Pentameric Clusters Research Articles

DFT and TD‐DFT Study of Many‐Body and Hydrogen Bonding Interactions: Nitrosamine Oligomers

AbstractThis study focuses on the properties and intermolecular interactions of nitrosamine oligomers, which are important in both semiconductor manufacturing and nuclear waste management. The study explores various configurations of nitrosamine oligomers, ranging from monomers to pentamers in linear, ladder, and cyclic clusters, with the finding that dimer cyclic forms and hexamers and above are unstable. Many‐body analysis revealed that two‐body interaction energies made remarkable contributions to the binding energy, while the sum of 3‐, 4‐, and 5‐body energy contributed less, indicating the decrease in stability of nitrosamine from dimer to pentamer clusters. Using advanced computational techniques, such as dispersion‐corrected B3LYP‐D3 and TD‐DFT, the study investigates the vibrational modes and electronic absorption spectra of nitrosamine oligomers. The results reveal that different configurations can significantly affect the vibrational modes and electronic properties of nitrosamine oligomers. The NH2 symmetric and asymmetric modes were particularly intense in various forms of nitrosamine oligomers. The wavelengths of electronic transition, oscillator strength, and HOMO to LUMO gap were reported. Additionally, the study reports on nitrosamine oligomers’ hydrogen‐bonded cooperativity and binding energy contributions. Overall, these findings offer valuable insights into the stability and properties of nitrosamine oligomers, with potential applications in materials science and chemical engineering.

Phase Diagram and Quantum Entanglement Properties of a Pentamer S = 1/2 Heisenberg Spin Cluster.

Cluster molecular magnets prove their potential for applications in quantum technologies, encouraging studies of quantum entanglement in spin systems. In the paper we discuss quantum entanglement properties of pentamer cluster composed of spins S=1/2 forming a tetrahedron with additional spin in its center, with geometry reproducing the smallest nonplanar graph. We model the system with isotropic Heisenberg Hamiltonian including external magnetic field and use exact diagonalization approach to explore the ground-state phase diagram and thermodynamic properties within canonical ensemble formalism. We focus the interest on two-spin entanglement quantified by Wootters concurrence. For ground state, we find two states with total cluster spin equal to 3/2 exhibiting entanglement, occurring preferably for antiferromagnetic interactions. For finite temperatures, we predict the presence of magnetic-field-induced entanglement as well as temperature-induced entanglement.

SARS-CoV-2 Envelope Protein Forms Clustered Pentamers in Lipid Bilayers.

The SARS-CoV-2 envelope (E) protein is a viroporin associated with the acute respiratory symptoms of COVID-19. E forms cation-selective ion channels that assemble in the lipid membrane of the endoplasmic reticulum Golgi intermediate compartment. The channel activity of E is linked to the inflammatory response of the host cell to the virus. Like many viroporins, E is thought to oligomerize with a well-defined stoichiometry. However, attempts to determine the E stoichiometry have led to inconclusive results and suggested mixtures of oligomers whose exact nature might vary with the detergent used. Here, we employ 19F solid-state nuclear magnetic resonance and the centerband-only detection of exchange (CODEX) technique to determine the oligomeric number of E’s transmembrane domain (ETM) in lipid bilayers. The CODEX equilibrium value, which corresponds to the inverse of the oligomeric number, indicates that ETM assembles into pentamers in lipid bilayers, without any detectable fraction of low-molecular-weight oligomers. Unexpectedly, at high peptide concentrations and in the presence of the lipid phosphatidylinositol, the CODEX data indicate that more than five 19F spins are within a detectable distance of about 2 nm, suggesting that the ETM pentamers cluster in the lipid bilayer. Monte Carlo simulations that take into account peptide–peptide and peptide–lipid interactions yielded pentamer clusters that reproduced the CODEX data. This supramolecular organization is likely important for E-mediated virus assembly and budding and for the channel function of the protein.

Confocal Raman microscopic evidence for cyclic water Pentamer, at high temperatures in a supramolecular host of [Cu(cyclam)(N3)2]·4H2O

Here, we report the existence of a pentameric water cluster in the host framework of [Cu(cyclam)(N3)2]·4H2O, that is stable upto 167 °C, well above the boiling point of water. The pentameric cluster structure embedded in the host framework is evident from the single crystal studies. The high thermal stability is confirmed by TGA and temperature dependent confocal Raman microscopic studies, where loss of water bands is well captured between 167 and 170 °C, besides its existence through SCXRD studies. To the best of our knowledge, this is the first report where temperature dependent confocal Raman microscopic investigation is used to study the stability of water in crystal environment. The study promises that temperature dependent confocal Raman microscopy can be an efficient tool to investigate the existence and stability of small water clusters, precisely in restricted environments.

Quantifying Effects of Active Site Proximity on Rates of Methanol Dehydration to Dimethyl Ether over Chabazite Zeolites through Microkinetic Modeling.

Control of the spatial proximity of Brønsted acid sites within the zeolite framework can result in materials with properties that are distinct from materials synthesized through conventional crystallization methods or available from commercial sources. Recent experimental evidence has shown that turnover rates of different acid-catalyzed reactions increase with the fraction of proximal sites in chabazite (CHA) zeolites. The catalytic conversion of oxygenates is an important research area, and the dehydration of methanol to dimethyl ether (DME) is a well-studied reaction as part of methanol-to-olefin chemistry catalyzed by solid acids. Published experimental data have shown that DME formation rates (per acid site) increase systematically with the fraction of proximal acid sites in the six-membered ring of CHA. Here, we probe the effect of acid site proximity in CHA on methanol dehydration rates using electronic structure calculations and microkinetic modeling to identify the primary causes of this chemistry and their relationship to the local structure of the catalyst at the nanoscale. We report a density functional theory-parametrized microkinetic model of methanol dehydration to DME, catalyzed by acidic CHA zeolite with direct comparison to experimental data. Effects of proximal acid sites on reaction rates were captured quantitatively for a range of operating conditions and catalyst compositions, with a focus on total paired acid site concentration and reactant clustering to form higher nuclearity complexes. Next-nearest neighbor paired acid sites were identified as promoting the formation of methanol trimer clusters rather than the inhibiting tetramer or pentamer clusters, resulting in large increases in the rate for DME production due to the lower energy barriers present in the concerted methanol trimer reaction pathway. The model framework developed in this study can be extended to other zeolite materials and reaction chemistries toward the goal of rational design and development of next-generation catalytic materials and chemical processes.

Electronic Structure and Electron Delocalization in Bare and Dressed Boron Pentamer Clusters.

The electronic structures of the lowest energy spin-states of the cationic, neutral and anionic bare boron pentamer clusters have been investigated by means of high level multiconfigurational type calculations, in view of the large static and dynamical electron correlation effects for these species. We found that resembles a singlet spin-state perfect pentagon, which bears no intra-annular chemical bonding interactions, as shown by our analysis of the electron delocalization carried out in terms of the normalized Giambiagi ring-current index, and the total and adjacent atom-pair delocalization indices. However, its lowest-energy triplet and quintet spin-state isomers have C2v symmetry, with large intra-annular chemical bonding interactions. This geometrical feature extends to both the neutral and the anionic species. Namely, the lowest-energy isomers of boron pentamer neutral and anionic clusters have peripheral and intra-annular sizable bonding interactions reflected in the delocalization of both π- and σ-type valence natural orbitals over the whole molecular plane, which impart large structural stability. In accordance to our calculations, the lowest energy triplet spin-state isomer of the anionic boron pentamer cluster has C2 symmetry, and consequently, it should show optical activity. Finally, we have studied the change of the geometrical structure of the boron pentamer clusters from planar to compact three-dimensional structures caused by the bonding of ligands to the boron atoms. Our explicit all-electron calculations have been rationalized in terms of the shell-closure of the delocalized valence orbitals of the clusters as predicted by the jellium model extended to nonspherical confinement potentials, circumscribing the role of the ligand to modulate the total number of valence electrons assigned to the core cluster.

Mechanism of proton transport in water clusters and the effect of electric fields: A DFT study

Proton transport inside metal organics frameworks (MOFs) plays an important role to understand and develop a new type of material for a high conductivity application. One of the possible pathways of this process is via water cluster which is confined inside the MOFs structure. In this work, the mechanism of proton transport is investigated within the Density Functional Theory (DFT) calculations. Different water clusters from dimer to pentamer and octamer, which are equivalent to water structures inside the tetrahedral and cubic cavities of MOF-801, respectively, were systematically considered. The results show that proton transfer inside the pentamer cluster has the lowest barrier around 16 kJ/mol. Moreover, the presence of electric fields has a strong effect on the mechanism and energy profile of the proton transfer in both pentamer and octamer cluster. Our DFT prediction of proton migration energies is supported by experimental data of high conducting MOFs such as MOF-801.

Role of supramolecular interactions in crystal packing of Strandberg-type cluster-based hybrid solids

Two new Strandberg-type cluster-based phosphomolybdates {H-2a3mp}5[{PO3(OH)}{PO4}Mo5O15], 1 and {H-2a4mp}5[{PO3(OH)}{PO4}Mo5O15]·6H2O, 2 have been crystallized via solvent evaporation technique using 2-amino-3-methylpyridine (2a3mp) and 2-amino-4-methylpyridine (2a4mp) respectively. The solids were characterized using single-crystal X-ray diffraction, powder X-ray diffraction, fourier transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy and cyclic voltammetry. The solid 1 crystallized in monoclinic system with space group P21/c, a = 8.394(1), b = 27.398(6), c = 21.521(4) A, β = 97.68(3)°, Z = 4. The solid 2 crystallized in triclinic system with space group P-1, a = 11.728(1), b = 14.234(1), c = 19.589(1) A, α = 68.906(3), β = 89.454(3), γ = 66.559(3)°, Z = 2. The solids 1 and 2 formed a supramolecular framework stabilized by hydrogen bonding interaction between cluster anions and organic moieties. CH…π interactions between the organic moieties reinforced the crystal packing in 1 and 2. While crystal packing effects resulted in the formation of solvent-accessible voids in 1; aggregation of lattice water molecules in 2 facilitated the formation of pentameric water cluster. In addition, electrochemical behavior of 1 and 2 has also been investigated. Two new Strandberg-type cluster based phosphomolybdates, 1 and 2 have been crystallized via solvent evaporation technique using 2-amino-3-methylpyridine and 2-amino-4-methylpyridine. Detailed structural analysis revealed the role of supramolecular interactions in the crystal packing of these solids. In addition, electrochemical behavior of 1 and 2 has also been investigated.

Two-Dimensional Correlation Spectroscopy (2D-COS) of Gas-Phase Pyrrole Clusters in a Supersonic Jet: Treatment of Sharp Bands on a Broad Background.

Two-dimensional correlation spectroscopy (2D-COS) is a useful technique to analyze any intensity behavior of optical spectra that exhibit a complicated feature with overlapped bands. In this study, we apply 2D-COS to the infrared (IR) spectra of gas-phase pyrrole (Py) clusters. The NH stretching vibrations of the Py clusters are measured by cavity ringdown spectroscopy. The observed IR spectra of the Py clusters consist of sharp bands, full width half-maximum (FWHM) ∼1 cm-1, and a broad background (FWHM >50 cm-1). The 2D asynchronous correlation spectra reveal that the sharp bands and a broad background are assigned to small clusters of dimer to pentamer and large clusters with bulk-like structures, respectively, which support the results of our previous study. The sharp bands are also analyzed using another 2D asynchronous correlation spectrum, which is obtained by decomposing the observed IR spectra into sharp and broad components. Because the asynchronous signals are consistent with those obtained from the IR spectra without decomposition, the result would suggest that we need not to decompose the IR spectra into sharp and broad components before applying 2D-COS. However, our model simulations of 2D-COS showed a counterexample that gives an incorrect result without removing a broad background component from the IR spectra. This study strongly suggests that we need to undertake a careful treatment of the complicated IR spectrum with various widths of bands.

Ionized water clusters , n = 2 to 6: A high‐accuracy study of structures and energetics

AbstractIonized water clusters, , have been of remarkable interest owing to their crucial roles in many chemical and biological processes. Small cationic water clusters , n = 2 to 6 serve as reasonable models for understanding the nature of the ionized water. In this study, employing high‐level ab initio quantum chemical methods, such as the density‐fitted orbital‐optimized linearized coupled‐cluster doubles (DF‐OLCCD), coupled‐cluster singles and doubles (CCSD), and coupled‐cluster singles and doubles with perturbative triples [CCSD(T)], a high‐accuracy study of structures and energetics for cationic water clusters [, n = 2‐6] is presented. In this study, 2 dimer, 8 trimer, 18 tetramer, 23 pentamer, and 25 hexamer clusters are reported. Most of the structures considered are reported for the first time. Relative, binding, and vertical attachment energies (VAEs), for the first time, are presented at the complete basis set (CBS) limit, extrapolating energies of the aug‐cc‐pVTZ and aug‐cc‐pVQZ basis sets, to provide the most accurate energetics to date. Our results demonstrate that as cluster size increases, the VAE value decreases, which indicates that large‐size clusters better compensate for the electron deficiency compared with small‐size clusters. The VAE values for pentamer and hexamer clusters are 118.5 to 165.5 and 121.9 to 153.7 kcal mol−1, respectively. Further, our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in cationic clusters due to hydrogen bond interactions. The average binding energy per water molecule varies from −16.6 to −21.8 kcal mol−1 for the clusters considered. Hence, we present the most extensive and accurate study on ionized water clusters to date. Further, our results indicate that the DF‐OLCCD method is very promising for ionic molecular clusters, and its accuracy approaches the CCSD(T) quality. The inexpensive analytic gradients of DF‐OLCCD, compared with CCSD(T), make it very helpful for high‐accuracy studies of molecular geometries.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics.

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol-1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol-1. Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol-1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Soft Templating of Water Aggregates Disrupts π–π Stacking in Crystalline Poly(3-hexylthiophene)

The π–π stacking robustness of the photoactive layer is key to maintaining efficiency of organic photovoltaics (OPVs). We show local disruption more than 2 A on average in the π–π stack of crystalline poly(3-hexylthiophene) (P3HT), one of the most common materials used in OPVs, through formation of a chainlike water structure with limited growth and mostly pentameric cluster ends. In contrast, a 3D aggregated water cluster with constant growth is observed in amorphous P3HT. Dynamics of water molecules that form the largest aggregates in crystalline P3HT show the effect of limited mobility, when compared to amorphous P3HT, due to dual confinement from both alkyl side groups and thiophene backbone. We term this dual confinement soft templating and quantify its effect on nature, size, and hydrogen bond participation of water aggregates in crystalline and amorphous P3HT using all-atom molecular dynamics with in-house developed potentials that were previously shown to represent the interfacial and wetting beha...

Hydrogen Peroxide Insular Dodecameric and Pentameric Clusters in Peroxosolvate Structures

AbstractPeroxosolvates of 2‐aminonicotinic acid (I) and lidocaine N‐oxide (II) including the largest insular hydrogen peroxide clusters were isolated and their crystal structures were determined by single‐crystal X‐ray diffraction. An unprecedented dodecameric hydrogen peroxide insular cluster was found in I. An unusual cross‐like pentameric cluster was observed in the structure of II. The topology of the (H2O2)12 assembly was never observed for small‐molecule clusters. In I and II new double and triple cross‐orientational disorders of H2O2 were found. Cluster II is the first example of a peroxosolvate crystal structure containing H2O2 molecules with a homoleptic hydrogen peroxide environment. In II, a hydrogen bond between an H2O2 molecule and a peptide group ‐CONH⋅⋅⋅O2H2 was observed for the first time.

Hydrogen Peroxide Insular Dodecameric and Pentameric Clusters in Peroxosolvate Structures.

Peroxosolvates of 2-aminonicotinic acid (I) and lidocaine N-oxide (II) including the largest insular hydrogen peroxide clusters were isolated and their crystal structures were determined by single-crystal X-ray diffraction. An unprecedented dodecameric hydrogen peroxide insular cluster was found in I. An unusual cross-like pentameric cluster was observed in the structure of II. The topology of the (H2 O2 )12 assembly was never observed for small-molecule clusters. In I and II new double and triple cross-orientational disorders of H2 O2 were found. Cluster II is the first example of a peroxosolvate crystal structure containing H2 O2 molecules with a homoleptic hydrogen peroxide environment. In II, a hydrogen bond between an H2 O2 molecule and a peptide group -CONH⋅⋅⋅O2 H2 was observed for the first time.

C–H···O Hydrogen Bonding in Pentamers of Isatin

Self-assembled monolayers of 1H-indole-2,3-dione (isatin), 3-methyl 2-oxindole, and 7-fluoroisatin are observed on the Au(111) surface via scanning tunneling microscopy (STM). We observed that isatin forms pentamers with density functional theory providing support for a cyclic structure stabilized by both N–H···O and C–H···O hydrogen bonds between neighboring molecules. The C–H···O bond is made between the 7-position C–H acting as the hydrogen bond donor and the 3-position carbonyl as the hydrogen bond acceptor, and calculations show that the isatin pentamer structure is 12 kJ/mol more stable than the dimer. When the 3-position carbonyl is removed and replaced with a methyl group (3-methyl 2-oxindole), we observe a monolayer with a mixture of catemer chains and pentameric clusters that are qualitatively different from those of isatin. Pentamer formation is completely broken when the 7-position hydrogen is removed and replaced with fluorine; the monolayer of 7-fluoroisatin is composed of a mixture of close...

Geometric and Electronic Structures of Vanadium Sub-nano Clusters, Vn (n = 2-5), and their Adsorption Complexes with CO and O2 Ligands: A DFT-NBO Study

In this study, electronic structures of ground state of pure vanadium sub-nano clusters, Vn (n=2-5), and their interactions with small ligands for example CO and triplet O2 molecules are investigated by using density functional theory (DFT) calibration at the mPWPW91/QZVP level of theory. The favorable orientations of these ligands in interaction with pure vanadium sub-nano clusters were determined. Multiplicities of these pure clusters are triple, doublet, singlet and doublet for dimer, trimer, tetramer and pentamer, respectively. While the CO molecule is associatively adsorbed on vanadium clusters, triplet O2 is dissociated over adsorption. Primary and secondary hyper-conjugation concepts have been employed to show stabilization of vanadium oxide complexes. Natural bond orbital (NBO) and natural resonance theory (NRT) analysis revealed that trimer, tetramer and pentamer clusters are relatively delocalized and have some resonance structures.

Classification of self-assembling protein nanoparticle architectures for applications in vaccine design.

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.

A series of s-block (Ca, Sr and Ba) metal–organic frameworks: synthesis and structure–property correlation

A series of metal–organic frameworks based on alkaline earth metal ions (Ca, Sr and Ba) and 1,3,5-benzenetribenzoic acid (BTB) have been synthesized and characterized. These are [H2N(CH3)2][Ca7(BTB)5(H2O)8(DMF)4]·4H2O (1), [H2N(CH3)2]2[Sr5(H2O)6(BTB)4] (2) and [H2N(CH3)2][Ba(H2O)(BTB)] (3). All the structures are three-dimensional in nature with different secondary building units. Compound 1 contains one-dimensional Ca–O–Ca zigzag chains while compound 2 contains Sr5O28 pentameric clusters and compound 3 contains one-dimensional Ba–O–Ba chains. Both compounds 1 and 3 form (3,6)-net connectivity while compound 2 forms (3,12)-net connectivity. Optical band gap energy measurements show that compound 1 (2.65 eV) has low band gap energy compared to 2 (3.22 eV) and 3 (3.32 eV). This variation in band gap energy may be due to the difference in structural arrangement. Compound 3 crystallizes in a non-centrosymmetric space group (Pna21), which belongs to the polar point group C2v. This compound displays a strong SHG response and good ferroelectric and piezoelectric properties.

Green approach to stereoselective synthesis of benzo[d]chromeno[3,4- h]oxathiazonine derivatives via MCRs in water: a combined experimental and DFT study.

(7S, 14S, 16R)- dialkyl 6-oxo-6,7,13,14-tetrahydro-7,14-methanobenzo[d]chromeno[3,4- h][1,6,3]oxathiazo-nine-14,16-dicarboxylates 4 and (S)-methyl 2-(2-methoxy-2-oxoethyl)-2,3- dihydrobenzo[d]thiazole-2-carboxylates 5 were readily synthesized in a ratio 3:1 and moderated yield by multicomponent reactions of 4-hydroxycoumarin and acetylenic esters with benzothiazole without using a catalyst. Also, The GIAO/DFT approach at the B3LYP/6-31G** level of theory was used to calculate the (1)H, (15)N, (17)O and (13)C NMR chemical shifts of product 4b. These computations are performed on the basis of X-ray structural data which are collected at 120(2) K temperature. In order to take into account intermolecular hydrogen bonds and the van der Waals effects, two different sizes of clusters (two model of trimeric and pentameric clusters) have been considered. A comparison between the experimental (Exp.) and calculated (Cal.) (1)H and (13)C NMR chemical shifts may reveal that the solution contains monomer, trimer1, trimer2, and pentamer models.

Curvature Concentrations on the HIV-1 Capsid

Abstract It is known that the retrovirus capsids possess a fullerene-like structure. These caged polyhedral arrangements are built entirely from hexagons and exactly 12 pentagons according to the Euler theorem. Viral capsids are composed of capsid proteins, which create the hexagon and pentagon shapes by groups of six (hexamer) and five (pentamer) proteins. Different distributions of these 12 pentamers result in icosahedral, tubular, or conical shaped capsids. These pentamer clusters introduce declination and hence curvature on the capsids. This paper provides explicit and quantitative characterization of curvature on virus capsids. The concept of curvature concentration is also introduced. For the HIV (5,7)-cone, it is shown that the curvature concentration at the narrow end is about at least four times higher than that at the broad end. Our modeling results about curvature concentrations on HIV-1 capsids echo the results in the literature that the pentamers are in the regions with the highest stress, although the connection between the two approaches (curvature concentration and stress) is to be explored. This also leads to a conjecture that “HIV-1 capsid narrow end may close last during maturation but open first during entry into a host cell".