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.

Structure prediction in low dimensions: concepts, issues and examples.

Structure prediction of stable and metastable polymorphs of chemical systems in low dimensions has become an important field, since materials that are patterned on the nano-scale are of increasing importance in modern technological applications. While many techniques for the prediction of crystalline structures in three dimensions or of small clusters of atoms have been developed over the past three decades, dealing with low-dimensional systems-ideal one-dimensional and two-dimensional systems, quasi-one-dimensional and quasi-two-dimensional systems, as well as low-dimensional composite systems-poses its own challenges that need to be addressed when developing a systematic methodology for the determination of low-dimensional polymorphs that are suitable for practical applications. Quite generally, the search algorithms that had been developed for three-dimensional systems need to be adjusted when being applied to low-dimensional systems with their own specific constraints; in particular, the embedding of the (quasi-)one-dimensional/two-dimensional system in three dimensions and the influence of stabilizing substrates need to be taken into account, both on a technical and a conceptual level. This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

Synthesis, Characterization, and Electronic Properties of ZnO/ZnS Core/Shell Nanostructures Investigated Using a Multidisciplinary Approach.

ZnO/ZnS core/shell nanostructures, which are studied for diverse possible applications, ranging from semiconductors, photovoltaics, and light-emitting diodes (LED), to solar cells, infrared detectors, and thermoelectrics, were synthesized and characterized by XRD, HR-(S)TEM, and analytical TEM (EDX and EELS). Moreover, band-gap measurements of the ZnO/ZnS core/shell nanostructures have been performed using UV/Vis DRS. The experimental results were combined with theoretical modeling of ZnO/ZnS (hetero)structures and band structure calculations for ZnO/ZnS systems, yielding more insights into the properties of the nanoparticles. The ab initio calculations were performed using hybrid PBE0 and HSE06 functionals. The synthesized and characterized ZnO/ZnS core/shell materials show a unique three-phase composition, where the ZnO phase is dominant in the core region and, interestingly, the auxiliary ZnS compound occurs in two phases as wurtzite and sphalerite in the shell region. Moreover, theoretical ab initio calculations show advanced semiconducting properties and possible band-gap tuning in such ZnO/ZnS structures.

Short-Range Structural Correlations in Amorphous 2D Polymers.

Many 2D covalent polymers synthesized as single layers on surfaces show inherent disorder, expressed for example in their ring-size distribution. Systems which are expected to form the thermodynamically favored hexagonal lattice usually deviate from crystallinity and include high numbers of pentagons, heptagons, and rings of other sizes. The amorphous structure of two different covalent polymers in real space using scanning tunneling microscopy is investigated. Molecular dynamics simulations are employed to extract additional information. We show that short-range correlations exist in the structure of one polymer, i. e. that polygons are not tessellating the surface randomly but that ring neighborhoods have preferential compositions. The correlation is dictated by the energy of formation of the ring neighborhoods.

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.

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.

The threshold algorithm: Description of the methodology and new developments.

Understanding the dynamics of complex systems requires the investigation of their energy landscape. In particular, the flow of probability on such landscapes is a central feature in visualizing the time evolution of complex systems. To obtain such flows, and the concomitant stable states of the systems and the generalized barriers among them, the threshold algorithm has been developed. Here, we describe the methodology of this approach starting from the fundamental concepts in complex energy landscapes and present recent new developments, the threshold-minimization algorithm and the molecular dynamics threshold algorithm. For applications of these new algorithms, we draw on landscape studies of three disaccharide molecules: lactose, maltose, and sucrose.

A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide.

We present a scheme, called the threshold-minimization method, for globally exploring the energy landscapes of small systems of biomolecular interest where typical exploration moves always require a certain degree of subsequent structural relaxation in order to be efficient, e.g., systems containing small or large circular carbon chains such as cyclic peptides or carbohydrates. We show that using this threshold-minimization method we can not only reproduce the global minimum and relevant local minima but also overcome energetic barriers associated with different types of isomerism for the example of a cyclic peptide, cyclo-(Gly)4. We then apply the new method to the disaccharide α-d-glucopyranose-1-2-ß-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.

Energy landscape exploration of sub-nanometre copper-silver clusters.

The energy landscapes of sub-nanometre bimetallic coinage metal clusters are explored with the Threshold Algorithm coupled with the Birmingham Cluster Genetic Algorithm. Global and energetically low-lying minima along with their permutational isomers are located for the Cu(4)Ag(4) cluster with the Gupta potential and density functional theory (DFT). Statistical tools are employed to map the connectivity of the energy landscape and the growth of structural basins, while the thermodynamics of interconversion are probed, based on probability flows between minima. Asymmetric statistical weights are found for pathways across dividing states between stable geometries, while basin volumes are observed to grow independently of the depth of the minimum. The DFT landscape is found to exhibit significantly more frustration than that of the Gupta potential, including several open, pseudo-planar geometries which are energetically competitive with the global minimum. The differences in local minima and their transition barriers between the two levels of theory indicate the importance of explicit electronic structure for even simple, closed shell clusters.

Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.

We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.

How can Databases assist with the Prediction of Chemical Compounds?

An overview is given on the ways databases can be employed to aid in the prediction of chemical compounds, in particular inorganic crystalline compounds. Methods currently employed and possible future approaches are discussed.

Sterically active electron pairs in lead sulfide? An investigation of the electronic and vibrational properties of PbS in the transition region between the rock salt and the α-GeTe-type modifications.

Recently, we have investigated the energy landscape of PbS for many different pressures on the ab initio level by using Hartree-Fock and density functional theory to globally search for possible thermodynamically stable and metastable structures. The perhaps most fascinating observation was that besides the experimentally known modification exhibiting the rock salt structure a second minimum exists close-by on the landscape showing the low-temperature α-GeTe-type structure. In the present study, we investigate the possible reasons for the existence of this metastable modification; in particular we address the question, whether the α-GeTe-type modification might be stabilized (and conversely the rock salt modification destabilized) by steric effects of the non-bonding electron pair.

Tetrahelix conformations and transformation pathways in Pt1Pd12 clusters.

The threshold method is used to explore the potential energy surface of the Pt(1)Pd(12) bimetallic cluster, defined by the Gupta semiempirical potential. A set of helical structures, which follow a Bernal tetrahelix pattern, correspond to local minima for the Pt(1)Pd(12) cluster, characterizing the region of the energy landscape where these structures are present. Both right-handed and left-handed chiral forms were discovered in our searches. Energetic and structural details of each of the tetrahelices are reported as well as the corresponding transition probabilities between these structures and with respect to the icosahedron-shaped global minimum structure via a disconnectivity graph analysis.

Theoretical and experimental exploration of the energy landscape of the quasi-binary cesium chloride/lithium chloride system.

As a case study, the energy landscape of the cesium chloride/lithium chloride system was investigated by combining theoretical and experimental methods. Global optimization for many compositions of this quasi-binary system gave candidates for possible modifications that constitute promising targets for subsequent syntheses based on solid-state reactions. Owing to the synergetic and complementary nature of the computational and experimental approaches, a substantially better efficiency of exploration was achieved. Several new phases were found in this system, for the compositions CsLiCl(2) and CsLi(2)Cl(3), and their thermodynamic ranking with respect to the already-known phases was clarified. In particular, the new CsLiCl(2) modification was shown to be the low-temperature phase, whilst the already-known modification for this composition corresponded to a high-temperature phase. Based on these results, an improved cesium chloride/lithium chloride phase diagram was derived, and this approach points the way to more rational and more efficient solid-state synthesis.

Addressing chemical diversity by employing the energy landscape concept.

Exploring the structural diversity of a chemical system rests on three pillars. First, there is the global exploration of its energy landscape that allows one to predict which crystalline modifications can exist in a chemical system at a given temperature and pressure. Next, there is the development of new synthesis methods in solid-state chemistry, which require only very low activation energies such that even metastable modifications corresponding, for example, to minima on the landscape surrounded by low barriers can be realized. Finally, there is the theoretical design of optimal synthesis routes, again based on the study of the system's energy landscape. In this paper the energy landscape approach to the prediction of stable and metastable compounds as a function of temperature and pressure is presented, with a particular focus on possible phase transitions. Furthermore, several examples are presented, where such predicted compounds were subsequently successfully synthesized, often employing a newly developed synthesis method, low-temperature atom-beam deposition.