Cluster Geometry Research Articles

Green Emissive Copper(I) Coordination Polymer Supported by the Diethylpyridylphosphine Ligand as a Luminescent Sensor for Overheating Processes.

Tertiary diethylpyridylphosphine was synthesized by the reaction of pyridylphosphine with bromoethane in a suberbasic medium. The reaction of phosphine with the copper(I) iodide led to the formation of a copper(I) coordination polymer, which, according to the X-ray diffraction data, has an intermediate structure with a copper-halide core between the octahedral and stairstep geometries of the Cu4I4 clusters. The obtained coordination polymer exhibits a green emission in the solid state, which is caused by the 3(M+X)LCT transitions. The heating up of the copper(I) coordination polymer to 138.5 °C results in its monomerization and the formation of a new solid-state phase. The new phase exhibits a red emission, with the emission band maximum at 725 nm. According to the experimental data and quantum chemical computations, it was concluded that depolymerization probably leads to a complex that is formed with the octahedral structure of the copper-halide core. The resulting solid-state phase can be backward-converted to the polymer phase via recrystallization from the acetone or DMF. Therefore, the obtained coordination polymer can be considered a sensor or detector for the overheating of processes that should be maintained at temperatures below 138 °C (e.g., engines, boiling liquids, solar heat systems, etc.).

Substituent effects on the [1-closo-CB9H10]− anion geometry: experimental and DFT studies

Five new structures of the [closo-1-CB9H10]− anion substituted at the apical position(s) are reported. C(1) and B(10) apical substituents affect the {closo-1-CB9} cluster geometry in different ways, and the effect correlates with the Hammett substituent parameters.

Structural stability and lithium storage property of Sn clusters (x ≤ 6) deposited on graphene based on first-principles calculation

First-principles calculation based on the density functional theory are performed to investigate the structural stability and lithium (Li) storage property of tin (Sn) clusters (i.e., Snx; where x is the number of Sn atoms) deposited on a graphene substrate, i.e., Snx/Gr (x ≤ 6). The latter is a promising candidate for anode material in a lithium-ion battery (LIB). The geometry and electronic properties of Snx clusters on graphene are systematically studied. Our results confirm that Snx clusters (x ≤ 4) tend to be deposited on graphene in a two-dimensional configuration parallel to the graphene plane, while Snx clusters (x ≥ 5) are usually deposited on graphene in a three-dimensional configuration. With the increase of the number of Sn atoms x, the charge transfer between Snx clusters and graphene decreases, and the interface binding between them weakens, resulting in a decrease in the structural stability of the Snx/Gr compound system. Furthermore, the adsorption energy of Li atoms on the Snx/Gr system are further calculated to examine the lithium storage property of Snx/Gr composites. Li atoms are preferentially stored on graphene and then adsorbed around Snx clusters. The complex synergistic effect of Snx clusters and graphene enhances the structural stability of Li adsorption. However, the structural stability of yLi-Snx/Gr system decreases with the increase of the number of Li atoms.

Redox-active carborane clusters in bond activation chemistry and ligand design.

Icosahedral closo-dodecaboranes have the ability to accept two electrons, opening into a dianionic nido-cluster. This transformation can be utilized to store electrons, drive bond activation, or alter coordination to metal cations. In this feature article, we present cases for each of these applications, wherein the redox activity of carborane facilitates the generation of unique products. We highlight the effects of exohedral substituents on reactivity and the stability of the products through conjugation between the cluster and exohedral substituents. Futher, the utilization of the redox properties and geometry of carborane clusters in the ligand design is detailed, both in the stabilization of low-valent complexes and in the tuning of ligand geometry.

STRUCTURE AND VIBRATIONS OF FREE NIN CLUSTERS (N < 20)

The binding energy, equilibrium geometry, and vibration frequencies of small free Nin clusters (n < 20) were calculated using interatomic interaction potentials calculated in an embedded atom method. Calculations of the energy parameter of stability АЕ2 and dissociation energy showed that the most energetically stable clusters are those with the magic numbers of atoms n = 4, 6, 13, 19. Calculations of atomic vibrations revealed that the dynamic contribution to the stability of clusters is determined by the minimum vibration frequency, whose extreme values fall on clusters with the magic numbers of atoms n = 4, 6, 13, 19. The maximum vibration frequency varies nonmonotonically and for clusters with n < 19 it has no clear extreme values. This result is consistent with available experimental data on stable structures of small and medium-sized metal clusters.

Nanostructured supramolecular networks from self-assembled diamondoid molecules under ultracold conditions.

Diamondoid molecules and their derivatives have attracted attention as fascinating building blocks for advanced functional materials. Depending on the balance between hydrogen bonds and London dispersion interactions, they can self-organize in different cluster structures with functional groups tailored for various applications. Here, we present a new approach to supramolecular aggregation where self-assembly of diamondoid acids and alcohols in the ultracold environment of superfluid helium nanodroplets (HNDs) was analyzed by a combination of time-of-flight mass spectrometry and computational tools. Experimentally observed magic numbers of the assembled cluster sizes were successfully identified and computed cluster structures gave valuable insights into a different conglomeration mode when compared to previously explored less-polar diamondoid derivatives. We have confirmed that functional groups acting as good hydrogen bond donors completely take over the self-organization process, resulting in fascinating pair-wise or cyclic supramolecular assemblies. Particularly noteworthy is that mono- and bis-substituted diamondoid derivatives of both series engage in completely different modes of action, which is reflected in differing non-covalent cluster geometries. Additionally, formed cyclic clusters with a polar cavity in the center and a non-polar diamondoid outer layer can be of high interest in porous material design and provide insights into the structural requirements needed to produce bulk materials with desired properties.

Mechanistic understanding of N2 activation: a comparison of unsupported and supported Ru catalysts.

N2 dissociative adsorption is commonly the rate-determining step in thermal ammonia synthesis. Herein, we performed density functional theory (DFT) calculations to understand the N2 dissociation mechanism on models of unsupported Ru(0001) terraces, Ru B5 sites, and polar MgO(111)-supported Ru8 cluster mimicking a B5 site geometry, denoted (Ru8(B5-like)/MgO(111)). The activation energy of N2 dissociative adsorption on the Ru8(B5-like)/MgO(111) model (Ea = 0.33 eV) is much lower than that on the unsupported Ru(0001) terrace (Ea = 1.74 eV) and Ru B5 (Ea = 0.62 eV) models. The lower N2 dissociation barrier on Ru B5 sites is facilitated by the enhanced σ donation and π* back-donation between N2(σ, π*) and Ru(d) orbitals resulting in the stronger activation of the molecular side-on N2* dissociation precursor. The Ru8(B5-like)/MgO(111) also exhibits enhanced σ donation because of the B5-like cluster geometry. Furthermore, the Ru cluster of the bare Ru8(B5-like)/MgO(111) model is positively charged. This induced an unusual π donation from N2(π) to Ru(d) orbitals as revealed by analyses of the density of states and partial charge densities. The combined σ and π donation resulted in an increased synergistic π* back-donation. The total interactions between N2(σ, π, π*) and Ru(d) resulted in an overall electron transfer to the adsorbed N2 from the Ru atoms in the B5-like site with no direct involvement of the MgO(111) substrate. Analyses of bond stretching vibrations and bond lengths show that the N2(σ, π, π*) and Ru(d) interactions lead to a weaker N-N bond and stronger Ru-N bonds. These correspond to a lower barrier of N2 dissociation on the Ru8(B5-like)/MgO(111) model, where the highest red-shift of N-N vibration and the longest N-N bond length were observed after side-on N2* adsorption. These results demonstrate that an electron-deficient Ru catalyst are not always inhibited from donating electrons to adsorbed N2. Rather, this study shows that the electron deficiency of Ru can promote π* back-donation and N2 activation. These new insights may therefore open new avenues to design supported Ru catalysts for nitrogen activation.

Revealing the governing factors for long-term radiation damage evolution in multi-principal elemental alloys through atomistically-informed cluster dynamics

Multi-principal elemental alloys (MPEAs) exhibit unusual mechanical properties and irradiation resistance. It has been reported that the irradiation tolerance of MPEAs originates from the long-term defect evolution stage rather than the ballistic collision phase. However, understanding the long-term evolution of MPEAs is exceptionally challenging due to intrinsic chemical disorder. In this work, we apply atomistically-informed cluster dynamics to study defect evolution in MPEAs for the first time, which enables us to elucidate the critical features responsible for the irradiation performance of MPEAs. With suitable irradiation parameters, our obtained cluster size distributions are in good agreement with experiments. We further discuss the influences of defect migration energy heterogeneity, cluster geometry, and temperature on the produced defect cluster forms. Our results suggest that the small clusters during the collision phase in MPEAs suppress the formation of large-sized defect clusters in the long term. Contrary to the common belief, a broader migration energy distribution due to chemical disorder cannot reduce the maximal defect cluster size but increase the proportion of small clusters. Our results thus reveal that the major role of chemical complexity in MPEAs is to modify the growth mechanism of clusters by promoting small cluster formation and suppressing overall defect diffusivities.

Phosphine-Stabilized Hidden Ground States in Gold Clusters Investigated via a Aun(PH3)m Database.

Nanoclusters are promising materials for catalysis and sensing due to their large surface areas and unique electronic structures which can be tailored through composition, geometry, and chemistry. However, relationships correlating synthesis parameters directly to outcomes are limited. While previous computational studies have mapped the potential energy surface of specific systems of bare nanoclusters by generating and calculating the energies of reasonable structures, it is known that environmental ions and ligands crucially impact the final shape and size. In this work, phosphine-stabilized gold is considered as a test system and DFT calculations are performed for clusters with and without ligands, producing a database containing >10000 structures for Aun(PH3)m (n ≤ 12). We find that the ligation of phosphines affects the thermodynamic stability, bonding, and electronic structure of Au nanoclusters, specifically such that "hidden" ground state cluster geometries are stabilized that are dynamically unstable in the pure gold system. Further, the addition of phosphine introduces steric effects that induce a transition from planar to nonplanar structures at 4-5 Au atoms rather than up to 13-14 Au atoms, as previously predicted for bare clusters. This work highlights the importance of considering the ligand environment in the prediction of nanocluster morphology and functionality, which adds complexity as well as a rich opportunity for tunability.

Preliminary verification of multi-group cross-sections generation and locally heterogeneous transport calculation using OpenMC with CEFR start-up tests benchmark

The multi-group (MG) Monte-Carlo (MC) scheme is a hybrid method based on MC solvers and deterministic strategies. This paper focuses on the study of MG schemes for the analysis of fast reactors. The MG scheme in this paper is composed of two steps. In the cross-section generation step, the OpenMC continuous-energy (CE) mode is used with 2D or 3D high-fidelity cluster geometry. In the core calculation step, both homogeneous and locally heterogeneous core models are computed using OpenMC in multi-group mode. The MG schemes are applied and validated in the China Experimental Fast Reactor (CEFR) start-up tests and compared to the CE scheme. The results show an overprediction of core criticality. The locally heterogeneous scheme improves significantly the accuracy in predicting control rod worth. Moreover, synthesizing the results from deterministic code, the locally heterogeneous scheme exhibits a stable performance across different codes, core sizes, and control rod designs. The locally heterogeneous core model with cross-sections generated from the 3D cluster has a good ability in the prediction of feedback coefficients including the sodium void reactivity, temperature reactivity, and subassembly swap reactivity. The computation speed of the locally heterogeneous MG scheme is almost the same as the homogenous MG scheme and its core calculation uses only 7.2% computation time of the reference CE scheme.

Insights of hydrogen adsorption and dissociation on Ni doped Mg4 clusters: A DFT study

Hydrogen adsorption and dissociation on Mg4 and NiMg3 clusters are studied using DFT method. Physisorption of hydrogen molecule on Mg4 is extremely weak, which however significantly strengthens on Ni doped Mg4 cluster. Following the physisorption mechanism, NiMg3 cluster can adsorb three H2 molecules at most and the cluster geometry plays an important role here. On the other hand, physisorption followed by chemisorption facilitates the growth of hydrogen adsorption process in both Mg4 and NiMg3 clusters. Further, dissociation and diffusion of H2 become more favourable on Ni doped Mg4 cluster resulting in a larger number of H2 adsorbed on NiMg3 compared to that on Mg4. NiMg3 is found to exhibit practically attainable H2 desorption energies lower than those for bare Mg4 clusters.

Dimethylformamide clusters: non-covalent bondings, structures and temperature-dependence

Thermodynamics properties as well as infrared spectra of liquids can be determined using the quantum cluster equilibrium (QCE) theory. The QCE theory requires the knowledge of the structures of the clusters formed by the solvent molecules. In prelude to this determination, in this work, we studied the non-covalent bondings, the structures and the temperature-dependence of the clusters of dimethylformamide (DMF) from dimer to tetramer. To perform this study, we used classical molecular dynamics to sample initial geometries of DMF clusters. Then, optimisation of the geometries is carried out at the MP2/aug-cc-pVDZ level of theory. Besides, we carried out a quantum theory of atoms in molecule analysis. The results show that the structures of the DMF dimer exhibit a stacking configuration, and mainly stabilised by CH··· O hydrogen bondings. For the DMF trimer and DMF tetramer, the structures exhibit an amorphous behaviour. Moreover, it has been found that the CH··· O hydrogen bondings are the main non-covalent bondings in DMF clusters. CH··· C, CH··· N, N··· O, N··· C, C··· O and H··· H bonding interactions are also located in the studied DMF clusters. In addition, the temperature-dependence study shows that only isomers with relative energy within ∼ 1.0 kcal/mol have meaningful contribution to the population of DMF clusters.

Self-Assembly of Optimally Packed Cylindrical Clusters inside Spherical Shells.

Systems with short-range attraction and long-range repulsion can form ordered microphases in bulk and under confinement. Using grand canonical Monte Carlo simulations, we study a colloidal system with competing interactions under confinement in narrow spherical shells at thermodynamic conditions at which the hexagonal phase of cylindrical clusters is stable in bulk. We observe spontaneous formation of different ordered structures. The results of the simulations are in a very good agreement with the predictions of a simple mathematical model based on the geometry and optimal packing of colloidal clusters. The results of the simulations and the explanation provided by a relatively simple geometric model may be helpful in manufacturing copolymer nanocapsules and may indicate possible ways of coiling DNA strands on spherical objects.

DAMQT 3: Advanced suite for the analysis of molecular density and related properties in large systems

A new version of the DAMQT package specially developed for large systems is reported. The graphical part has been entirely redesigned, using new OpenGL libraries (versions 3.3 or higher) for 3D display. Several 2D plotters and 3D viewers can be launched now in the same session and more than one molecule can be loaded in the same 3D window. Algorithms have been rescaled and modified to work with densities coming from ZDO computations in very big molecular systems (up to thousands of atoms) at a very moderate cost. New functionalities have been added including computation of molecular electrostatic potential over a molecular surface determined as a user-defined density isosurface. The method of Electrostatics for Intermolecular Complexation has been added to the package to serve as an auxiliary tool for cluster geometry optimization. Examples are provided which prove the good performance of the algorithms. Program summaryProgram Title: DAMQT_3CPC Library link to program files:https://doi.org/10.17632/2rxvgbsnhx.2Licensing provisions: GPLv3Programming language: Fortran90, C++ and PythonSupplementary material: Quick-start guide and User's manual in PDF format included in the package. User's manual is also accessible from the GUI.External routines/libraries: Qt (5.10 or higher), OpenGL (3.3 or higher), ffmpeg (3.4 or higher), OpenBabel (2.3 or higher, optional)Nature of problem: Analysis and visualization of the molecular electron density, electrostatic potential, critical points, gradient paths, atomic basins, electric field and Hellmann-Feynman forces on nuclei, clusters optimization with EPIC.Solution method: Molecular electron density is partitioned into (pseudo)atomic fragments by means of the method of Deformed Atoms in Molecules [1]. Electron densities of the fragments are expanded as a series of spherical harmonics times radial factors. The partition is used for defining molecular density deformations and for the fast calculation of several properties associated with density, including electrostatic potential, electric field and Hellmann-Feynman forces over nuclei. Exploration of density and potential topology is facilitated, and the computation of electrostatic potential over an isodensity surface is implemented. Cluster optimization facility with EPIC is also implemented.Additional comments including restrictions and unusual features: Density matrix must come from an LCAO calculation (any computational level) with spherical (not Cartesian) Slater or Gaussian functions.The program contains an OPEN statement to binary files (stream) in several files. This statement does not have a standard syntax in Fortran 90. Two possibilities are considered in conditional compilation: Intel's ifort and Fortran2003 standard. This latter is applied to compilers other than ifort (gfortran uses this one, for instance).

Electronic structure and reactivity indexes of cobalt clusters, both pure and mixed with NO and [Formula: see text] ([Formula: see text], [Formula: see text] and [Formula: see text]).

Among the most popular motivations for environmental scientists is improving materials that could be useful to fight or avoid pollution. This work shows a study of neutral and cationic cobalt clusters from 4 to 9 atoms ([Formula: see text], q = 0,1 and n = 4-9) to model their separate interaction with contaminant nitric and nitrous oxides. This study is within the framework of the density functional theory in the Kohn-Sham scheme by using BPW91 functional and 6-311G and 6-31G* basis sets to calculate global and local reactivity indexes. The effect of spin multiplicity is also determined. Results on the geometries of pure cobalt clusters agree with previously reported structures. Global minimum energy structures showed a marked preference towards the interaction of nitric and nitrous oxide molecules with cobalt clusters through chemisorptive dissociation, with the dissociation of the corresponding nitrogen oxide. Reactivity indexes reveal an even-odd alternate, which is related to electron counts. Moreover, the chemical potential is lowering after interaction with nitrogen oxides. The Fukui function illustrates the reactive zones with a high probability of chemisorption of more nitrogen oxide molecules.

Assessment of Simultaneous Global Optimization of Geometry and Total Spin of Small Iron Clusters.

In this work, simultaneous global optimization of geometry and total spin of small iron clusters Fen (3 ≤ n ≤ 40) is assessed using Simulated Annealing (SA) simulations with forces calculated at the DFT-based Tight-Binding (DFTB) level of theory. In order to optimize the total spin, the occupancies of α and β densities were allowed to relax at each SA step, resulting in a continuous variation of the total spin along the trajectory. The behavior and performance of the procedure were investigated running two series of 10 independent "long" molecular dynamics simulations and one series of 100 independent "short" simulations. Cluster structures optimized with the assessed methodology reproduced geometries and magnetic moments reported in a previous work very well where multiple fixed total spin and geometries of iron clusters were individually probed, and for some clusters, more stable global minima were found. Other properties such as binding energies and second energy differences were also calculated in order to compare with previously reported theoretical and experimental values. The few mismatches were found to be driven by quasi degenerated ground states with different magnetic moments or by states with crossing free energies at high temperatures.

Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks.

Super-resolution imaging techniques have provided a better understanding of the relationship between the nanoscale organization and function of ryanodine receptors (RyRs) in cardiomyocytes. Recent data have indicated that this relationship is disrupted in heart failure (HF), as RyRs are dispersed into smaller and more numerous clusters. However, RyRs are also hyperphosphorylated in this condition, and this is reported to occur preferentially within the cluster centre. Thus, the combined impact of RyR relocalization and sensitization on Ca2+ spark generation in failing cardiomyocytes is likely complex and these observations suggest that both the nanoscale organization of RyRs and the pattern of phosphorylated RyRs within clusters could be critical determinants of Ca2+ spark dynamics. To test this hypothesis, we used computational modeling to quantify the relationships between RyR cluster geometry, phosphorylation patterns, and sarcoplasmic reticulum (SR) Ca2+ release. We found that RyR cluster disruption results in a decrease in spark fidelity and longer sparks with a lower amplitude. Phosphorylation of some RyRs within the cluster can play a compensatory role, recovering healthy spark dynamics. Interestingly, our model predicts that such compensation is critically dependent on the phosphorylation pattern, as phosphorylation localized within the cluster center resulted in longer Ca2+ sparks and higher spark fidelity compared to a uniformly distributed phosphorylation pattern. Our results strongly suggest that both the phosphorylation pattern and nanoscale RyR reorganization are critical determinants of Ca2+ dynamics in HF.

Seismogenic structure beneath the northern Longitudinal Valley revealed by the 2018–2021 Hualien earthquake sequences and 3-D velocity model

This study uses the 3D crustal velocity model and the relocated earthquake hypocenters, including the 2018–2021 earthquake sequences, to re-assess the seismogenic structures at the northern Longitudinal Valley. Earthquake focal mechanisms and relocated hypocenters from earthquake clusters suggest a gentle west-dipping fault existing under the Longitudinal Valley and the Coastal Range. Earthquake clusters associated with this west-dipping fault indicate it develops along the base of high-velocity Central Range metamorphic rocks and is likely branched out from the previously recognized Central Range Fault (CRF). Both the 3D velocity model and the geometry of earthquake clusters suggest this structure truncates the Longitudinal Valley Fault north of 23.7° N, separating the northernmost LVF into the shallow and the deep segments. The shallow segment then plausibly evolves to be a transpressional fault system that mainly accommodates the left-lateral motions. This interpretation coincides with the geomorphological and geodetic observations showing that the northern LVF is dominated by the left-lateral faulting, instead of showing a significant reverse component as in the southern Longitudinal Valley. The limited fault width and geometry of the shallow LVF segment also imply its seismic potential is relatively limited, while the underling west-dipping fault and the deeper segment of the LVF are the major seismogenic structure. Such development of the major CRF-related west-dipping structure could accommodate the northwestward subduction of the Philippine Sea Plate and also likely reactivate part of the Offshore Eastern Taiwan Thrust Belt.

Structural, electronic, thermodynamic and optical properties of SnlSemSn clusters: A DFT study

• DFT study of electronic, thermodynamic and optical properties of SnlSemSn clusters. • Band gap energy of Sn l Se m S n clusters lie in the semiconducting range (1.035–3.463 eV). • Sn 1 Se 1 S 2 is found to be the most reactive cluster. • Absorption spectra can be tailored by varying thecomposition of atoms in clusters. Density Functional Theory (DFT) calculations are performed to investigate the structural, electronic, thermodynamic, and optical properties of Sn l Se m S n clusters with the variation in the number of Sn, Se, and S atoms using B3LYP/321-G ∗ level of theory. We have obtained 23 optimized clusters and their calculated properties are dependent on the size, geometry, and structure of clusters. We observed that Sn 1 Se 1 S 2 is found to be highly reactive owing to its largest values of electronegativity, vertical ionization potential, vertical electron affinity with the least values of binding energy and band gap energy. The least reactive cluster is Sn 1 Se 1 S 8 with the maximum values of band gap and hardness. The band gap energies of all clusters lie in the semiconducting range (1.035 eV–3.463 eV). The optical absorption is observed in ultraviolet and visible regions. The theoretically computed absorption spectrum for excited states is compared experimentally confirming their applications in optoelectronics.

Clusteromics III: Acid Synergy in Sulfuric Acid-Methanesulfonic Acid-Base Cluster Formation.

Acid–base molecular clusters are an important stage in atmospheric new particle formation. While such clusters are most likely multicomponent in nature, there are very few reports on clusters consisting of multiple acid molecules and multiple base molecules. By applying state-of-the-art quantum chemical methods, we herein study electrically neutral (SA)1(MSA)1(base)0–2 clusters with base = ammonia (A), methylamine (MA), dimethylamine (DMA), trimethylamine (TMA) and ethylenediamine (EDA). The cluster structures are obtained using a funneling approach employing the ABCluster program, semiempirical PM7 calculations and ωB97X-D/6-31++G(d,p) calculations. The final binding free energies are calculated at the DLPNO-CCSD(T0)/aug-cc-pVTZ//ωB97X-D/6-31++G(d,p) level of theory using the quasi-harmonic approximation. Based on the calculated cluster geometries and thermochemistry (at 298.15 K and 1 atm), we find that the mixed (SA)1(MSA)1(base)1–2 clusters more resemble the (SA)2(base)1–2 clusters compared to the (MSA)2(base)1–2 clusters. Hence, some of the steric hindrance and lack of hydrogen bond capacity previously observed in the (MSA)2(base)1–2 clusters is diminished in the corresponding (SA)1(MSA)1(base)1–2 clusters. Cluster kinetics simulations reveal that the presence of an MSA molecule in the clusters enhances the cluster formation potential by up to a factor of 20. We find that the SA–MSA–DMA clusters have the highest cluster formation potential, and thus, this system should be further extended to larger sizes in future studies.