Effects of Hydration on the Conformational Behavior of Flexible Molecules with Two Charge Centers.

The hydration behavior of alkyl-diammonium di-cations and alkyl-dicarboxylate di-anions, of varying alkyl chain length, was examined using basin-hopping (BH) global optimization techniques. For every di-ion investigated, a conformational transition from linear to folded is observed at a critical hydration number, n*, specific to each di-ion. A stepwise hydration study has been undertaken for alkyl-dicarboxylate di-anions in finite water clusters containing 1-12 water molecules, and low-energy structures have been examined for larger water clusters. An even number of carbons in the alkyl chain gives rise to more stable conformations in unhydrated, implicitly solvated, and explicitly solvated conditions. This work provides valuable information on how the hydration of ammonium and carboxylate ions influence larger biomolecules' conformations.

Modelling free and oxide-supported nanoalloy catalysts: comparison of bulk-immiscible Pd-Ir and Au-Rh systems and influence of a TiO2 support.

The relative stabilities of different chemical arrangements of Pd-Ir and Au-Rh nanoalloys (and their pure metal equivalents) are studied, for a range of compositions, for fcc truncated octahedral 38- and 79-atom nanoparticles (NPs). For the 38-atom NPs, comparisons are made of pure and alloy NPs supported on a TiO2(110) slab. The relative energies of different chemical arrangements are found to be similar for Pd-Ir and Au-Rh nanoalloys, and depend on the cohesive and surface energies of the component metals. For supported nanoalloys on TiO2, the interaction with the surface is greater for Ir (Rh) than Pd (Au): most of the pure NPs and nanoalloys preferentially bind to the TiO2 surface in an edge-on configuration. When Au-Rh nanoalloys are bound to the surface through Au, the surface binding strength is lower than for the pure Au NP, while the Pd-surface interaction is found to be greater for Pd-Ir nanoalloys than for the pure Pd NP. However, alloying leads to very little difference in Ir-surface and Rh-surface binding strength. Comparing the relative stabilities of the TiO2-supported NPs, the results for Pd-Ir and Au-Rh nanoalloys are the same: supported Janus NPs, whose Ir (Rh) atoms bind to the TiO2 surface, bind most strongly to the surface, becoming closer in energy to the core-shell configurations (Ir@Pd and Rh@Au) which are favoured for the free particles.

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters.

We present putative global minima for the micro-hydrated sulfite SO32-(H2O) N and chlorate ClO3-(H2O) N systems in the range 3≤N≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤N≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems.This article is part of the theme issue 'Modern theoretical chemistry'.

Chemical bonding in initial building blocks of semiconductors: Geometrical structures and optical absorption spectra of isolated CdSe 2 + and Cd2 Se 2 + species.

We present the first experimental optical absorption spectra of isolated CdSe 2 + and Cd2 Se 2 + species in the photon energy range ℏω = 1.9-4.9 eV. We probe the optical response by measuring photodissociation cross sections and combine our results with time-dependent density functional theory and equation-of-motion coupled cluster calculations. Structural candidates for the time-dependent excited state calculations are generated by a density functional theory based genetic algorithm as a global geometry optimization tool. This approach allows us to determine the cluster geometries present in our molecular beams by a comparison of experimental spectra with theoretical predictions for putative global minimum candidates. For CdSe 2 + , an excellent agreement between the global minimum and the experimental results is presented. We identify the global minimum geometry of Cd2 Se 2 + as a trapezium, which is built up of a neutral Se2 and a cationic Cd 2 + unit, in contrast to what was previously proposed. We find an excellent overall agreement between experimental spectra and excited state calculations. We further study the influence of total and partial charges on the optical and geometric properties of Cd2Se2 and compare our findings to CdSe quantum dots and to bulk CdSe.

Engineering Bimetallic Ag-Cu Nanoalloys for Highly Efficient Oxygen Reduction Catalysts: A Guideline for Designing Ag-Based Electrocatalysts with Activity Comparable to Pt/C-20.

Development of highly active and stable Pt-free oxygen reduction reaction catalysts from earth-abundant elements remains a grand challenge for highly demanded metal-air batteries. Ag-based alloys have many advantages over platinum group catalysts due to their low cost, high stability, and acceptable oxygen reduction reaction (ORR) performance in alkaline solutions. Nevertheless, compared to commercial Pt/C-20%, their catalytic activity still cannot meet the demand of commercialization. In this study, a kind of catalysts screening strategy on Agx Cu100-x nanoalloys is reported, containing the surface modification method, studies of activity enhancement mechanism, and applied research on zinc-air batteries. The results exhibit that the role of selective dealloying (DE) or galvanic displacement (GD) is limited by the "parting limitation", and this "parting limitation" determines the surface topography, position of d-band center, and ORR performance of Agx Cu100-x alloys. The GD-Ag55 Cu45 and DE-Ag25 Cu75 catalysts alloys present excellent ORR performance that is comparable to Pt/C-20%. The relationship between electronic perturbation and specific activity demonstrates that positive shift of the d-band center (≈0.12 eV, relative to Ag) for GD-Ag55 Cu45 is beneficial for ORR, which is contrary to Pt-based alloys (negative shift, ≈0.1 eV). Meanwhile, extensive electrochemical and electronic structure characterization indicates that the high work function of GD-Ag55 Cu45 (4.8 eV) is the reason behind their excellent durability for zinc-air batteries.

Activity Trends of Binary Silver Alloy Nanocatalysts for Oxygen Reduction Reaction in Alkaline Media.

The electrocatalytic activity of Pt-based alloys exhibits a strong dependence on their electronic structures, but a relationship between electronic structure and oxygen reduction reaction (ORR) activity in Ag-based alloys is still not clear. Here, a vapor deposition based approach is reported for the preparation of Ag75 M25 (M = Cu, Co, Fe, and In) and Agx Cu100-x (x = 0, 25, 45, 50, 55, 75, 90, and 100) nanocatalysts and their electronic structures are determined by valence band spectra. The relationship of the d-band center and ORR activity exhibits volcano-shape behaviors, where the maximum catalytic activity is obtained for Ag75 Cu25 alloys. The ORR enhancement of Ag75 Cu25 alloys originates from the 0.12 eV upshift in d-band center relative to pure Ag, which is different from the downshift in the d-band center in Pt-based alloys. The activity trend for these Ag75 M25 alloys is in the order of Ag75 Cu25 > Ag75 Fe25 > Ag75 Co25 . These results provide an insight to understand the activity and stability enhancement of Ag75 Cu25 and Ag50 Cu50 catalysts by alloying.

DFT study of the structure, chemical ordering and molecular adsorption of Pd-Ir nanoalloys.

The structures and surface adsorption sites of Pd-Ir nanoalloys are crucial to the understanding of their catalytic performance because they can affect the activity and selectivity of nanocatalysts. In this article, density functional theory (DFT) calculations are performed on bare Pd-Ir nanoalloys to systematically explore their stability and chemical ordering properties, before studying the adsorption of CO on the nanoalloys. First, the structural stability of 38-atom and 79-atom truncated octahedral (TO) Pd-Ir nanoalloys are investigated. Then the adsorption properties and preferred adsorption sites of CO on 38-atom Pd-Ir nanoalloys are considered. The PdshellIrcore structure, which has the lowest energy of all the considered isomers, exhibits the highest structural stability, while the PdcoreIrshell configuration is the least stable. In addition, the adsorption strength of CO on Ir atoms is found to be greater than on Pd for Pd-Ir nanoclusters. The preferred adsorption sites of CO on pure Pd and Ir clusters are in agreement with calculations and experiments on extended Pd and Ir surfaces. In addition, d-band center and charge effects on CO adsorption strength on Pd-Ir nanoalloys are analyzed by comparison with pure clusters. The study provides a valuable theoretical insight into catalytically active Pd-Ir nanoalloys.

Global optimization of small bimetallic Pd-Co binary nanoalloy clusters: a genetic algorithm approach at the DFT level.

The global optimisation of small bimetallic PdCo binary nanoalloys are systematically investigated using the Birmingham Cluster Genetic Algorithm (BCGA). The effect of size and composition on the structures, stability, magnetic and electronic properties including the binding energies, second finite difference energies and mixing energies of Pd-Co binary nanoalloys are discussed. A detailed analysis of Pd-Co structural motifs and segregation effects is also presented. The maximal mixing energy corresponds to Pd atom compositions for which the number of mixed Pd-Co bonds is maximised. Global minimum clusters are distinguished from transition states by vibrational frequency analysis. HOMO-LUMO gap, electric dipole moment and vibrational frequency analyses are made to enable correlation with future experiments.

DFT global optimisation of gas-phase and MgO-supported sub-nanometre AuPd clusters.

The Birmingham Parallel Genetic Algorithm (BPGA) has been adopted for the global optimization of free and MgO(100)-supported Pd, Au and AuPd nanocluster structures, over the size range N = 4-10. Structures were evaluated directly using density functional theory, which has allowed the identification of Pd, Au and AuPd global minima. The energetics, structures, and tendency of segregation have been evaluated by different stability criteria such as binding energy, excess energy, second difference in energy, and adsorption energy. The ability of the approach in searching for putative global minimum has been assessed against a systematic homotop search method, which shows a high degree of success.

A comparative study of AumRhn (4 ≤ m + n ≤ 6) clusters in the gas phase versus those deposited on (100) MgO.

A comparative theoretical study has been performed of the gas phase and deposited AumRhn (4 ≤ m + n ≤ 6) clusters. The combined use of a genetic algorithm and Density Functional Theory (DFT) calculations allows us to explore the potential energy surface and, therefore, find efficiently and automatically the global minimum configuration for each composition. Our results show interesting effects on the geometries of the clusters on deposition. This occurs because the rhodium atoms (electronically) prefer to be in contact with the MgO surface, sometimes promoting planar clusters to become three-dimensional when deposited, and three-dimensional clusters in the gas phase to become two-dimensional. Together with the change in geometries, the magnetic moment is reduced from the gas phase, as the electrons rearrange themselves when the cluster interacts with the substrate.

Isomers and Energy Landscapes of Perchlorate-Water Clusters and a Comparison to Pure Water and Sulfate-Water Clusters.

Hydrated ions are crucially important in a wide array of environments, from biology to the atmosphere, and the presence and concentration of ions in a system can drastically alter its behavior. One way in which ions can affect systems is in their interactions with proteins. The Hofmeister series ranks ions by their ability to salt-out proteins, with kosmotropes, such as sulfate, increasing their stability and chaotropes, such as perchlorate, decreasing their stability. We study hydrated perchlorate clusters as they are strongly chaotropic and thus exhibit different properties than sulfate. In this study we simulate small hydrated perchlorate clusters using a basin-hopping geometry optimization search with empirical potentials. We compare topological features of these clusters to data from both computational and experimental studies of hydrated sulfate ions and draw some conclusions about ion effects in the Hofmeister series. We observe a patterning conferred to the water molecules within the cluster by the presence of the perchlorate ion and compare the magnitude of this effect to that observed in previous studies involving sulfate. We also investigate the influence of the overall ionic charge on the low-energy structures adopted by these clusters.

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.

Theoretical study of the structures and chemical ordering of cobalt-palladium nanoclusters.

Global optimization of 1 : 1 compositions of (Co-Pd)N/2 up to N = 150 and all compositions of 34- and 38-atom binary clusters has been performed using a genetic algorithm, coupled with the Gupta empirical potential to model interatomic interactions. An ab initio approach based on density functional theory (DFT) has been used to reoptimize the "putative" global minimum GM structures for 1 : 1 compositions of (Co-Pd)N/2 up to N = 50 and all compositions of 34- and 38-atom binary clusters. A detailed analysis of Co-Pd structural motifs and segregation effects is presented. Gupta potential calculations on Co-Pd clusters with 1 : 1 compositions have shown that the putative GM has Co(core)Pd(shell) segregation. A variety of structural motifs is observed for 34- and 38-atom CoPd clusters. From the excess energy analysis at Gupta and DFT level, we find different stable compositions for 34- and 38-atom CoPd clusters. In addition to this, low energy isomers of 38-atom (for the composition range Co25Pd13-Co13Pd25) clusters are also investigated at DFT level and the excess energies of Gupta and DFT levels are compared.

The Effect of Dispersion Correction on the Adsorption of CO on Metallic Nanoparticles.

The effect of dispersion corrections at a range of theory levels on the chemisorption properties of metallic nanoparticles is presented. The site preference for CO on Pt, Au, Pd, and Ir nanoparticles is determined for two geometries, the 38-atom truncated octahedron and the 55-atom icosahedron using density functional theory (DFT). The effects of Grimme's DFT-D2 and DFT-D3 corrections and the optPBE vdW-DF on the site preference of CO is then compared to the "standard" DFT results. Functional behavior is shown to depend not only on the metal but also on the geometry of the nanoparticle with significant effects seen for Pt and Au. There are both qualitative and quantitative differences between the functionals, with significant energetic differences in the chemical ordering of inequivalent sites and adsorption energies varying by up to 1.6 eV.

Chiral effects on helicity studied via the energy landscape of short (D, L)-alanine peptides.

The homochirality of natural amino acids facilitates the formation of regular secondary structures such as α-helices and ß-sheets. Here, we study the relationship between chirality and backbone structure for the example of hexa-alanine. The most stable stereoisomers are identified through global optimisation. Further, the energy landscape, a database of connected low-energy local minima and transition points, is constructed for various neutral and zwitterionic stereoisomers of hexa-alanine. Three order parameters for partial helicity are applied and metric disconnectivity graphs are presented with partial helicity as a metric. We also apply the Zimm-Bragg model to derive average partial helicities for Ace-(L-Ala)6-NHMe, Ace-(D-Ala-L-Ala)3-NHMe, and Ace-(L-Ala)3-(D-Ala)3-NHMe from the database of local minima and compare with previous studies.

The Nature of Bonding between Argon and Mixed Gold-Silver Trimers.

The controversial nature of chemical bonding between noble gases and noble metals is addressed. Experimental evidence of exceptionally strong Au-Ar bonds in Ar complexes of mixed Au-Ag trimers is presented. IR spectra reveal an enormous influence of the attached Ar atoms on vibrational modes, particularly in Au-rich trimers, where Ar atoms are heavily involved owing to a relativistically enhanced covalency. In Ag-rich trimers, vibrational transitions of the metal framework predominate, indicating a pure electrostatic character of the Ag-Ar bonds. The experimental findings are analyzed by means of DFT calculations, which show how the relativistic differences between Au and Ag are manifested in stronger Au-Ar binding energies. Because of the ability to vary composition and charge distribution, the trimers serve as ideal model systems to study the chemical nature of the bonding of noble gases to closed-shell systems containing gold.

Visualizing energy landscapes with metric disconnectivity graphs.

The visualization of multidimensional energy landscapes is important, providing insight into the kinetics and thermodynamics of a system, as well the range of structures a system can adopt. It is, however, highly nontrivial, with the number of dimensions required for a faithful reproduction of the landscape far higher than can be represented in two or three dimensions. Metric disconnectivity graphs provide a possible solution, incorporating the landscape connectivity information present in disconnectivity graphs with structural information in the form of a metric. In this study, we present a new software package, PyConnect, which is capable of producing both disconnectivity graphs and metric disconnectivity graphs in two or three dimensions. We present as a test case the analysis of the 69-bead BLN coarse-grained model protein and show that, by choosing appropriate order parameters, metric disconnectivity graphs can resolve correlations between structural features on the energy landscape with the landscapes energetic and kinetic properties.

Modeling nanoscale inhomogeneities for quantitative HAADF STEM imaging.

High-angle annular dark-field scanning transmission electron microscopy in conjunction with image simulation is an important tool to determine the structure of nanomaterials. We show that molecular dynamics calculations can be combined with multislice image simulations to account for the large effects of surface-enhanced thermal vibrations and structural relaxation on image intensities. Application to a catalytically important gold cluster shows that the image intensity is sensitive to these surface dominated effects with important implications for three-dimensional structural characterizations.

A theoretical study of the structures and optical spectra of helical copper-silver clusters.

The structures and optical response of helical clusters ("Bernal spirals") with compositions Ag12Cu1(+) and Ag1Cu12(+) are calculated within Kohn-Sham density functional theory and the configuration interaction singles variant of time dependent density functional theory. The effects of dopant position within the cluster on the vertical excitation spectrum are investigated according to the underlying electronic structure of the major transitions. The roles of symmetry and geometry are investigated by calculating the optical response of helical, icosahedral and nanorod-like clusters of Ag13(+), finding local structure to be significant in driving the resultant optical response at the subnanometre scale. Further, it is noted that helical clusters have optical properties which are quite distinct from those of nanorods of similar dimensions. The effect of multiple doping is studied by introducing copper atoms into the centre of the silver helix, over the composition range Ag13(+) to Ag6Cu7(+). There is a complex variation of the major plasmon-like peak over this range, attributed to subtle variations in the influence of the copper 3d band on the excitations and charge transfer for different sites within the cluster. This work suggests that coinage metal nanohelices have unusual, tunable electronic properties, which in addition to their inherent chirality makes them interesting systems to study for chiral catalysis and optoelectronics.

DFT studies of oxygen dissociation on the 116-atom platinum truncated octahedron particle.

Density functional theory calculations are performed to investigate oxygen dissociation on 116-atom truncated octahedron platinum particles. This work builds on results presented previously [Jennings et al., Nanoscale, 2014, 6, 1153], where it was shown that shell flexibility played an important role in facilitating fast oxygen dissociation. In this study, through investigation of the larger particle size, it is shown that oxygen dissociation on the (111) facet of pure platinum species is still aided by shell flexibility at larger sizes. Only the hollow sites close to the edges of the (111) facet mediate oxygen dissociation; oxygen is bound too weakly at other hollow sites for dissociation to occur. Further studies are performed on the (100) facet, which is larger for the Pt116 particle than for either the Pt38 or Pt79 ones. Much higher dissociation barriers are found on the (100) facet compared to the (111) facet, where the bridge sites are favourable for oxygen dissociation.