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.

A new theoretical model for hexagonal ice, Ih(d), from first principles investigations

Due to their great importance in science, technology, and the life sciences, water and ice have been extensively investigated over many years. In particular, hexagonal ice Ih has been of great interest since it is the most common form of ice, and several modifications, Ih(a), Ih(b) and Ih(c) are known, whose structural details are still under discussion. In this study, we present an alternative theoretical model, called Ih(d), for the hexagonal ice modification in space group P63/mmc (no. 194), based on first-principles calculations that have been performed using DFT-LDA, GGA-PBE, and hybrid B3LYP and PBE0 functionals.

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.

We rationalize the experimentally observed variety of trehalose assemblies on Cu(100) by modeling based on STM images and global optimization.

ZnO/ZnS (hetero)structures: ab initio investigations of polytypic behavior of mixed ZnO and ZnS compounds

The range of feasible ZnO/ZnS polytypes has been explored, predicting alternative structural arrangements compared with previously suggested or observed structural forms of ZnO/ZnS compounds, including bulk crystal structures, various nanostructures, heterostructures and heterojunctions. All calculations were performed ab initio using density functional theory–local density approximation and hybrid Heyd–Scuseria–Ernzerhof functionals. Specifically, pure ZnO and ZnS compounds and mixed ZnO1–x S x compounds (x = 0.20, 0.25, 0.33, 0.50, 0.60, 0.66 and 0.75) are investigated and a multitude of possible stable polytypes for ZnO/ZnS compounds creating new possibilities for synthesis of new materials with improved physical and chemical properties are identified.

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-β-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.

Prediction and clarification of structures of (bio)molecules on surfaces

The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.

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.

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.

Evolution of order in amorphous-to-crystalline phase transformation of MgF2

Structural disorder and distortion play a significant role in phase transformations. Experimentally, electron diffraction in the transmission electron microscope offers the ability to characterize disorderviathe pair distribution function (PDF) at high spatial resolution. In this work, energy-filteredin situelectron diffraction is applied to measure PDFs of different phases of MgF2from the amorphous deposit through metastable modifications to the thermodynamically stable phase. Despite the restriction of thick specimens resulting in multiple electron scattering, elaborate data analysis enabled experimental and molecular dynamics simulation data to be matched, thus allowing analysis of the evolution of short-range ordering. In particular, it is possible to explain the theoretically not predicted existence of a metastable phase by the presence of atomic disorder and distortion. The short-range ordering in the amorphous and crystalline phases is elucidated as three steps: (i) an initial amorphous phase exhibiting CaCl2-type short-range order which acts as a crystallization nucleus to guide the phase transformation to the metastable CaCl2-type phase and thus suppresses the direct appearance of the rutile-type phase; (ii) a metastable CaCl2-type phase containing short-range structural features of the stable rutile type; and (iii) the formation of a large volume fraction of disordered intergranular regions which stabilize the CaCl2-type phase. The structure evolution is described within the energy landscape concept.

Structure prediction of binary pernitride MN2 compounds (M=Ca, Sr, Ba, La, and Ti)

Metal-pernitride compounds belong to a class of chemical systems in which both the complex ions and the non-bonding electrons may play roles in the formation of their modified crystalline structures. To investigate this issue, the energy landscapes of pernitrides of metals with different maximum valence (M=Ca, Sr, Ba, La, and Ti) were globally explored on the ab initio level at standard and high pressures, thereby yielding possible (meta)stable modifications in these systems together with information on how the landscape changed as function of the valence of the metal cation. For all of the systems in which no compounds had been synthesized so far, we predicted the existence of kinetically stable modifications that should, in principle, be experimentally accessible. In particular, TiN2 should crystallize in a new structure type, TiN2-I.

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.

Finite-time thermodynamics and the gas-liquid phase transition

In this paper, we study the application of the concept of finite-time thermodynamics to first-order phase transitions. As an example, we investigate the transition from the gaseous to the liquid state by modeling the liquification of the gas in a finite time. In particular, we introduce, state, and solve an optimal control problem in which we aim at achieving the gas-liquid first-order phase transition through supersaturation within a fixed time in an optimal fashion, in the sense that the work required to supersaturate the gas, called excess work, is minimized by controlling the appropriate thermodynamic parameters. The resulting set of coupled nonlinear differential equations is then solved for three systems, nitrogen N2, oxygen O2, and water vapor H2O.

Possible Existence of Alkali Metal Orthocarbonates at High Pressure

We investigate the possible existence of crystalline alkali metal orthocarbonates, A(4)CO(4), where A=Li, Na, K, Rb, and Cs. We study the equilibrium between the possible modifications of the orthocarbonate A(4)CO(4) and the binary mixture of the possible modifications of the alkali oxide A(2)O and those of the alkali metal carbonate A(2)CO(3) as function of pressure. In all cases, the orthocarbonate should be stable at sufficiently high pressure ranging from 22-32 GPa (Rb(4)CO(4)) to 200-220 GPa (Cs(4)CO(4)).

Ab initioprediction of the low-temperature phase diagrams in the systems KBr–NaBr, KX–RbX, and LiX–RbX (X=Cl,Br)

The authors have calculated the low-temperature phase diagrams for the ternary alkali halides KBr-NaBr, KX-RbX, and LiX-RbX (X=Cl,Br) systems on the ab initio level without any recourse to experimental information. Via global exploration of the enthalpy landscapes for many different compositions in these systems, candidates for both ordered stoichiometric modifications and crystalline solid solution phases have been identified. Next, their free enthalpies were computed on ab initio level, and the respective low-temperature phase diagram has been derived. They find miscibility gaps in the systems KBr-NaBr and KX-RbX (X=Cl,Br), while in LiX-RbX (X=Cl,Br) only crystalline ordered phases should be present, in agreement with available experimental data. Furthermore, they predict several new thermodynamically stable and metastable phases in these systems.

Ab Initio Computation of the Low-Temperature Phase Diagrams of the Alkali Metal Iodide−Bromides: MBrxI1-x (0 ≤ x ≤ 1), Where M = Li, Na, K, Rb, or Cs

We have studied the low-temperature phase diagrams of the systems MBr-MI (M = Li, Na, K, Rb, or Cs) via global exploration of the enthalpy landscapes for many different compositions, leading to candidates for solid solution-like and ordered crystalline phases. For all of these candidates the free enthalpies are computed at the ab initio level, and the low-temperature phase diagrams of the five chemical systems are derived. We find not only the expected stable solid solution in the rocksalt structure type but also metastable solid solutions based on the CsCl type for the RbBr-RbI and CsCl-CsI systems. Furthermore, additional metastable structure candidates exhibiting ordered crystalline structures exist for several compositions. In the case of the LiBr-LiI system, the metastable solid solution based on the wurtzite type was generated, and the location of the miscibility gap was predicted.

The Route to the Structure Determination of Amorphous Solids: A Case Study of the Ceramic Si3B3N7

Si(3)B(3)N(7) is the parent compound of a new class of amorphous ceramics containing silicon, boron, nitrogen, and carbon that display a unique spectrum of properties. It consists of a random network in which the constituent elements are linked by predominantly covalent bonds. Similarly to quartz glass, the composition of amorphous Si(3)B(3)N(7) is virtually stoichiometric. As all three of its constituent elements can serve as the objects of various structural probes, Si(3)B(3)N(7) was selected as the basis of a systematic structural investigation, in which methods for the structure determination of solids without translational symmetry could be validated and improved. However, as the complete amorphous structure cannot be deduced from experimental data, these results must be complemented by computer simulations. Thus, five classes of structure models were generated and compared to experimental results. Only the models generated by following the actual synthesis route as closely as possible agreed well with the experimental data.

Ab initio computation of low-temperature phase diagrams exhibiting miscibility gaps

A new methodology for the computation of the low-temperature part of phase diagrams without recourse to any experimental information is presented. A central element is a procedure for deciding whether formation of crystalline solid solution phases can take place in the chemical system. Via global exploration of the enthalpy landscapes for many different compositions in the system, candidates for ordered stoichiometric and crystalline solid solution phases are identified. Next, their free enthalpies are computed at ab initio level and a low-temperature phase diagram is derived. As examples, the low-temperature phase diagrams for the ternary alkali halides NaCl/LiCl NaBr/LiBr and NaCl/KCl are presented.

Nonequilibrium Dynamics in Amorphous Si3B3N7

We present extensive numerical investigations of the structural relaxation dynamics of a realistic model of the amorphous high-temperature ceramic a-Si3B3N7, probing the mean-square displacement of the atoms, the bond survival probability, the average energy, the specific heat, and the two-point energy average. Combining the information from these different sources, we identify a transition temperature Tc approximately 2000 K below which the system is no longer ergodic and physical quantities observed over a time t(obs) show a systematic parametric dependence on the waiting time t(w), or age, elapsed after the quench. The aging dynamics "stiffens" as the system becomes older, which is similar to the behavior of highly idealized models such as Ising spin glasses and Lennard-Jones glasses.

Structure prediction of high-pressure phases for alkali metal sulfides

For a given chemical system we present a systematic approach to predict structures, which may exist at high pressure, by investigating the global enthalpy landscape. We combine global optimizations, based on empirical potential energy functions, and local optimizations (volume, cell shape, and atomic positions) on both Hartree-Fock and density functional theory level. We predict the existence of high-pressure phases for the alkali metal sulfides of the composition M2S (M = Li, Na, K, Rb, Cs), together with the transition pressures among these phases.

Computational Design and Prediction of Interesting Not-Yet-Synthesized Structures of Inorganic Materials by Using Building Unit Concepts

The computational design of new and interesting inorganic materials is still an ongoing challenge. The motivation of these efforts is to aid the often difficult task of crystal structure determination, to rationalize different but related structure types, or to help limit the domain of structures that are possible in a given system. Over the past decade, simulation methods have continuously evolved towards the prediction of new structures using minimal input information in terms of symmetry, cell parameters, or chemical composition. So far, this task of identifying candidate structures through an analysis of the energy landscape of chemical systems has been particularly successful for predominantly ionic systems with relatively small numbers of atoms or ions in the simulation cell. After an introductory section, the second section of this work presents the historical developments of such simulation methods in this area. The following sections of the work are dedicated to the introduction of the building unit concept in simulation methods: we present simulation approaches to structure prediction employing both primary (aggregate of atoms) and secondary (aggregate of coordination polyhedra) building units. While structure prediction with primary units is a straightforward extension of established approaches, the AASBU method (automated asssembly of secondary building units) focusses on the topology of network-based structures. This method explores the possible ways to assemble predefined inorganic building units in three-dimensional space, opening the way to the manipulation of very large building units (up to 84 atoms in this work). As illustrative examples we present the prediction of candidate structures for Li(4)CO(4), the identification of topological relationships within a family of metalphosphates, ULM-n and MIL-n, and finally the generation of new topologies by using predefined large building units such as a sodalite or a double-four-ring cage, for the prediction of new and interesting zeolite-type structures.