dimers are then compared to the differences between the total DFT energies of dimers and those of sums over the energies of monomers. The comparison allows us to estimate the weight of the Van der Waals contribution to the total interaction energy since the DFT values include all contributions such as weak chemical interaction or Pauli repulsion to the binding energy. We show that the interaction energy computed with vdW-DF-cx exchange-correlation functional is almost identical with the one computed using Wannier orbitals. By analyzing the properties of Wannier orbitals in monomer and dimer structures, we check the fact the Van der Waals energy can be accurately calculated by using only the orbitals corresponding to the single molecule, which is useful from a practical perspective.

Dip Pen Nanolithography technique has been employed for patterning L-Glutathione tripeptide (l-y-glutamyl-l-cysteinyl-glycine) nanostructures at specific locations on metallic Au(111) substrate. The formed supramolecular architectures were designed through straight lines and dots serving as precursors for building blocks assemblies in nano-bio-electronics applications or as template structures for functionalized particles in the form of host-guest networks. Tween 20 polyoxyethylene surfactant concentrations ranging from 0.005 to 0.1% (v/v) into initial l-Glutathione tripeptide (2 mg mL(-1)) ink solutions were sequentially tested for the improvement of the ink delivery process and to assure an optimum uniformity and homogeneity over the patterned space. A strong relationship was found between the coated atomic force microscope (AFM) cantilever within the highly effective Tween 20 activator adjuvant and the molecular diffusion along concentration gradients. An increase in the driving force for ink transport from the AFM tip has been demonstrated within the highest 0.1% (v/v) TW 20 surfactant concentration, favoring the patterning of GSH molecules routinely with sub-100 nm resolution. Self-assembled monolayers of GSH were also fabricated and characterized in the light of X-ray photoemission spectroscopy (XPS) and ellipsometric optical measurements. Adsorption from water of l-Glutathione to the gold substrate is proven to be made by the thiol group of cysteine. Theoretical DFT approaches were applied for quantum chemical studies dedicated to electronic processes underneath molecular GSH/Au(111) systems.

In this work the surface-enhanced Raman total half band widths of seven genomic DNAs from leaves of chrysanthemum (Dendranthema grandiflora Ramat.), common sundew (Drosera rotundifolia L.), edelweiss (Leontopodium alpinum Cass), Epilobium hirsutum L., Hypericum richeri ssp. transsilvanicum (Čelak) Ciocârlan, rose (Rosa x hybrida L.) and redwood (Sequoia sempervirens D. Don. Endl.) have been measured. We have shown that surface-enhanced Raman spectroscopy (SERS) can be used to study the fast subpicosecond dynamics of DNA in the proximity of a metallic surface. The dependencies of the total half band widths and the global relaxation times, on the DNA molecular subgroup structure and on the type of genomic DNA, are reported. In our study, the full widths at half-maximum (FWHMs) for the SERS bands of genomic DNAs from different leaf tissues are typically in the wavenumber range from 15 to 55 cm(-1). Besides, it can be observed that molecular relaxation processes studied in this work have a global relaxation time smaller than 0.71 ps and larger than 0.19 ps. A comparison between different ranges of FT-Raman and SERS band parameters, respectively, corresponding to DNA extracted from leaf tissues is given. It is shown that the interaction between DNA and a metallic surface has the potential to lead to a shortening of the global relaxation times, as compared with molecular dynamics in solution. We have found that the surface dynamics of molecular subgroups in plant DNA is, in some cases, about two times faster than the solution dynamics of nucleic acids. This can be rationalized in a qualitative manner by invoking the complex landscape of the interaction energy between the molecule and the silver surface.

We present density functional theory investigations on the electronic structure properties for three derivatives of trioxotriangulene that were recently used as electrode materials in Li–ion batteries. We compare the results obtained by standard GGA exchange–correlation functionals with those based on recently developed van der Waals exchange–correlation functionals for the free molecules and bulk structures. This allows us to point out the importance of van der Waals interaction for the stability of the structures as well as the main characteristics of the electronic structures.

The physical properties of cysteine clusters formed on the Au(110)-(1 × 1) surface are investigated by means of density-functional theory. We take into account the clusters formed from three types of rotational conformers of cysteine; for each structure we investigate the protonated and unprotonated forms. Our investigations are based on three different geometrical models for the surface–adsorbate system, allowing us to describe the formation of new nucleation centers on the surface as well as the properties of long chains of cysteine molecules adsorbed on the Au(110)-(1 × 1) surface. We point out significant differences between the relaxed structures formed by each conformer as well as the specific physicochemical properties leading to formation of new nucleation centers compared with those of already formed large cysteine structures. In particular, we emphasize the role of the NH2 group of cysteine in these processes, by correlating our data with its relative position with respect to the gold surface.

Using first-principles calculations, we study the electronic and transport properties of rutheniumterpyridine molecules sandwiched between two Au(111) electrodes. We analyse both single and packed molecular devices, more amenable to scaling and realistic integration approaches. The devices display all together robust negative differential resistance features at low bias voltages. Remarkably, the electrical control of the spin transport in the studied systems implies a subtle distribution of the magnetisation density within the biased devices and highlights the key role of the Au(111) electrical contacts.

We performed simulations of the vibrational properties of the adenine adsorbed on Au(1 0 0) gold surface by using three different geometric models. For each geometric model we used two approximations to build partial the Hessian matrix: in the first one the gold atoms were allowed to vibrate while in the second one they are pinned to their relaxed positions. The influence of the vibrations of the first layers in the gold surface upon the vibrational bands of the adenine as well as the influence of a point-like defect in the surface is discussed in detail. The comparison with experimental results indicates that two maxima of the SERS signals are present (just above 300 and 600 cm −1 ) while the values obtained from our calculations are 327 cm −1 and 625 cm −1 . For the frequencies ranging between 0 and 700 cm −1 we note shifts of up to 40 cm −1 caused by the use of different computational models. For the frequencies larger than 700 cm −1 there are practically no differences between the models used by us. The presence of a point-like defect on the surface leads to important modification of the vibrational properties of adenine in the low frequency regime. While in the case of VbDOS projected over the gold atoms the presence of the defect leads to minimal changes of the vibrational density of states, the influence of the defect of the adenine’s atoms is more important. This is clearly visible by comparing the VbDOS at low frequencies.

We have investigated the ballistic transport for Mn, Fe-porphyrin molecules in contact with Au(111) electrodes by using density functional theory. We show that the information resulted from the projected density of electronic states does not provide a complete picture of the transport mechanism. Instead, we propose a methodology based on the concept of the orbital projected transmissions for selected groups of atoms. We have found that the transmission channels for occupied states can be assigned to short range scattering processes at gold-molecule interface, while for the states above Fermi level the transmission takes place via long range scattering processes. The interplay between these two conduction mechanisms is responsible for the transport path in metal-porphyrin; our model is in qualitative agreement with the existing experimental data on transport pathway on single porphyrin molecules.

Previous investigation of coding sequence lengths (CDS) in the bacterial circular chromosome revealed short range correlation in the series of these data. We have further analyzed the averaged periodograms of these series and we found that the organization of CDS can be well described by first order autoregressive processes. This involves interaction between the neighboring terms. The autoregressive analysis may have great potential in modeling various physical and biological processes like light emission of galaxies, protein organization, cell flickering, cognitive processes and perhaps others., 11 pages, 5 figures, 2 tables

We provide qualitative results for the physical properties of the lead alloys at atomic scale by using DFT calculations. Our approach is based on the two assumptions: (i) the geometric structure of lead atoms provides a matrix where the alloying elements can take their positions in the structure as substitutions and (ii) there is a small probability of a direct interaction between the alloying elements, thus the interactions of each alloying element may be approximated by the interactions to the lead matrix. DFT calculations are used to investigate the interaction between several types of impurities and the lead matrix for low concentrations of the alloying element. We report results such as the enthalpy of formation, charge transfer and mechanical stress induced by the impurities in the lead matrix; these results can be used as qualitative guide in tuning the physico-chemical properties of the lead alloys.

The binding effects of Mg2+, Ca2+, and Cu2+ ions on the vibrational properties of guanine-cytosine base pairs have been performed using density functional theory investigations. Both Watson-Crick and Hoogsteen configurations of the base pairs were investigated. In Watson-Crick configuration, the metal was coordinated at N7 atom of guanine, while in the case of Hoogsteen configuration, the coordination is at N3 atom of guanine. We have pointed out the geometric properties of the metal-GC base pairs structure, as well as the vibrational bands that can be used to detect the presence of metallic ions in the Watson-Crick and Hoogsteen GC structures. For the geometric models used by us, the vibrational amplitudes of metallic atoms were stronger for wavenumbers lower than 500 cm−1. This suggests that in the experimental studies on DNA the presence of the three metallic atoms (Mg, Ca, and Cu) can be explicitly detected at low frequencies.

We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LCAO basis sets or geometric models for the adsorption of the molecules on the surface, the binding energy can vary up to 100 %. A critical analysis of the physical parameters resulting from the calculations is presented for each exchange-correlation functional.

The binding effects of Mg²⁺, Ca²⁺, and Cu²⁺ ions on the vibrational properties of guanine-cytosine base pairs have been performed using density functional theory investigations. Both Watson-Crick and Hoogsteen configurations of the base pairs were investigated. In Watson-Crick configuration, the metal was coordinated at N7 atom of guanine, while in the case of Hoogsteen configuration, the coordination is at N3 atom of guanine. We have pointed out the geometric properties of the metal-GC base pairs structure, as well as the vibrational bands that can be used to detect the presence of metallic ions in the Watson-Crick and Hoogsteen GC structures. For the geometric models used by us, the vibrational amplitudes of metallic atoms were stronger for wavenumbers lower than 500 cm⁻¹. This suggests that in the experimental studies on DNA the presence of the three metallic atoms (Mg, Ca, and Cu) can be explicitly detected at low frequencies.

Periodic density functional theory calculations were used to investigate relevant aspects of adsorption mechanisms of cysteine dimers in protonated form on Au(111) and Au(110) surfaces. The projected densities of states are explicitly discussed for all main chemical groups of cysteine, i.e. the amino group (NH2), the thiol group (SH) and the carboxylic group (COOH) to identify differences in adsorption mechanism. Special emphasis is put on the analysis of changes in the electronic structure of molecules adsorbed on Au(111) and Au(110) surfaces as well as the accompanying charge transfer mechanisms at molecule-substrate interaction.

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

The controlled self-assembly of functional molecular species on well defined surfaces is a promising approach toward the design of nanoscale architectures. By using this methodology, regular low-dimensional systems such as supramolecular clusters, chains, or nanoporous arrays can be fabricated. Small biological molecules such as amino acids represent an important class of building blocks that are of interest for molecular architecture on surfaces because they inherently qualify for molecular recognition and self-assembly. The interaction between amino acids and solid surfaces is decisive for the development of bioanalytical devices or biocompatible materials as well as for a fundamental understanding of protein-surface bonding. Their practical implementation often involves surface structural defects. We investigated the adsorbtion mechanism of the cysteine on Au(111) defect surfaces by means of crystal orbital overlap population (COOP) analysis and also the dependence of the COOP curves on the type of surface defects.

Autoregressive processes (AR) have typical short-range memory. Detrended Fluctuation Analysis (DFA) was basically designed to reveal long range correlation in non stationary processes. However DFA can also be regarded as a suitable method to investigate both long-range and short range correlation in non-stationary and stationary systems. Applying DFA to AR processes can help understanding the non uniform correlation structure of such processes. We systematically investigated a first order autoregressive model AR(1) by DFA and established the relationship between the interaction constant of AR(1) and the DFA correlation exponent. The higher the interaction constant the higher is the short range correlation exponent. They are exponentially related. The investigation was extended to AR(2) processes. The presence of a distant positive interaction in addition to a near by interaction will increase the correlation exponent and the range of correlation while the effect of a distant negative interaction will decrease significantly only the range of interaction. This analysis demonstrate the possibility to identify and AR(1) model in an unknown DFA plot or to distinguish among AR(1) and AR(2) models. The analysis was performed on medium long series of 1000 terms., 7 pages, 6 figures, submitted to Fluctuation and Noise Letters

The electrochemical behavior and electronic properties of redox-active ferrocenes grafted onto semiconductor Si(100) substrate were investigated theoretically by first-principles calculations. Organic molecules were attached via the formation of Si-C covalent bonds through two different linkers: vinyl (direct grafting), and N3(CH2)11 (indirect grafting). Redox energies and the electronic properties relating to different spacers in hybrid ferrocene Fc/Si and ferrocenium Fc+/Si structures were theoretically extracted and compared with experimental cyclic voltametry data. Electronic charge transfers are discussed through the alignment positions of the frontier orbitals of the molecule with respect to the Si substrate gap. Periodic boundary conditions were used to investigate the Si(100) as a slab surface and hybrid Fc/Si structures. The resulting projected density of states (PDOS) were compared with molecular results and discussed in the light of experimental data.

Cysteine clusters of various sizes are investigated, as free structures and adsorbed on the Au(110)−(1 × 1) surface, by using density-functional theory. We analyse the adsorption of clusters in protonized and deprotonized forms. The presence of a trend for the values of bonding energy per adsorbed cysteine molecule as a function of cluster size is pointed out. To explain these findings we analyse the electronic density of states of the clusters and the charge transfer occurring between the surface and cysteine molecules. We emphasize the broadening of the molecular density of states as a function of cluster size. Details of the geometrical structure of the adsorbed clusters in protonized and deprotonized forms are compared and discussed from the perspective provided by the electronic structure calculation. By investigating the redistribution of the electron density upon the adsorption we point out the significant features of the molecule–surface charge transfer. In particular we show that the charge redistribution occurs only at the thiol end while the electronic density of the carboxylic group is not affected in the adsorbed state.

The adsorption mechanisms of l- and ll-cysteine dimers on Au(111) surface was investigated by means of periodic density functional theory calculations. The computed binding energies suggest that ll dimer is stabilized by the interaction occurring between the COOH groups. Results for different molecular configurations show that for all the investigated adsorption geometries the l and ll molecules are physisorbed at a relatively high position with respect to the gold surface. By analysing the electronic structure of the adsorbate, we noted that upon the adsorption of ll dimer there is no competition between the mechanism of dimer formation and that of dimer adsorption on the gold surface. The calculated projected density of states allows us to locate the l- and ll-cysteine molecular orbitals with respect to the metal's Fermi level.

The erythrocyte membrane fluctuations analysis was performed for two suspension media, plasma and phosphate buffered saline (PBS) respectively. The investigation methods consist of detrended fluctuation analysis (DFA) and spectral analysis applied on data series formed by successive values of cellular area which were obtained by managing the sequential images set for each cell. We have shown that the suspension media influences significantly the membrane fluctuation characteristics. Detrended fluctuation analysis revealed two short range correlations both for cells suspended in their natural medium and artificial medium. Moreover, we found out the strength on interaction between terms in series by using spectral analysis and autoregressive modeling. The correlation between parameters obtained by the above mentioned methods was evidenced by theoretical models and certified by our experiments.