Exploring Molecular Energy Landscapes by Coupling the DFTB Potential with a Tree-Based Stochastic Algorithm: Investigation of the Conformational Diversity of Phthalates.

Exploring the global energy landscape of relatively large molecules at the quantum level is a challenging problem. In this work, we report the coupling of a nonredundant conformational space exploration method, namely, the robotics-inspired iterative global exploration and local optimization (IGLOO) algorithm, with the quantum-chemical density functional tight binding (DFTB) potential. The application of this fast and efficient computational approach to three close-sized molecules of the phthalate family (DBP, BBP, and DEHP) showed that they present different conformational landscapes. These differences have been rationalized by making use of descriptors based on distances and dihedral angles. Coulomb interactions, steric hindrance, and dispersive interactions have been found to drive the geometric properties. A strong correlation has been evidenced between the two dihedral angles describing the side-chain orientation of the phthalate molecules. Our approach identifies low-energy minima without prior knowledge of the potential energy surface, paving the way for future investigations into transition paths and states.

Low-Energy Transformation Pathways between Naphthalene Isomers.

The transformation pathways between low-energy naphthalene isomers are studied by investigating the topology of the energy landscape of this astrophysically relevant molecule. The threshold algorithm is used to identify the minima basins of the isomers on the potential energy surface of the system and to evaluate the probability flows between them. The transition pathways between the different basins and the associated probabilities were investigated for several lid energies up to 11 eV, this value being close to the highest photon energy in the interstellar medium (13.6 eV). More than a hundred isomers were identified and a set of 23 minima was selected among them, on the basis of their energy and probability of occurrence. The return probabilities of these 23 minima and the transition probabilities between them were computed for several lid energies up to 11 eV. The first connection appeared at 3.5 eV while all minima were found to be connected at 9.5 eV. The local density of state was also sampled inside their respective basins. This work gives insight into both energy and entropic barriers separating the different basins, which also provides information about the transition regions of the energy landscape.

Coordination of Ethylamine on Small Silver Clusters: Structural and Topological (ELF, QTAIM) Analyses.

Amine ligands are expected to drive the organization of metallic centers as well as the chemical reactivity of silver clusters early growing during the very first steps of the synthesis of silver nanoparticles via an organometallic route. Density functional theory (DFT) computational studies have been performed to characterize the structure, the atomic charge distribution, and the planar two-dimensional (2D)/three-dimensional (3D) relative stability of small-size silver clusters (Agn, 2 ≤ n ≤ 7), with or without an ethylamine (EA) ligand coordinated to the Ag clusters. The transition from 2D to 3D structures is shifted from n = 7 to 6 in the presence of one EA coordinating ligand, and it is explained from the analysis of the Ag-N and Ag-Ag bond energies. For fully EA saturated silver clusters (Agn-EAn), the effect on the 2D/3D transition is even more pronounced with a shift between n = 4 and 5. Subsequent electron localization function (ELF) and quantum theory of atoms in molecules (QTAIM) topological analyses allow for the fine characterization of the dative Ag-N and metallic Ag-Ag bonds, both in nature and in strength. Electron transfer from ethylamine to the coordinated silver atoms induces an increase of the polarization of the metallic core.

Convertible and conformationally constrained nucleic acids (C2NAs).

We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and ß can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.

Evidencing the relationship between isomer spectra and melting: the 20- and 55-atom silver and gold cluster cases.

The present work highlights the links between melting properties and structural excitation spectra of small gold and silver clusters. The heat capacity curves are computed for Ag20, Au20, Ag55, Au55 and their ions, using a parallel-tempering molecular dynamics scheme to explore the density functional based tight binding (DFTB) potential energy surfaces and the multiple histogram method. It is found that clusters having very symmetric lowest energy structures (Au20, Ag55 and their ions) present sharp or relatively sharp solid-to-liquid transitions and large melting temperatures, important structural excitation energies and a discrete isomer spectrum. Opposite trends are observed for less ordered clusters (Ag20, Au55 and their ions). Regarding the structural evolution with temperature, very symmetric clusters exhibit minor evolution up to the starting melting temperature. The present study also highlights that, in contrast with the case of Au20, a single electron excess or deficiency is not determinant regarding the melting characteristics, even quantitatively, for clusters containing 55 atoms, for gold as for silver.

Carbohydrate Self-Assembly at Surfaces: STM Imaging of Sucrose Conformation and Ordering on Cu(100).

Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self-assembly of the disaccharide sucrose on a Cu(100) surface with subunit-level imaging. By employing a multistage modeling approach in combination with the experimental data, we can rationalize the conformation on the surface as well as the interactions between the sucrose molecules, thereby yielding models of the observed self-assembled patterns on the surface.

Melting of the Au20 Gold Cluster: Does Charge Matter?

We investigate the dependence upon the charge of the heat capacities of magic gold cluster Au20 obtained from density functional-based tight binding theory within parallel tempering molecular dynamics and the multiple histogram method. The melting temperatures, determined from the heat capacity curves, are found to be 1102 K for neutral Au20 and only 866 and 826 K for Au20+ and Au20-. Both the canonical and the microcanonical aspects of the transition are discussed. A convex intruder, associated with a negative heat capacity, is evidenced in the microcanonical entropy in the case of the neutral cluster but is absent in the melting processes of the ions. The present work shows that a single charge quantitatively affects the thermal properties of the gold 20mer.

Au147 nanoparticles: Ordered or amorphous?

Structural aspects of the Au147 cluster have been investigated through a density functional based tight binding global optimization involving a parallel tempering molecular dynamics scheme with quenching followed by geometries relaxation at the Density Functional Theory (DFT) level. The focus is put on the competition between relaxed ordered regular geometries and disordered (or amorphous) structures. The present work shows that Au147 amorphous geometries are relevant low energy candidates and are likely to contribute in finite temperature dynamics and thermodynamics. The structure of the amorphous-like isomers is discussed from the anisotropy parameters, the atomic coordinations, the radial and pair distribution functions, the IR spectra, and the vibrational DOS. With respect to the regular structures, the amorphous geometries are shown to be characterized by a larger number of surface atoms, a less dense volume with reduced coordination number per atom, a propensity to increase the dimension of flat facets at the surface, and a stronger anisotropy. Moreover, all amorphous clusters have similar IR spectra, almost continuous with active frequencies over the whole spectral range, while symmetric clusters are characterized by a few lines with large intensities.

Theoretical study of the atrazine pesticide interaction with pyrophyllite and Ca(2+) -montmorillonite clay surfaces.

Atrazine, a pesticide belonging to the s-triazine family, is one of the most employed pesticides. Due to its negative impact on the environment, it has been forbidden within the European Union since 2004 but remains abundant in soils. For these reasons, its behavior in soils and water at the atomic scale is of great interest. In this article, we have investigated, using DFT, the adsorption of atrazine onto two different clay surfaces: a pyrophyllite clay and an Mg-substituted clay named montmorillonite, with Ca2+ compensating cations on its surface. The calculations show that the atrazine molecule is physisorbed on the pyrophyllite surface, evidencing the necessity to use dispersion-corrected computational methods. The adsorption energies of atrazine on montmorillonite are two to three times larger than on pyrophyllite, depending on the adsorption pattern. The computed adsorption energy is of about -30 kcal mol-1 for the two most stable montmorillonite-atrazine studied isomers. For these complexes, the large adsorption energy is related to the strong interaction between the chlorine atom of the atrazine molecule and one of the Ca2+ compensating cations of the clay surface. The structural modifications induced by the adsorption are localized: for the surface, close to substitutions and particularly below the Ca2+ cations; in the molecule, around the chlorine atom when Ca2+ interacts strongly with this basic site in a monodentate mode. This study shows the important role of the alkaline earth cations on the adsorption of atrazine on clays, suggesting that the atrazine pesticide retention will be significant in Ca2+ -montmorillonite clays. © 2016 Wiley Periodicals, Inc.

Adsorption energy of small molecules on core-shell Fe@Au nanoparticles: tuning by shell thickness.

The adsorption of several small molecules on different gold surfaces, Au(001), strained Au(001) and Au(001) epitaxied on Fe(001), has been characterized using density functional theory. The surface strain leads to a less energetically favourable adsorption for all studied molecules. Moreover, the presence of the iron substrate induces an additional decrease of the binding energy, for 1 and 2 Au monolayers. For carbon monoxide (CO), the structural and energetic variations with the number of Au monolayers deposited on Fe have been analyzed and correlated with the distance between the carbon atom and the gold surface. The effect of the subsurface layer has been evidenced for 1 and 2 monolayers. The other molecules show different quantitative behavior depending on the type of their interaction with the gold surface. However, the iron substrate weakens the interaction, either for the chemisorbed species or for the physisorbed species. 2 Au monolayers seem to be the best compromise to decrease the reactivity of the gold surface towards adsorption while preventing the Fe oxidation.

Benchmarking Density Functional Based Tight-Binding for Silver and Gold Materials: From Small Clusters to Bulk.

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) parameters for silver and gold clusters as well as for bulk materials. In the former case, our benchmarks focus on both the structural and energetic properties of small-size AgN and AuN clusters (N from 2 to 13), medium-size clusters with N = 20 and 55, and finally larger nanoparticles with N = 147, 309, and 561. For bulk materials, structural, energetics and elastic properties are discussed. We show that SCC-DFTB is quite satisfactory in reproducing essential differences between silver and gold aggregates, in particular their 2D-3D structural transitions, and their dependency upon cluster charge. SCC-DFTB is also in agreement with DFT and experiments in the medium-size regime regarding the energetic ordering of the different low-energy isomers and allows for an overall satisfactory treatment of bulk properties. A consistent convergence between the cohesive energies of the largest investigated nanoparticles and the bulk's is obtained. On the basis of our results for nanoparticles of increasing size, a two-parameter analytical extrapolation of the cohesive energy is proposed. This formula takes into account the reduction of the cohesive energy for undercoordinated surface sites and converges properly to the bulk cohesive energy. Values for the surface sites cohesive energies are also proposed.

Investigation on the Synthesis of Shigella flexneri Specific Oligosaccharides Using Disaccharides as Potential Transglucosylase Acceptor Substrates.

Chemo-enzymatic strategies hold great potential for the development of stereo- and regioselective syntheses of structurally defined bioactive oligosaccharides. Herein, we illustrate the potential of the appropriate combination of a planned chemo-enzymatic pathway and an engineered biocatalyst for the multistep synthesis of an important decasaccharide for vaccine development. We report the stepwise investigation, which led to an efficient chemical conversion of allyl α-d-glucopyranosyl-(1→4)-α-l-rhamnopyranosyl-(1→3)-2-deoxy-2-trichloroacetamido-ß-d-glucopyranoside, the product of site-specific enzymatic α-d-glucosylation of a lightly protected non-natural disaccharide acceptor, into a pentasaccharide building block suitable for chain elongation at both ends. Successful differentiation between hydroxyl groups features the selective acylation of primary alcohols and acetalation of a cis-vicinal diol, followed by a controlled per-O-benzylation step. Moreover, we describe the successful use of the pentasaccharide intermediate in the [5 + 5] synthesis of an aminoethyl aglycon-equipped decasaccharide, corresponding to a dimer of the basic repeating unit from the O-specific polysaccharide of Shigella flexneri 2a, a major cause of bacillary dysentery. Four analogues of the disaccharide acceptor were synthesized and evaluated to reach a larger repertoire of O-glucosylation patterns encountered among S. flexneri type-specific polysaccharides. New insights on the potential and limitations of planned chemo-enzymatic pathways in oligosaccharide synthesis are provided.

Adaptive Smith-Waterman residue match seeding for protein structural alignment.

The POLYFIT rigid-body algorithm for automated global pairwise and multiple protein structural alignment is presented. Smith-Waterman local alignment is used to establish a set of seed equivalences that are extended using Needleman-Wunsch dynamic programming techniques. Structural and functional interaction constraints provided by evolution are encoded as one-dimensional residue physical environment strings for alignment of highly structurally overlapped protein pairs. Local structure alignment of more distantly related pairs is carried out using rigid-body conformational matching of 15-residue fragments, with allowance made for less stringent conformational matching of metal-ion and small molecule ligand-contact, disulphide bridge, and cis-peptide correspondences. Protein structural plasticity is accommodated through the stepped adjustment of a single empirical distance parameter value in the calculation of the Smith-Waterman dynamic programming matrix. Structural overlap is used both as a measure of similarity and to assess alignment quality. Pairwise alignment accuracy has been benchmarked against that of 10 widely used aligners on the Sippl and Wiederstein set of difficult pairwise structure alignment problems, and more extensively against that of Matt, SALIGN, and MUSTANG in pairwise and multiple structural alignments of protein domains with low shared sequence identity in the SCOP-ASTRAL 40% compendium. The results demonstrate the advantages of POLYFIT over other aligners in the efficient and robust identification of matching seed residue positions in distantly related protein targets and in the generation of longer structurally overlapped alignment lengths. Superposition-based application areas include comparative modeling and protein and ligand design. POLYFIT is available on the Web server at http://polyfit.insa-toulouse.fr.

Influence of air exposure on structural isomers of silver nanoparticles.

Up to date, the influence of ambient air exposure on the energetics and stability of silver clusters has rarely been investigated and compared to clusters in vacuum. Silver clusters up to 3000 atoms in size, on an amorphous carbon film, have been exposed to ambient air and investigated by atomic-resolution imaging in the aberration-corrected Scanning Transmission Electron Microscope. Ordered structures comprise more than half the population, the rest are amorphous. Here, we show that the most common ordered isomer structures is the icosahedron. These results contrast with the published behaviour of silver clusters protected from atmospheric exposure, where the predominant ordered isomer is face-centred cubic. We propose that the formation of surface oxide or sulphide species resulting from air exposure can account for this deviation in stable isomer. This interpretation is consistent with density functional theory calculations based on silver nanoclusters, in the size range 147-201 atoms, on which methanethiol molecules are adsorbed. An understanding of the effects of ambient exposure on the atomic structure and therefore functional properties of nanoparticles is highly relevant to their real-world performance and applications.

Silica-induced electron loss of silver nanoparticles.

Despite the frequent use of silver nanoparticles (Ag NPs) embedded in materials for medical or optical applications, the effect of the matrix on the nanoparticle properties remains largely unknown. This study aims to shed light on the effect of an amorphous silica matrix on the structure and charge distribution of 55- and 147-atom silver nanoparticles by means of dispersion-corrected DFT calculations. Particular attention is paid to nanoparticle size and concentration effects and to the impact of the presence of native defects in the matrix. Covalent bonding between the silver nanoparticles and the matrix is found to occur at the interface. Such interface reconstruction involves the breaking of Si-O bonds, which systematically leads to the formation of Ag-Si bonds, and in some cases, to the formation of Ag-O ones. Interestingly, these interface reconstructions are accompanied by electron depletion of the nanoparticles, a substantial number of electrons being transferred from the two outer shells of the Ag NPs to the surrounding silica medium. The electrons lost by the nanoparticles are captured by the Si atoms involved in the interface bonds, but also, unexpectedly, by the undercoordinated silica defects that act as electron pumps and by the atoms of the silica network inside a few angströms spherical shell around the silver nanoparticle. The numbers of interface bonds and electrons transferred to the surrounding silica shell appear to be proportional to the surface area of the Ag NP. The electronic extension within silica goes beyond that attributable to the Ag NP spill-out. The presence of additional electrons in the matrix, especially on defects, is consistent with the experimental literature.

Dehydrogenation versus deprotonation of disaccharide molecules in vacuum: a thorough theoretical investigation.

Dehydrogenation and deprotonation of sucrose and trehalose molecules in vacuum is theoretically studied by using ab initio calculations in the framework of the density functional theory. The differences in the structural, electronic, energetic and vibrational properties of dehydrogenated and deprotonated molecules are discussed, depending on the site from which the hydrogen atom or the proton has been removed. The dehydrogenated molecules are found to be stable, regardless of which hydrogen atom is removed. This contrasts with the instability of the deprotonated molecules, where break-ups or structural reorganizations of the molecule are observed in 20-30% of the cases, but only when the hydrogen atom whose proton is removed was bonded to a carbon atom. Considering the stability and possible rearrangements of the hydrogen network of the deprotonated/dehydrogenated molecule, the formation of additional hydrogen-bridge bonds compared with the nominal molecule appears to be more pronounced for the deprotonated molecules than for the dehydrogenated ones. Moreover, our calculations show that the hydrogen-transfer energy barriers are usually larger for the deprotonated molecules than for the dehydrogenated ones. Finally, compared with the nominal molecule, the vibrational frequency spectrum is shifted to lower frequencies for both the dehydrogenated and the deprotonated molecules.

Importance of Defective and Nonsymmetric Structures in Silver Nanoparticles.

Scanning transmission electron microscopy experiments indicate that face-centered cubic (FCC) is the predominant ordered structure for Ag309 ± 7 nanoclusters, synthesized in vacuum. Historically, experiments do not present a consensus on the morphology at these sizes, whereas theoretical studies find the icosahedral symmetry for Ag309 and the decahedral shape for nearby sizes. We employ density functional theory calculations to rationalize these observations, considering both regular and defective Ag nanoparticles (281-321 atoms). The change of stability induced by the presence of defects, symmetry loss, and change of number of atoms is evaluated by the nanoparticle surface energy, which was measured previously. FCC and decahedral symmetries are found to be more favorable than icosahedral, consistent with our measurements of clusters protected from extended atmospheric exposure. In addition, an energy-free descriptor, surface atomic density, is proposed and qualitatively reproduces the surface energy data. Nonsymmetric and defective structures may be preferred over perfectly regular ones within a given size range.

Density-functional tight-binding: basic concepts and applications to molecules and clusters.

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu(100).

Saccharides, also commonly known as carbohydrates, are ubiquitous biomolecules, but little is known about their interaction with surfaces. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy now provides access to the molecular details of the surface assembly of this important class of bio-molecules. Among carbohydrates, the disaccharide trehalose is outstanding as it enables strong anhydrobiotic effects in biosystems. This ability is closely related to the observed polymorphism. In this work, we explore the self-assembly of trehalose on the Cu(100) surface. Molecular imaging reveals the details of the assembly properties in this reduced symmetry environment. Already at room temperature, we observe a variety of self-assembled motifs, in contrast to other disaccharides like e.g. sucrose. Using a multistage modeling approach, we rationalize the conformation of trehalose on the copper surface as well as the intermolecular interactions and the self-assembly behavior.

Theoretical study of specific hydrogen-bonding effects on the bridging P-OR bond strength of phosphate monoester dianions.

It has been proposed that the driving force for the initial phosphoryl transfer step of protein tyrosine phosphatases (PTPases) could be activation of the substrate ROPO32- by means of an enforced hydrogen-bonding interaction between an aspartic general acid and the bridging oxygen atom O (Zhang et al. Biochemistry 1995, 34, 16088-16096). The potential catalytic effect of this type of interaction, with regard to P-OR bond cleavage, was investigated computationally through simple model systems in which an efficient intramolecular hydrogen bond can take place between a H-bond donor group and the bridging oxygen atom of the dianionic phosphate. The dielectric effect of the environment (epsilon = 1, 4, and 78) was also explored. The results indicate that this interaction causes significant lengthenings of the scissile P-OR bond in all media but with more extreme effects observed in the low dielectric fields epsilon = 1 and epsilon = 4. It is interesting that, in all cases examined, this interaction actually contributes to stabilize the reactant state while causing its P-OR bond to lengthen. Overall, our results support the idea that this specific hydrogen-bonding situation might well be used by PTPases as an important driving force for promoting phosphoryl transfer reactions through highly dissociative transition states.