Trimeric Clusters Research Articles

Hydrogen bonding in 2,2,2-trifluoroethanol.

2,2,2-Trifluoroethanol (TFE) is known as a membrane mimetic solvent. The IR spectrum, 1H NMR spectrum, 13C NMR spin‒lattice relaxation times (T1), and nuclear Overhauser effect (NOE) data are consistent with extensive hydrogen bonding in TFE, but do not lead to structural features of the hydrogen bonding. Hence, DFT computations were carried out. The results predict the existence of a set of H-bonded dimers and trimers. The bond lengths and dihedral angles in these complexes are obtained, together with their dissociation energies. Computations were also performed for the geometry of the two conformers of the isolated monomer. The structure of one of the dimers consists of a 7-member cyclic fragment with a free CF3CH2 side chain. One set of the trimer structures involves the OH of a third monomer H-bonding to one of the F atoms in the CF3 group of the side chain of this dimer, thereby creating three trimer isomers. A fourth trimer cluster is formed from three monomers in which three OH∙∙∙O bonds create a cyclic fragment with three CF3CH2 side chains. The high dissociation energy (with respect to three monomers) indicates the high stability of the trimer complexes. The structural features of the trimer complexes resemble the structure of a conventional liquid crystal molecule and are postulated to resemble the latter in properties and function in solution, but at a much shorter timescale because of the noncovalent bonding. This hydrogen bonding phenomenon of TFE may be related to its function as a membrane memetic solvent. Initially, IR and NMR spectroscopic methods were used. Standard procedures were followed. For the computations, a hybrid DFT method with empirical dispersion, ωB97X-D, was used. The basis set, 6-311++G**, is of triple-ζ quality, in which polarization functions and diffuse functions were added for all atoms.

Self-Association and Microhydration of Phenol: Identification of Large-Amplitude Hydrogen Bond Librational Modes.

The self-association mechanisms of phenol have represented long-standing challenges to quantum chemical methodologies owing to the competition between strongly directional intermolecular hydrogen bonding, weaker non-directional London dispersion forces and C-H⋯π interactions between the aromatic rings. The present work explores these subtle self-association mechanisms of relevance for biological molecular recognition processes via spectroscopic observations of large-amplitude hydrogen bond librational modes of phenol cluster molecules embedded in inert neon "quantum" matrices complemented by domain-based local pair natural orbital-coupled cluster DLPNO-CCSD(T) theory. The spectral signatures confirm a primarily intermolecular O-H⋯H hydrogen-bonded structure of the phenol dimer strengthened further by cooperative contributions from inter-ring London dispersion forces as supported by DLPNO-based local energy decomposition (LED) predictions. In the same way, the hydrogen bond librational bands observed for the trimeric cluster molecule confirm a pseudo-C3 symmetric cyclic cooperative hydrogen-bonded barrel-like potential energy minimum structure. This structure is vastly different from the sterically favored "chair" conformations observed for aliphatic alcohol cluster molecules of the same size owing to the additional stabilizing London dispersion forces and C-H⋯π interactions between the aromatic rings. The hydrogen bond librational transition observed for the phenol monohydrate finally confirms that phenol acts as a hydrogen bond donor to water in contrast to the hydrogen bond acceptor role observed for aliphatic alcohols.

Ultrafast spin dynamics in magnetic trimer and tetramer clusters: a step towards prototypic spin-SHIFT registers

Ultrafast magnetic dynamics is a necessary ingredient for magnetic recording and ultrafast information processing. The shift functionality, although not mandatory for Boolean logic, is always implemented in CMOS CPUs and therefore must be also present in magnetic logic. In this respect, using ab initio calculations we show ultrafast spin dynamics in molecular clusters such as Co3 +CO and Ni4. In this work, we establish that clusters with magnetic atoms can provide a theoretical toolbox for efficient spin charge dynamics whose operation time can range up to a few picoseconds. The prime underlying mechanism for all spin manipulation scenarios in the above mentioned clusters are laser-induced Λ processes where the laser parameters are fully optimized using a genetic algorithm. In general, a structural asymmetry enforces substantial spin localization on the active centers of both magnetic clusters. Keeping in mind the shift functionality, we theoretically suggest a series of spin-transfer scenarios between the Co and Ni atoms in each of these two clusters independently to construct a 3-bit and a 4-bit cyclic spin-SHIFT register, respectively. The maximum operational time for both logic devices is 2 ps, which is much faster than the response time of conventional spintronic devices. Additionally, for a better understanding of the transfer cycles, their feasibility and reversibility are also investigated through the analysis of the optical spectra of the related states. Our results provide important theoretical guidance for ultrafast spin manipulation in molecular structures as well as their potential spin functionality, and thus step closer to the realization of future spin-based logic devices and quantum computation. This effectively motivates the investigation and precise establishment of the shift functionality in magnetic trimers and tetramers.

Net-Shaped DNA Nanostructure-Based Lateral Flow Assays for Rapid and Sensitive SARS-CoV-2 Detection.

Lateral flow assay (LFA)-based rapid antigen tests are experiencing extensive global uptake as an expeditious and highly effective modality for the screening of viral infections during the COVID-19 pandemic. While these devices have played a significant role in alleviating the burden on the public healthcare system, their specificity and sensitivity fall short compared with molecular tests. In this study, we endeavor to address both limitations through the utilization of DNA nanotechnology in LFA format, wherein we substitute the target-specific antibody with designer DNA nanostructure-based molecular probes for recognizing the SARS-CoV-2 virus via multivalent, pattern-matching interactions. We meticulously designed a Net-shaped DNA nanostructure and strategically arranged trimeric clusters of aptamers that specifically recognize the spike proteins of SARS-CoV-2. This approach has proven instrumental in bolstering virus-binding affinity on the LFAs. Our findings indicate high LFA sensitivity, enabling the detection of viral loads ranging from 103 to 108 viral copies/mL. This notable sensitivity is maintained across various SARS-CoV-2 viral strains, obviating the need for intricate sample preparation protocols. The significance of this heightened sensitivity lies in the crucial role played by the designer DNA nanostructure, which facilitates the detection of extremely low levels of viral loads. This not only enhances the overall reliability of self-testing but also reduces the likelihood of false-negative results, especially in cases of low viral load within patient samples.

Computational design of spatially confined triatomic catalysts for nitrogen reduction reaction

The electrocatalytic process of nitrogen reduction reactions (NRR) offers a promising approach towards achieving sustainable ammonia production, acting as an environmentally friendly replacement for the conventional Haber-Bosch method. Density functional theory calculations have been utilized to design and investigate a set of catalysts known as triple-atom catalysts (TACs) for electrochemical NRR, which are supported on graphite-C3N3 nanosheets. Herein, we have systematically evaluated these TACs using stringent screening to assess their catalytic performance. Among the candidates, supported Pt3, Re3, and Ru3 trimers emerged as highly active with decent selectivity, involving a limiting potential range of -0.35~-0.11 V. According to analysis of electronic properties, we determined that high NRR activity stems from the d -π* electron-accepting and -donating mechanism. Significantly, the correlation between chemical activity of TACs and electronic structure was established as a pivotal physical parameter, which has led to the conclusion that we can precisely control the catalytic behavior of transition metal trimer clusters by selecting appropriate metal elements and designing moderate cluster-substrates interactions. In summary, these theoretical studies not only enhance our understanding of how catalytic properties are governed by metal-support interactions, regulating stability, activity, and selectivity, but also offer a useful method for screening and designing novel TACs for NRR.

Graphitic carbon nitride supported trimeric metal clusters as electrocatalysts for N2 reduction reaction

As a cleaner and more energy-efficient alternative, the electrochemical reduction of N2 to NH3 under mild conditions has emerged as a promising avenue for environmental protection. However, developing catalysts with both high activity and selectivity has been a challenging task. The advent of atomically dispersed catalysts is revolutionizing the field of catalysis. Drawing inspiration from the successful fabrication of Ru trimer on graphitic carbon nitride (g-C3N4) nanosheets, herein, we adopted a series of trimeric metal clusters anchored on g-C3N4 monolayer (TM3@g-C3N4, TM = 3d, 4d and 5d transition metal atom), as well as utilized the criteria range to describe the stability, activity, energy cost and selectivity of supported trimers for N2 reduction reaction based on ab initio calculations combined with multi-level screening strategies. Finally, 5 candidate TM3@g-C3N4 (TM = Rh, Ru, V, Mo, and Re) exhibits decent catalytic activity with limiting potential ranging of –0.50 – –0.02 V. These spatially confined triatomic metal centers demonstrated proficiency in activating N2 molecules while exhibiting tunable surficial reactivity through modulation of the metal elements and interfacial electron coupling between trimers and underlying substrates. More importantly, a structure–activity relationship was established, which provides crucial insights for precise design of highly efficient atomically-precise catalysts at an atomic level for hydrogen fuel storage.

Metamagnetism in a coordination polymer built of trimeric cobalt units and melamine.

A coordination polymer of linear trimeric cobalt units and melamine has been synthesized. The magnetic isotherms of violet coloured crystals as long as 400 μm show a field-induced transition in an external field of about 2 T at temperatures approximately below 2 K. It is addressed that by assuming the coexistent positive and negative exchange between the nearest-neighbour spins in the linear trimer, this metamagnetism can be interpreted as a transition from antiferromagnetic to ferromagnetic exchange within each trimeric spin cluster. Although weak inter-cluster or inter-chain exchange to yield a long-range magnetic order is another possible and often attributed origin of metamagnetism in low-dimensional spin systems, this study demonstrates the significance of the exchange flip within each cluster in clustered spin networks.

Sulfur Centered Hydrogen Bonding in Thioglycolic Acid and Its Clusters: A Computational Exploration.

The conformational landscape of thioglycolic acid (TGA) was investigated by using the CCSD/cc-pVTZ level of theory. The GGC conformer was identified as the global minimum, followed by the GAC conformer. The calculated rotational constant for the GGC conformer exhibited good agreement with the previously reported experimental results. Subsequently, the study delved into the exploration of sulfur-centered hydrogen bonding in TGA's dimer and trimer clusters, employing the CCSD/cc-pVDZ level of theory. These clusters revealed the participation of both oxygen and sulfur atoms in noncovalent H-bonding, contributing to their stability. The presence of these noncovalent interactions in TGA clusters was elucidated through Atoms in Molecule (AIM), reduced density gradient (RDG), and natural bond order (NBO) analysis, while electrostatic potential (ESP) charge and vibrational mode analysis further supported these findings.

Self-Organization of 1-Propanol at H-ZSM-5 Brønsted Acid Sites.

In situ Al K-edge X-ray absorption near edge structure (XANES) and Extended X-ray absorption fine structure (EXAFS) spectroscopy in conjunction with ab initio molecular dynamics (AIMD) simulations show that adsorption of 1-propanol alters the structure of the Brønsted acid site through changes in the associated aluminum-oxygen tetrahedron in zeolite H-MFI. The decreasing intensity of the pre-edge signal of the in situ Al K-edge XANES spectra with increasing 1-propanol coverage shows that Al T-sites become more symmetric as the sorbed alcohol molecules form monomers, dimers, and trimers. The adsorption of monomeric 1-propanol on Brønsted acid sites reduces the distortion of the associated Al T-site, shortens the Al-O distance, and causes the formation of a Zundel-like structure. With dimeric and trimeric alcohol clusters, the zeolite proton is fully transferred to the alcohols and the aluminum-oxygen tetrahedron becomes fully symmetric. The subtle changes in Al-K-edge XANES in the presence of sorbate structures, with the use of theory, are used to probe the local zeolite structures and provide a basis to predict the population and chemical state of the sorbed species.

Multi-Modular Design of Stable Pore-Space-Partitioned Metal-Organic Frameworks for Gas Separation Applications.

Pore space partition (PSP) is an effective materials design method for developing high-performance small-pore materials for storage and separation of gas molecules. The continued success of PSP depends on broad availability and judicious choice of pore-partition ligands and better understanding of each structural module on stability and sorption properties. Here, by using substructural bioisosteric strategy (sub-BIS), a dramatic expansion of pore-partitioned materials is targeted by using ditopic dipyridyl ligands with non-aromatic cores or extenders, as well as by expanding heterometallic clusters to uncommon nickel-vanadium and nickel-indium clusters rarely known before in porous materials. The dual-module iterative refinement of pore-partition ligands and trimers leads to remarkable enhancement of chemical stability and porosity. Here a family of 23 pore-partitioned materials synthesized from five pore-partition ligands and seven types of trimeric clusters is reported. New materials with such compositionally and structurally diverse framework modules reveal key factors that dictate stability, porosity, and gas separation properties. Among these, materials based on heterometallic vanadium-nickel trimeric clusters give rise to the highest long-term hydrolytic stability and remarkable uptake capacity for CO2 , C2 H2 /C2 H4 /C2 H6 , and C3 H6 /C3 H8 hydrocarbon gases. The breakthrough experiment shows the potential application of new materials for separating gas mixtures such as C2 H2 /CO2 .

The synergistic effect of organic and inorganic sulfonic acids promotes new particle formation

New particle formation (NPF) represents a significant source of aerosol particles in the atmosphere; however, the NPF mechanisms remain uncertain, hindering the understanding and assessment of its environmental effects. Hence, we investigated the nucleation mechanisms in multicomponent systems including two inorganic sulfonic acids (ISAs), two organic sulfonic acids (OSAs), and dimethylamine (DMA) by combining quantum chemical (QC) calculations and molecular dynamics (MD) simulations, and evaluated the comprehensive effect of ISAs and OSAs on DMA-driven NPF. The QC results showed that the (Acid)2(DMA)0–1 clusters were strongly stable, and the (ISA)2(DMA)1 clusters exhibited higher stability than the (OSA)2(DMA)1 clusters because ISAs (sulfuric and sulfamic acids) provided more H-bonds and stronger proton transfer than OSAs (methanesulfonic and ethanesulfonic acids). ISAs readily engaged in dimer formation, whereas the stability of trimer clusters was mainly regulated by the synergistic effects of ISAs and OSAs. OSAs participated in cluster growth earlier than ISAs. Our results revealed that ISAs promote cluster formation, whereas OSAs facilitate the growth of clusters. The synergistic effect of ISAs and OSAs should be further investigated in areas with high [OSAs]: [ISAs].

Efficient Electrochemical Reduction of CO2 on g-C3 N4 Monolayer-supported Metal Trimer Catalysts: A DFT Study.

The electrochemical reduction of CO2 into valuable chemicals and fuels is a promising but challenging method to realize the carbon cycle. In this work, a series of transition metal trimer clusters supported on g-C3 N4 catalysts (M3 @g-C3 N4 , M=Cr, Mn, Fe, Co, Ni, Cu, and Ru) for electrochemical CO2 reduction (CO2 RR) toward C1 and C2 products were systemically studied using density functional theory (DFT) calculations. Our results show that CO2 could be adsorbed and activated effectively on M3 @g-C3 N4 from adsorption configurations and electronic structures analyses. Cu3 @g-C3 N4 is a promising electrocatalyst for CH4 production with a limiting potential of -0.42 V. Cr3 @g-C3 N4 , Fe3 @g-C3 N4 , and Co3 @g-C3 N4 produce a low limiting potential of -0.64 V, -0.45 V, and -0.64 V for C2 H4 production, respectively. Hydrogen evolution reaction is refrained on Cu3 @g-C3 N4 , Cr3 @g-C3 N4 , and Co3 @ g-C3 N4 . This work provides useful insights into transition metal trimer cluster catalysts with enhanced activity and selectivity in CO2 RR.

Insights into molecular cluster materials with adamantane-like core structures by considering dimer interactions.

A class of adamantane-like molecular materials attracts attention because they exhibit an extreme non-linear optical response and emit a broad white-light spectrum after illumination with a continuous-wave infrared laser source. According to recent studies, not only the nature of the cluster molecules, but also the macroscopic structure of the materials determines their non-linear optical properties. Here we present a systematic study of cluster dimers of the compounds AdR4 and [(RT)4 S6 ] (T=Si, Ge, Sn) with R=methyl, phenyl or 1-naphthyl to gain fundamental knowledge about the interactions in the materials. For all compounds, a similar type of dimer structures with a staggered arrangement of substituents was determined as the energetically most favorable configuration. The binding energy between the dimers, determined by including London dispersion interactions, increases with the size of the core and the substituents. The cluster interactions can be classified as substituent-substituent-dominated (small cores, large substituents) or core-core-dominated (large cores, small substituents). Among various possible dimer conformers, those with small core-core distances are energetically preferred. Trimer and tetramer clusters display similar trends regarding the minimal core-core distances and binding energies. The much lower energy barrier determined for the rotation of substituents as compared to the rotation of the cluster dimers past each other indicates that the rotation of substituents more easily leads to different conformers in the material. Thus, understanding the interaction of the cluster dimers allows an initial assessment of the interactions in the materials.

Synthesis, structure and dielectric behavior study of Mn (II)-4,4′-sulfonyldibenzoate-auxiliary ligand system based coordination polymers (CPs)

Based on MnCl2.4H2O, V-shaped ligand 4,4′-sulfonyldibenzoic acid (H2SBA), and two N-containing auxiliary ligands three new coordination polymers (CPs), namely: [Mn3(SBA)2(pyzc)2(DMA)2].DMA.H2O 1, [Mn3(SBA)2(phen)2(OAc)2].2DMA 2, and [Mn3(SBA)2(phen)2(OAc)2].2EtOH 3 [where, SBA = 4,4′-sulfonyldibenzoate, pyzc = 2-pyrazinecarboxylate, phen = 1,10-phenanthroline, OAc = acetate, DMF = N, N'-dimethylformamide, DMA = N, N'-dimethylacetamide] were synthesized using mixture of polar protic/aprotic solvents under solvothermal conditions. Single crystal X-ray study revealed that solid 1 is composed of tetrameric {Mn4O20N2} and dimeric units {Mn2O8N2}, whereas solids 2 and 3 are built of trimeric cluster {Mn3N2O14}. The structurally similar 2D coordination solids 2 and 3 showed comparable dielectric constant (ɛ'∼15.0) at room temperature. Solid 1 exhibited a higher value of dielectric constant (ɛ'∼30.5) probably due to the contribution from disordered polar guest solvent molecules, and 1D manganese carboxylate chains interaction. The crystal engineering of soluble 1:1 manganese carboxylate complex species, with or without coordination with an auxiliary ligand, is also explained mechanistically in this study. The approach not only provides a rationale for the composition and variation in the coordination linkage but also describes the crystal packing in terms of the dominant directional coordination and H-bonding forces.

Trimeric Ruthenium Cluster-Derived Ru Nanoparticles Dispersed in MIL-101(Cr) for Catalytic Transfer Hydrogenation

The synthesis of highly dispersed metal nanoparticles supported on metal–organic frameworks has been widely studied as a means to provide high-performance heterogeneous catalysts. Here, a Ru-nanoparticles-supported MIL-101(Cr) catalyst was prepared via a diamine and oxo-centered trimeric ruthenium cluster ([Ru3(μ3-O)(μ-CH3COO)6(H2O)3]CH3COO), Ru3 cluster sequential grafting, followed by alcohol reduction. Ethylenediamine (ED) acted as the linker, coordinating with unsaturated sites on both MIL-101(Cr) and the Ru3 cluster to produce Ru3-ED-MIL-101(Cr), after which selective alcohol reduction process provided the Ru/ED-MIL-101(Cr) catalyst. The synthesized Ru/ED-MIL-101(Cr) catalyst contained small, finely dispersed Ru nanoparticles, and the structural integrity of ED-MIL-101(Cr) was maintained. The Ru/ED-MIL-101(Cr) catalyst was tested for the transfer hydrogenation of benzene using isopropanol as the hydrogen source, where it was shown to outperform other Ru-based catalysts.

Quantitation of Enantiomeric Excess in an Achiral Environment Using Trapped Ion Mobility Mass Spectrometry.

We present a novel, straightforward method to determine the enantiomeric excess (ee) of tryptophan (Trp) and N-tert-butyloxycarbonyl-O-benzylserine (BBS) solutions without chiral additives. For this, lithium carbonate, sodium carbonate, or silver acetate was added to solutions of Trp or BBS. Singly negatively charged dimer and trimer clusters were then formed by electrospray ionization and analyzed using trapped ion mobility spectrometry (TIMS) and time-of-flight mass spectrometry. When a solution contains both enantiomers, homo- and heterochiral clusters are generated which can be separated in the TIMS-tunnel based on their different mobilities using a nitrogen buffer gas. The ratio of homochiral to heterochiral clusters shows a binomial distribution and can be calibrated with solutions of known ee to yield ee measurements of samples with better than 1% accuracy. Samples can be prepared rapidly, and measurements are completed in less than 5 min. Current instrumental limitations restrict this method to rigid molecules with large functional groups adjacent to the chiral centers. Nevertheless, we expect this method to be applicable to many pharmaceuticals and provide the example of 1-methyltryptophan to demonstrate this.

Cyclopropenylidene: Clustering and Interaction with Water Molecules.

Cyclopropenylidene (c-C3H2, abbreviated CPD) is a highly reactive, planar, partially aromatic carbene discovered in the interstellar medium, and, also recently, in the outer solar system. It is demonstrated herein on cogent quantum chemical grounds that CPD which possesses an electric dipole moment of 3.4 D is capable of forming stable dimer and trimer clusters through hydrogen-bonding. These attributes of CPD are conducive to the formation of stable hydrogen-bonded conformations with one- and two-water molecules. Having determined its consistency with the second-order Møller-Plesset perturbation theory MP2, we employ the ωB97xD hybrid density functional theory in conjunction with a 6-311++G(2d,2p) basis set for a credible description of noncovalent interactions involved in clustering. Molecular electrostatic potential (MESP) and characteristic vibrational frequency shifts upon clustering are presented.

Cluster quantum Monte Carlo study of two-dimensional weakly coupled frustrated trimer antiferromagnets

We report results from spin trimer-based cluster quantum Monte Carlo simulations for the thermodynamic properties of two-dimensional frustrated quantum antiferromagnets that are composed of weakly-coupled three-spin (trimer) clusters. In particular, we consider the spin-1/2 kagome lattice with a strong breathing distortion, and the triangle-square lattice model proposed previously for the cuprate La${}_4$Cu${}_3$MoO${}_{12}$. For both cases, we demonstrate that an appropriately chosen trimer-based computational basis allows us to significantly reduce the quantum Monte Carlo sign problem down to the low-temperature regime. Besides exploring the thermodynamic behavior for the triangle-square lattice model we also assess a mean field theory-based prediction for the onset of chiral order. For the breathing distorted kagome lattice model, we observe a robust two-peak structure in the specific heat, both in the quantum spin liquid and the lattice-nematic regimes.

Near field FEM simulations of plasmonic gold nanoparticle based SERS substrate with experimental validation

Surface enhanced Raman spectroscopy or surface enhanced Raman scattering (SERS) being a very powerful technique for quantitative and qualitative analysis finds application in low concentration detection of chemical and biological samples. In this work, we have presented a complete methodology of simulating nanoparticles-based SERS substrate. Different configurations namely single nanoparticle, dimer, trimer and tetramer nanoparticle clusters are simulated and enhancement factor for each configuration is estimated. Presented simulations are carried out with COMSOL Multiphysics software using Electromagnetic Waves module (Wave Optics) in frequency domain. The model of gold nanoparticle is established to determine the scatter field, which was further used to estimate the enhancement factor. Simulation results thus obtained are then validated with experimental results. The simulation study using the COMSOL Multiphysics tool helps in the design and development of the SERS substrate for maximum electromagnetic enhancement at a particular wavelength. The presented simulation methodology will be helpful for various SERS related computational studies in future. Presented approach helps in understanding the effect of various parameters such as particle size, inter particle gap, excitation wavelength, etc. on the EM enhancement. Simulating various possibilities before fabrication helps in saving money and time. For device realization, gold nanoparticles are synthesized using Turkevich method to achieve uniform and spherical nanoparticles. Synthesized nanoparticles (40–45 nm radius) were drop casted on a porous cellulose paper substrate to realize a SERS substrate. Nanogaps created between nanoparticles become the hot-spot locations leading to electromagnetic coupling and hence the Raman signal enhancement. Paper based SERS substrate is tested with Rhodamine B (1 μM) test sample. Enhancement of 106 was observed with the developed SERS substrate. UV–Vis spectrometer and Raman spectrometers are used for various characterizations.

Computational Prediction of Graphdiyne-Supported Three-Atom Single-Cluster Catalysts

Computational Prediction of Graphdiyne-Supported Three-Atom Single-Cluster Catalysts