Dinuclear Research Articles

Theoretical study of a Ti4 cluster interacting with B-doped and non-doped multivacancy graphene

A density functional theory study was performed to understand the interactions of a small Ti4 cluster with multi-vacancy graphene. We also consider the effect produced by the B-doping of the vacancy defect. In this sense, we analyze the binding mechanisms of the metal cluster. The focus is set on its stability on the substrate, geometrical structure and the interactions participating between the cluster and graphene substrate. A qualitative study of the principal bonds was carried out employing overlap population and bond order chemical descriptors. Additionally, as an attempt to comprehend better the electronic structure and related properties, we performed total density of states, band structure and magnetic moment calculations to characterize the electrical and magnetic properties of the B-doped and non-doped systems.

Role of Explicit Solvation in Computational Modeling of Chemical Reactions: Mechanism of Cu(I) Transfer Between Thiolate-Based Chelators in Water.

Solvation plays important roles in controlling the thermodynamic and kinetic aspects of chemical reactions. The conventional approaches to treat solvation via electronic structure methods are likely to become inadequate, when the reacting solutes have strong electrostatic and hydrogen bonding interactions with the solvent and undergo significant structural changes during the course of the reaction. In this article, we present evidence of such solvent and structural effects in the computational study of the Cu(I) transfer reaction between thiolate-based chelators dithiobutylamine (DTBA) and dithiotheritol (DTT) in water, inspired from biological copper trafficking phenomena. We propose a general solution to the problem by combining classical molecular dynamics (MD) simulations of the bulk system and static quantum chemistry calculations. The fluctuating solvation shell was estimated from MD, and energetics was assessed by averaging QM energies of a series of molecular clusters constructed from the MD snapshots. Applying this approach, we propose a reaction pathway with estimates of relative intermediate stabilities and barriers, which suggest the overall reaction to be reversible in nature and likely to go through both two and three coordinated intermediates, confirming previous studies of similar protein analogues. An interesting fact that emerged from our study was the strong indication that the rate-determining step is the deprotonation of initial thiol bound Cu(I) complex, without involving any Cu(I)-S bonds. The proposed method will lead to a better treatment of solvations, and these mechanistic insights will aid our understanding of biological copper(I) trafficking.

Identification of key genes for atherosclerosis in different arterial beds

Atherosclerosis (AS) is the pathologic basis of various cardiovascular and cerebrovascular events, with a high degree of heterogeneity among different arterial beds. However, mechanistic differences between arterial beds remain unexplored. The aim of this study was to explore key genes and potential mechanistic differences between AS in different arterial beds through bioinformatics analysis. Carotid atherosclerosis (CAS), femoral atherosclerosis (FAS), infrapopliteal atherosclerosis (IPAS), abdominal aortic atherosclerosis (AAS), and AS-specific differentially expressed genes (DEGs) were screened from the GSE100927 and GSE57691 datasets. Immune infiltration analysis was used to identify AS immune cell infiltration differences. Unsupervised cluster analysis of AS samples from different regions based on macrophage polarization gene expression profiles. Weighted gene co-expression network analysis (WGCNA) was performed to identify the most relevant module genes with AS. Hub genes were then screened by LASSO regression, SVM-REF, and single-gene differential analysis, and a nomogram was constructed to predict the risk of AS development. The results showed that differential expression analysis identified 5, 4, 121, and 62 CAS, FAS, IPAS, AAS-specific DEGs, and 42 AS-common DEGs, respectively. Immune infiltration analysis demonstrated that the degree of macrophage and mast cell enrichment differed significantly in different regions of AS. The CAS, FAS, IPAS, and AAS could be distinguished into two different biologically functional and stable molecular clusters based on macrophage polarization gene expression profiles, especially for cardiomyopathy and glycolipid metabolic processes. Hub genes for 6 AS (ADAP2, CSF3R, FABP5, ITGAX, MYOC, and SPP1), 4 IPAS (CLECL1, DIO2, F2RL2, and GUCY1A2), and 3 AAS (RPL21, RPL26, and RPL10A) were obtained based on module gene, gender stratification, machine learning algorithms, and single-gene difference analysis, respectively, and these genes were effective in differentiating between different regions of AS. This study demonstrates that there are similarities and heterogeneities in the pathogenesis of AS between different arterial beds.

SERS analysis, DFT, and solution effects regarding the structural and optical characteristics of folic acid biomolecule adsorbed on a Cu3 metal cluster

The optical characteristics of folic acid (ABP) and metal clusters of copper (Cu3) at various locations were investigated by means of density functional theory (DFT) computations. Mulliken charge analysis and molecular electrostatic potential (MEP) surface show how charge moves from Cu3 to ABP through the various groups. The peak in the UV–Vis spectra of ABP-Cu3 is caused by bonding and anti-bonding orbitals. In both vacuum and aqueous conditions, the polarizability values of ABP-Cu3 cluster are significantly higher than those of pure ABP, indicating a possible enhancement of the nonlinear optical (NLO) effect. Our research investigates the possibility of using ABP adsorbed metal clusters for NLO materials. Surface enhanced Raman scattering (SERS) in the ABP adsorbed metal clusters enhances the vibrational modes of ABP. Adsorption energies are found to be in the range −17.08 to −58.52 kcal/mol in vacuum and −53.34 to −93.44 kcal/mol in aqueous medium for the different configurations for ABP-Cu3. It indicates that metal clusters adsorbed by ABP are stable in the aqueous media. Experimental IR and UV–Vis of ABP is in agreement with theoretically predicted ones.

Development of Heterometallic Annular Tetranuclear Clusters in Metal–Organic Frameworks for Methane Purification and Storage

Development of Heterometallic Annular Tetranuclear Clusters in Metal–Organic Frameworks for Methane Purification and Storage

Asymmetrical Interactions between Ni Single Atomic Sites and Ni Clusters in a 3D Porous Organic Framework for Enhanced CO2 Photoreduction.

3D porous organic frameworks, which possess the advantages of high surface area and abundant exposed active sites, are considered ideal platforms to accommodate single atoms (SAs) and metal nanoclusters (NCs) in high-performance catalysts; however, very little research has been conducted in this field. In the present work, a 3D porous organic framework containing Ni1 SAs and Nin NCs is prepared through the metal-assisted one-pot polycondensation of tetraaldehyde and hexaaminotriptycene. The single metal sites and metal clusters confined in the 3D space created a favorable micro-environment that facilitated the activation of chemically inert CO2 molecules, thus promoting the overall photoconversion efficiency and selectivity of CO2 reduction. The 3D-NiSAs/NiNCs-POPs, as a CO2 photoreduction catalyst, demonstrated an exceptional CO production rate of 6.24mmolg-1h-1, high selectivity of 98%, and excellent stability. The theoretical calculations uncovered that asymmetrical interaction between Ni1 SAs and Nin NCs not only favored the bending of CO2 molecules and reducing the CO2 reduction energy, but also regulated the electronic structure of the catalyst leading to the optimal binding strength of intermediates.

Tetrametallic mastery: Cluster-doped graphdiyne as a superior electrocatalyst for hydrogen evolution

Hydrogen evolution reaction (HER) is a promising route for sustainable hydrogen production. However, its efficiency is limited by kinetic barriers. Herein, we employ density functional theory (DFT) calculations to demonstrate a new strategy of embedding tetrametallic transition metal clusters (3TM1-TM2) into the pores of graphdiyne (GDY) to effectively optimize its HER performance. By screening 900 configurations, 10 prototypes displayed near-ideal hydrogen adsorption free energies. Among them, 3W–Hg@GDY with a ΔGH of −0.00035 eV was identified as the optimal candidate. Analysis of the electronic structure reveals hybridization between the metal d orbitals and GDY p orbitals near the Fermi level, creating partially filled impurity states to promote hydrogen adsorption. Additionally, coordination between the three TM1 atoms and active TM2 atom in the cluster enables precise tuning of TM2's electron density to achieve a moderate interaction with the adsorbed H, facilitating superior HER catalysis. Our findings showcase a new paradigm of cluster engineering for modulating GDY's reactivity that holds great promise as a universal approach for the design of high-performance GDY-based electrocatalysts beyond HER.

Direct formation of single crystalline molecular clusters with disulfide bonding from thiol-containing triptycene derivatives

Abstract When a DMF solution of 1,8,13-trimercaptotriptycene is allowed to stand under an inert atmosphere, a single crystalline molecular cluster with disulfide bonding results. Likewise, several thiol-containing triptycene derivatives yield single crystalline disulfide-containing clusters with different structural patterns. One of these clusters featuring a densely arranged tetrapod-like disulfide moiety exhibits a particularly high refractive index of 1.75, much higher than that of the others, although the sulfur contents of these clusters are comparable.

Water-Mediated Charge Transfer and Electron Localization in a Co3Fe2 Cyanide-Bridged Trigonal Bipyramidal Complex.

The effects of temperature and chemical environment on a pentanuclear cyanide-bridged, trigonal bipyramidal molecular paramagnet have been investigated. Using element- and oxidation state-specific near-ambient pressure X-ray photoemission spectroscopy (NAP-XPS) to probe charge transfer and second order, nonlinear vibrational spectroscopy, which is sensitive to symmetry changes based on charge (de)localization coupled with DFT, a detailed picture of environmental effects on charge-transfer-induced spin transitions is presented. The molecular cluster, Co3Fe2(tmphen)6(μ-CN)6(t-CN)6, abbrev. Co3Fe2, shows changes in electronic behavior depending on the chemical environment. NAP-XPS shows that temperature changes induce a metal-to-metal charge transfer (MMCT) in Co3Fe2 between a Co and Fe center, while cycling between ultrahigh vacuum and 2 mbar of water at constant temperature causes oxidation state changes not fully captured by the MMCT picture. Sum frequency generation vibrational spectroscopy (SFG-VS) probes the role of the cyanide ligand, which controls the electron (de)localization via the superexchange coupling. Spectral shifts and intensity changes indicate a change from a charge delocalized, Robin-Day class II/III high spin state to a charge-localized, class I low spin state consistent with DFT. In the presence of a H-bonding solvent, the complex adopts a localized electronic structure, while removal of the solvent delocalizes the charges and drives an MMCT. This change in Robin-Day classification of the complex as a function of chemical environment results in reversible switching of the dipole moment, analogous to molecular multiferroics. These results illustrate the important role of the chemical environment and solvation on underlying charge and spin transitions in this and related complexes.

From the Automated Calculation of Potential Energy Surfaces to Accurate Infrared Spectra.

Advances in the development of quantum chemical methods and progress in multicore architectures in computer science made the simulation of infrared spectra of isolated molecules competitive with respect to established experimental methods. Although it is mainly the multidimensional potential energy surface that controls the accuracy of these calculations, the subsequent vibrational structure calculations need to be carefully converged in order to yield accurate results. As both aspects need to be considered in a balanced way, we focus on approaches for molecules of up to 12-15 atoms with respect to both parts, which have been automated to some extent so that they can be employed in routine applications. Alternatives to machine learning will be discussed, which appear to be attractive, as long as local regions of the potential energy surface are sufficient. The automatization of these methods is still in its infancy, and the generalization to molecules with large amplitude motions or molecular clusters is far from trivial, but many systems relevant for astrophysical studies are already in reach.

Photoinduced Selective B-H Activation of nido-Carboranes.

The development of new synthetic methods for B-H bond activation has been an important research area in boron cluster chemistry, which may provide opportunities to broaden the application scope of boron clusters. Herein, we present a new reaction strategy for the direct site-selective B-H functionalization of nido-carboranes initiated by photoinduced cage activation via a noncovalent cage···π interaction. As a result, the nido-carborane cage radical is generated through a single electron transfer from the 3D nido-carborane cage to a 2D photocatalyst upon irradiation with green light. The resulting transient nido-carborane cage radical could be directly probed by an advanced time-resolved EPR technique. In air, the subsequent transformations of the active nido-carborane cage radical have led to efficient and selective B-N, B-S, and B-Se couplings in the presence of N-heterocycles, imines, thioethers, thioamides, and selenium ethers. This protocol also facilitates both the late-stage modification of drugs and the synthesis of nido-carborane-based drug candidates for boron neutron capture therapy (BNCT).

Revealing the adsorption nature of disulfiram on metal clusters (Au, Pt, Ag, Pd, Cu, and Ni): DFT analysis, SERS enhancement and sensor properties

The electrical and vibrational characteristics of disulfiram (DSM) with Au/Pt/Ag/Pd/Cu/Ni metal cages are analyzed using the DFT method. The current study shows that complexes have energy gaps that are distinct from those of pure metal clusters and are surprisingly stable. Reactivity descriptors including hardness, chemical potential and electrophilicity are estimated in order to thoroughly examine the electronic property. Raman modes are enhanced, particularly for complexesI, as a result of SERS effect. The DSM and metal clusters exchange charges, which induces a dipole moment. The change in the FMOs energy of the metal clusters after interaction has a substantial impact on electrical conductivity and work function. The metal clusters for DSM can be used as a work function-based sensor in addition to an electronic sensor. On the other hand, DSM with metal clusters has a longer recovery period, suggesting that it can be stored or taken out of a particular environment.

The Management of Phaeochromocytomas and Paragangliomas in the Era of Precision Medicine: Where Are We Now? Evidence-Based Systemic Treatment Options and Future Cluster Oriented Perspectives.

Pheochromocytomas (PCCs) and Paragangliomas (PGLs), commonly known as PPGLs to include both entities, are rare neuroendocrine tumors that may arise in the context of hereditary syndromes or be sporadic. However, even among sporadic PPGLs, identifiable somatic alterations in at least one of the known susceptibility genes can be detected. Therefore, about 3/4 of all PPGL patients can be assigned to one of the three molecular clusters that have been identified in the last years with difference in the underlying pathogenetic mechanisms, biochemical phenotype, metastatic potential, and prognosis. While surgery represents the mainstay of treatment for localized PPGLs, several therapeutic options are available in advanced and/or metastatic setting. However, only few of them hinge upon prospective data and a cluster-oriented approach has not yet been established. In order to render management even more personalized and improve the prognosis of this molecularly complex disease, it is undoubtable that genetic testing for germline mutations as well as genome profiling for somatic mutations, where available, must be improved and become standard practice. This review summarizes the current evidence regarding diagnosis and treatment of PPGLs, supporting the need of a more cluster-specific approach in clinical practice.

Unique Viscoelasticity and Hierarchical Relaxation Dynamics of Molecular Granular Materials.

Resulting from the dense packing of subnanometer molecular clusters, molecular granular materials (MGMs) are shown to maintain high elasticity far above their apparent glass transition temperature (Tg*). However, our microscopic understanding of their structure-property relationship is still poor. Herein, 1 nm polyhedral oligomeric silsesquioxanes (POSSs) are appended to a backbone chain in a brush configuration with different flexible linker chains. Assemblies of these brush polymers exhibit hierarchical relaxation dynamics with the glass transition arising from the cooperative dynamics of packed POSSs. The interaction among the assemblies can be strengthened by increasing the rigidity of linkers with the MGM relaxation modes changing from colloid- to polymer chain-like behavior, rendering their tunable viscoelasticity. This finally contributes to the decoupling of mechanical and thermal properties by showing elasticity dominant mechanical properties at a temperature 150 K above the Tg*.

Water molecule elimination from the protonated methanol dimer ion-An example of a size-selective intracluster reaction.

The abundance of extraterrestrial methanol makes the reaction between methanol molecules in a molecular cluster a possible key step in the search for mechanisms for the formation of more complex molecules under the conditions of the interstellar medium as well as circumstellar and planetary atmospheres. The reaction leading to the formation of the dimethyl ether ion from a methanol molecule interacting with a protonated methanol ion via the elimination of a water molecule is a basic mechanism for the formation of complex organic molecules. Here, we experimentally examine such reactions in the gas phase, analyzing the production and reactivity of protonated cluster ions formed by the ionization of a supersonic jet of methanol. Focusing especially on the post-collisional relaxation of the protonated methanol dimer and trimer ions after high-energy single collisions, the results indicate a strong size selectivity favoring the occurrence of this reaction only in the dimer ion. To elucidate this behavior, the velocity distribution of the eliminated water molecule was measured using an event-by-event coincidence analysis. These results are interpreted using quantum chemical calculations of the dissociation pathways. It turns out that in the dimer case, two transition states are able to contribute to this intracluster reaction. In the trimer case, methanol evaporation appears as the most energetically favorable relaxation pathway.

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems.

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree-Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. The accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, Rcut. Rcut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small Rcut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

Fragmentation of water clusters formed in helium nanodroplets by charge transfer and Penning ionization.

Helium nanodroplets ("HNDs") are widely used for forming tailor-made clusters and molecular complexes in a cold, transparent, and weakly interacting matrix. The characterization of embedded species by mass spectrometry is often complicated by the fragmentation and trapping of ions in the HNDs. Here, we systematically study fragment ion mass spectra of HND-aggregated water and oxygen clusters following their ionization by charge transfer ionization ("CTI") and Penning ionization ("PEI"). While the efficiency of PEI of embedded clusters is lower than for CTI by about factor 10, both the mean sizes of detected water clusters and the relative yields of unprotonated cluster ions are significantly larger, making PEI a "soft ionization" scheme. However, the tendency of ions to remain bound to HNDs leads to a reduced detection efficiency for large HNDs containing >104 helium atoms. These results are instrumental in determining optimal conditions for mass spectrometry and photoionization spectroscopy of molecular complexes and clusters aggregated in HNDs.

Metal Organic Frameworks Synthesis: The Versatility of Triethylamine.

Metal Organic Frameworks (MOFs) are organic-inorganic hybrid materials with exceptionally customizable composition and properties. MOFs intrinsically possess open metal sites, tunable pore size/shape and an ultra-large specific surface area, and have obtained significant attention over the past 30 years. Furthermore, through the integration of functional moieties such as, molecules, functional groups, noble metal clusters and nanocrystals or nanoparticles into MOFs, the resulting composites have greatly enriched the physical and chemical properties of pure MOFs, enabling their application in a wider range of fields. Triethylamine (TEA) as an organic base has consistently played a fundamental role in the development of MOFs. In this Concept, the versatility of triethylamine when involved in the synthesis of MOFs is discussed. Four sections are used to elaborate on the role of TEA including: (1) Single crystal synthesis; (2) Size and morphology control; (3) Counterion of MOFs; (4) MOFs composites synthesis. In the last part, we highlight the potential of TEA for further developments.

Isothermal and nonisothermal crystallization kinetics of modified hydroxyapatite-enhanced poly(3-hydroxybutyrate-co-4-hydroxybutyrate)

Poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P34HB) is a biodegradable material, and efforts have been devoted to enhancing its mechanical properties and biocompatibility for biomedical applications. However, there is a lack of research confirming the influence of nucleating agents on its crystallization behavior. In this study, the isothermal crystallization process was described using the Avrami model. The non-isothermal crystallization process was investigated using the Avrami-Jeziorny and Mo models. The effects of different calcium hydroxyapatite (CA-HA) contents on the nucleation activity, crystallization activation energy, and equilibrium melting point of P34HB/CA-HA composites were compared. The impact of CA-HA on the crystallization rate, nucleation rate, and crystal growth rate of the polymer matrix was discussed. The results indicate that with an increase in CA-HA content, the crystallization rate initially decreases and then increases. The minimum crystallization rate is observed at a CA-HA content of 9 wt%. Moreover, as the CA-HA content increases, nucleation activity is enhanced, suggesting that CA-HA acts as a nucleating agent, facilitating the nucleation process. When the CA-HA content exceeds 9 wt%, the increase in crystallization rate may be attributed to the further enlargement of molecular clusters formed by CA-HA, leading to a reduced dispersion of CA-HA in the polymer matrix. Furthermore, when the CA-HA content surpasses 9%, a significant decrease in crystallization activation energy is observed, indicating a reduction in the mobility of polymer chain segments.

Potential health risk assessment of mixtures of heavy metals in drinking water

Despite the potential to cause chronic adverse effects, heavy metals screenings are not typically as frequent or exhaustive as those for bacterial contamination. Additionally, there is a pressing need for collectively assessing heavy metals as a mixture rather than individual allowed limits. We tested a hypothesis that comprehensive methodical wide screening for heavy metals can inform the magnitude of potential exposures and aid in classifying heavy metals collectively as hazardous rather than individual level comparisons. A total of 297 samples were taken by proportional cluster sampling from different households in Irbid governorate, depending on population density in each district. We analyzed the samples using Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS). Our analysis looked at individual levels of heavy metal clustering in different water sources and regions and calculated a heavy metals pollution index (HPI) in five different types of drinking water: harvested rainwater, bottled water, spring water, water shop, and tap water. Pb and Fe were the main contaminants in drinking water, especially tap and harvested rainwater. High amounts of essential metals were found in tap, harvested rain, and spring waters compared to water shop and bottled water. HPI was above critical value in 29 samples, all of which were harvested rainwater samples, and most of which came from Wasateya and Taiba regions. Spring and tap water had similar heavy metal patterns. This experimental approach provides a guide for clustering water sources in their heavy metal patterns and for classification of heavy metals as mixtures rather than individual limits; it also fills crucial gaps in prioritization of heavy metal testing according to water type and metal correlations. Furthermore, this study presents the first data on drinking water quality in Jordan to be published in over a decade.