Boat-shaped Structure Research Articles

Exploring electronic structure and spectral properties of nitrogen-doped boron clusters [formula omitted]N with [formula omitted

This report demonstrates the effect of nitrogen atom doping on boron clusters. It investigates the lowest energy structure and electronic and spectral properties of nitrogen–boron clusters of sizes 10 to 20 using the ABCluster global search technique and the CALYPSO method in combination with density functional theory. The calculation results show that these clusters’ global minima are plane or quasi-plane structures at n = 11, 13, 15–20, bowl-like structures at n = 10, 12, and a boat-shaped structure at n = 14. The calculated HOMO–LUMO gaps suggest that the clusters possess typical semiconductor properties. Chemical bonding analysis and NPA reveal these clusters’ strong covalent bonds and molecular properties. Molecular electrostatic potential explores the nature of interactions. Infrared and Raman spectra indicate that these clusters have several characteristic peaks, which can be used to identify the structures of the clusters and make comparative analyses with future experiments. Moreover, the electronic absorption spectrum analysis reveals that these clusters’ first absorption peak is in the visible band.

S-Shaped Fused Azacorannulene Dimer: Structural and Redox Properties

S-Shaped Fused Azacorannulene Dimer: Structural and Redox Properties

Fully conjugated azacorannulene dimer as large diaza[80]fullerene fragment

A fully conjugated azacorannulene dimer with a large π-surface (76π system) was successfully synthesized from a fully conjugated bifunctional polycyclic aromatic azomethine ylide. This molecule represents an example of diaza[80]fullerene (C78N2) fragment molecule bearing two internal nitrogen atoms. X-ray crystallography analysis shows its boat-shaped structure with two terminal azacorannulenes bent in the same direction. The molecular shape leads to unique selective association with a dumbbell-shaped C60 dimer (C120) over C60 through shape recognition. Owing to its large π-surface and a narrow HOMO–LUMO gap, the azacorannulene dimer exhibits red fluorescence with a quantum yield of up to 31%. The utilization of the fully conjugated bifunctional azomethine ylide is a powerful method for the bottom-up synthesis of large multiazafullerene fragments, providing a step towards the selective total synthesis of multiazafullerenes.

Syntheses and structural characterization of heterometallic trinuclear {Cu(I), Ag(I)}-Ir(III) hydride complexes bridged by Ir metalloligands

The reactions of [Ir(H)2(PPh3)2(tptz)]PF6 (1) (tptz = 2,4,6-tris(2-pyridyl)-s-triazine) with {Cu(I), Ag(I)} salts under Ar afforded heterometallic trinuclear {Cu(I), Ag(I)}-Ir(III)-tptz hydride complexes [CuIr2(H)4(PPh3)4(tptz)2](PF6)3·2Me2CO (2), [AgIr2(H)4(PPh3)4(tptz)2](PF6)3·4Me2CO·H2O (3a) and [AgIr2(H)4(PPh3)4(tptz)2](CF3SO3)2(PF6)·4Me2CO (3b). We have demonstrated that Ir(III)-tptz complex 1 can serve as a potentially bridgeable Ir metalloligand. X-ray analyses showed that meaningful intramolecular π-π stacking interactions exist in {Cu(I), Ag(I)}-Ir(III)-tptz hydride complexes 2, 3a and 3b. These intramolecular π-π stacking interactions could be contributed to the structural stabilization of the distorted boat-shaped structure. 1H and 31P NMR analyses showed that the structures of {Cu(I), Ag(I)}-Ir(III)-tptz hydride complexes 2 and 3a are kept in solution. The significant 1H NMR upfield shifts could be induced by the ring current effect from the phenyl groups of adjacent PPh3 ligands.

Study on Band Gap Characteristics of Boat-Shaped Phononic Crystal

In this paper, we analyze the two-dimensional Boat-shaped structure based on the finite element method. We calculated its energy band structure and vibration transmission properties and found that the structure has band gaps at both high and low frequencies. Compared with common traditional two- dimensional phononic crystals, the boat-shaped phononic crystal has the advantage of larger bandgap design and modulation parameter space due to their structural complexity. In order to obtain better bandgap characteristics, we studied the influence of four key parameters, such as the rod length and the angle between the rods, on the bandgap. The results show that: for low frequency band gaps, the width of the band gap can be effectively changed by changing the size of the angle between the rods while rod length greatly affects the bandgap position; for high band gaps, the length of rods has a large effect on the band gap position. These laws have guiding significance for the bandgap regulation of boat-shaped phononic crystal.

GENETIC BARCODING AND BOTANICAL STUDIES ON POTHOS SCANDENS L. LEAVES-AN EXTRA-PHARMACOPOEIAL DRUG OF AYURVEDA

Objective: This study was undertaken to carry out genetic barcoding, pharmacognostical and phytochemical studies on leaves of Pothos scandens L. belonging to the family Araceae. Methods: P. scandens, was collected from Cochin, Kerala, during the month of August 2019. Its leaves were examined for pharmacognostical characters and physicochemical, qualitative analysis and HPTLC studies was carried out following standard protocols recommended by the Ayurvedic Pharmacopoeia of India. Genetic barcoding of the fresh tender leaves samples was carried out through following standard methods. Results: Leaves are simple, alternate, broadly winged petiole. Transverse section through winged petiole portion showed U-shaped, epidermal cell along with cluster crystals. Transverse section through midrib boat-shaped structure, mesophyll undifferentiated, consist parenchyma cell, epidermis with thick cuticle along with waxy coating. Leaves powder shows green in color and microscopy reveals the presence of prismatic crystals, raphides, fibres, acicular crystals and monocot type 1 stomata. The plant is identified as Pothos scandens based on sequence homology and phylogenic analysis. Qualitative results show the presence of carbohydrates, protein, alkaloids and tannins. HPTLC profile shows 7 spots at both short UV and long UV and ferulic acid and kaempferol were identified through quantitative HPTLC. Conclusion: Pothos scandens is a climber with simple, alternate leaves. Acicular crystals and raphides, mucilaginous cavities, undifferentiated mesophyll are key characters of the identification of its leaf. DNA Barcoding results helps in correct identification of Pothos scandens. The results obtained from the phytochemical study will be helpful in the determination of the strength of purity and also for further standardization of the plant.

Structures, Electronic, and Spectral Properties of Doped Boron Clusters MB12 0/- (M = Li, Na, and K).

Structures and electronic properties of alkali metal atom-doped boron clusters MB120/– (M = Li, Na, K) are determined using the CALYPSO method for the global minimum search followed by density functional theory. It is found that the global minima obtained for the neutral clusters correspond to the half-sandwich structure and those of the monoanionic clusters correspond to the boat-shaped structure. The neutral MB12 (M = Li, Na, K) can be considered as a member of the half-sandwich doped B12 clusters, and the geometrical pattern of anion MB12– (M = Li, Na, K) is a new structure that is different from other doped B12 clusters. Natural population and chemical bonding analyses reveal that the alkali metal atom-doped boron clusters MB12– are characterized as charge transfer complexes, M+B122–, resulting in symmetrically distributed chemical bonds and electrostatic interactions between cationic M+ and boron atoms. The calculated spectra indicate that MB120/– (M = Li, Na, K) has meaningful spectral features that can be compared with future experimental data. Our work enriches the varieties of geometrical structures of doped boron clusters and can provide much insight into boron nanomaterials.

A Nanoboat with Fused Concave N-Heterotriangulene.

The surface extension of all-carbon based bowl-shaped molecules, such as corannulene and sumanene, to synthesize even larger buckybowls has been widely studied, leaving other concave compounds with heteroatoms less considered. Herein we present a highly curved molecule synthesized via stepwise cyclization of fjords of a bisacridone derivative. Crystallographic analysis unambiguously confirmed a boat-shaped structure with deformed bottom benzene ring. Theoretical calculation unravels an inversion process with an S-shaped transition structure rather than a planar one. The enlarged boat demonstrates interesting properties, such as red shifts in absorption and emission spectra, enhanced emission intensity, and convergent frontier molecular orbital energy levels, in comparison to the related concave N-heterotriangulene.

CASSCF Calculations Reveal Competitive Chair (Pericyclic) and Boat (Pseudopericyclic) Transition States for the [3,3] Sigmatropic Rearrangement of Allyl Esters.

(10,8)CASPT2/6-31G**//(10,8)CASSCF/6-31G** and CCSD(T)/cc-pVDZ//(10,8)-CASSCF/6-31G** calculations have been performed on the potential surface for the [3,3] sigmatropic allyl ester rearrangements of cis-3-penten-2-yl acetate (16) to trans-3-penten-2-yl acetate (17) and 3-buten-2-yl acetate (21) to trans-2-buten-1-yl acetate (22). The results are compared to DFT (B3LYP/6-31G**) calculations on the known 16 → 17 rearrangement that reported it to be concerted and pseudopericyclic through a boat-shaped transition structure ( Birney, D. M. et al. J. Am. Chem. Soc. 2009 , 131 , 528 - 537 ). The CASSCF calculations, on the other hand, uncovered competitive concerted pathways for both the 16 → 17 and 21 → 22 rearrangements, though it was necessary to apply certain approximations in the former case. While one CASSCF pathway in each case involves a boat-shaped transition structure, similar to the one located through DFT calculations, the other pathway involves a chair-shaped transition structure. Preference for chair or boat is shown to be method dependent. Moreover, examination of the CASSCF active-space orbitals clearly confirms that the boat-shaped transition structures are pseudopericyclic but significantly also established that the chair-shaped transition structures are clearly pericyclic. Conclusions based on these results, and regarding our understanding of pericyclic vs pseudopericyclic reactions, are proffered.

Structural and magnetic properties of FeGen-/0 (n = 3-12) clusters: Mass-selected anion photoelectron spectroscopy and density functional theory calculations.

The structural, electronic, and magnetic properties of FeGen-/0 (n = 3-12) clusters were investigated by using anion photoelectron spectroscopy in combination with density functional theory calculations. For both anionic and neutral FeGen (n = 3-12) clusters with n ≤ 7, the dominant structures are exohedral. The FeGe8-/0 clusters have half-encapsulated boat-shaped structures, and the opening of the boat-shaped structure is gradually covered by the additional Ge atoms to form Gen cage from n = 9 to 11. The structures of FeGe10-/0 can be viewed as two Ge atoms symmetrically capping the opening of the boat-shaped structure of FeGe8, and those of FeGe12-/0 are distorted hexagonal prisms with the Fe atom at the center. Natural population analysis shows that there is an electron transfer from the Ge atoms to the Fe atom at n = 8-12. The total magnetic moment of FeGen-/0 and local magnetic moment of the Fe atom have not been quenched.

Photoelectron Spectroscopy and Density Functional Calculations of TiGen− (n=7–12) Clusters

The growth pattern and electronic properties of TiGen− (n=7–12) clusters were investigated using anion photoelectron spectroscopy and density functional theory calculations. For both anionic and neutral TiGen clusters, a half-encapsulated boat-shaped structure appears at n=8, and the boat-shaped structure is gradually covered by the additional Ge atoms to form Gen cage at n=9–11. TiGe12− cluster has a distorted hexagonal prism cage structure. According to the natural population analysis, the electron transfers from the Gen framework to the Ti atom for TiGen−/0 clusters at n=8–12, implying that the electron transfer pattern is related to the structural evolution.

The structural and electronic properties of NbSin-/0 (n = 3-12) clusters: anion photoelectron spectroscopy and ab initio calculations.

Niobium-doped silicon clusters, NbSin- (n = 3-12), were generated by laser vaporization and investigated by anion photoelectron spectroscopy. The structures and electronic properties of NbSin- anions and their neutral counterparts were investigated with ab initio calculations and compared with the experimental results. It is found that the Nb atom in NbSin-/0 prefers to occupy the high coordination sites to form more Nb-Si bonds. The most stable structures of NbSi3-7-/0 are all exohedral structures with the Nb atom face-capping the Sin frameworks. At n = 8, both the anion and neutral adopt a boat-shaped structure and the openings of the boat-shaped structures remain unclosed in NbSi9-10-/0 clusters. The most stable structure of the NbSi11- anion is endohedral, while that of neutral NbSi11 is exohedral. The global minima of both the NbSi12- anion and neutral NbSi12 are D6h symmetric hexagonal prisms with the Nb atom at the center. The perfect D6h symmetric hexagonal prism of NbSi12- is electronically stable as it obeys the 18-electron rule and has a shell-closed electronic structure with a large HOMO-LUMO gap of 2.70 eV. The molecular orbital analysis of NbSi12- suggests that the delocalized Nb-Si12 ligand interactions may contribute to the stability of the D6h symmetric hexagonal prism. The AdNDP analysis shows that the delocalized 2c-2e Si-Si bonds and multicenter-2e NbSin bonds are important for the structural stability of the NbSi12- anion.

Photoelectron Spectroscopy and Density Functional Calculations of VGen– (n = 3–12) Clusters

The structural, electronic and magnetic properties of VGen–/0 (n = 3–12) clusters were investigated using anion photoelectron spectroscopy in combination with density functional theory calculations. We found that the dominant geometries are exohedral for the VGen–/0 clusters with n ≤ 7. The VGe8–/0 clusters have half-encapsulated boat-shaped structures, and the opening of the boat-shaped structure is gradually covered by the additional Ge atoms to form Gen cage from n = 9–11. At n = 12, a D3d distorted hexagonal prism cage structure is formed. According to the natural population analysis, for both anionic and neutral VGen clusters of n = 8–12, there is electron transfer from the Gen framework to the V atom and the total magnetic moments decrease to the minima. The electron transfer pattern and the minimization of the magnetic moments for these clusters are related to their structural evolution.

A special place in the saltings? Survey and excavation of an Iron Age estuarine islet at An Dunan, Lewis, Western Isles

This is the third of a series of four papers that present the excavations undertaken on the Uig peninsula, Isle of Lewis, as part of the Uig Landscape Project. We present the archaeological evidence from An Dunan, a causewayed tidal islet in the salt marsh of Uig sands, a liminal and potentially ritual site dating to the Iron Age and medieval period. The first main Middle Iron Age phase was characterised by activities centred on an ash mound, demarcated by four large orthostats, within an essentially rectilinear structure containing internal cellular divisions. The activities within the structure have been interpreted as non-domestic in nature. The second main phase involved the medieval re-use of aspects of the Iron Age building to create a small boat-shaped structure, with very little associated material culture. The structural, artefactual and environmental evidence from the site is presented, before being interpreted within the wider research context of the archaeology of the Western Isles and Atlantic Scotland.

Observation of Posterior Precortical Vitreous Pocket Using Swept-Source Optical Coherence Tomography

To observe posterior precortical vitreous pockets (PPVPs) using swept-source optical coherence tomography (SS-OCT). We performed SS-OCT in both eyes of 58 volunteers (36 men, 22 women) using 12-mm horizontal vertical scans through the macula and optic disc. To minimize age-related changes (liquefaction or posterior vitreous detachment), all subjects were a mean of 26.2 years (range, 22-40 years). The refractive errors ranged from -9.5 diopters (D) to +3.0 D. To estimate the PPVP size, we measured the height between the fovea and the anterior border of the PPVP and the maximal width in the 12-mm horizontal scan through the fovea and disc. SS-OCT visualized the PPVPs as boat-shaped lacunae in the macular area bilaterally in all subjects (maximal width, 3114-9887 μm; mean width, 6420.6; central height, 208-1877 μm; mean height, 708.1 in the right eyes, with no significant difference in the left eyes). There was a significant correlation between the PPVP height and myopic refractive error. The posterior wall of the PPVP was a thin vitreous cortex, thinnest at the fovea. The septum was between the nasal border of the pocket and Cloquet's canal, which extended forward and tilted superiorly in all cases. A channel connected Cloquet's canal and the PPVPs bilaterally in 54 (93.1%) of 58 cases. SS-OCT clarified the boat-shaped PPVP structure in vivo. Although the central height increased with the myopic refractive error, the width was unchanged. A channel connecting Cloquet's canal and PPVP suggested the route of aqueous humor into the PPVP.

Theoretical study of the benzoquinone–tetrathiafulvalene–benzoquinone triad in neutral and oxidized/reduced states

This work presents a thorough DFT quantumchemical characterization of the structural and electronic properties of the benzoquinone–tetrathiafulvalene–benzoquinone (Q–TTF–Q) triad in its neutral and oxidized/ reduced states. The minimum-energy structure of the triad in its neutral state corresponds to a C2v boat conformation, although the planar D2h structure is also found to be a minimum- energy structure practically degenerate with the boat conformation. Upon oxidation, electrons are mainly extracted from the TTF backbone and the boat-shaped TTF structure evolves toward a planar D2hh and to a twisted D2 conformation in the cation and dication, respectively. The theoretical characterization of the triad in its radical anion and dianion states is performed with several hybrid (B3LYP, PBE0 and BHHLYP), meta-hybrid (M06-2X) and longrange- corrected (CAM-B3LYP, ωB97X and ωB97XD) functionals. In gas phase, BHHLYP, M06-2X, CAMB3LYP, ωB97X and ωB97XD functionals correctly predict the localized Q-–TTF–Q structure as the most stable structure, whereas the hybrid B3LYP and PBE0 functionals lead to a delocalized (Q–cTTF–Q)- structure. The incorporation of solvent effects is crucial to provide a qualitatively correct description of the anion species where the localized solutions are found to be minimum-energy structures for all the functionals evaluated. The (Q–TTF–Q)2- dianion is predicted to be a biradicaloid species in its electronic ground state. Calculations predict that both Q- → Q0 and TTF → Q0 charge-transfer electronic transitions are associated with the low-energy, broad absorption band experimentally observed for the localized Q-–TTF–Q anion.

Synthesis of pyrrolidine homoazasugars and 3,4-dihydroxy-5-hydroxymethylprolines using aldol additions of metalated bislactim ethers to 2,4-O-ethylidene-d-erythroses

A strategy for the synthesis of 2,5-dideoxy-2,5-iminohexitols and 2,5-dideoxy-2,5-iminoglyconic acids is described by using diastereoselective aldol additions of metalated bislactim ethers to 2,4-O-ethylidene-d-erythroses and intramolecular N-alkylation as key steps. The nature of the metal fragment of the azaenolate and the beta-alkoxy protecting group for the erythrose moiety were varied to modulate the level and the direction of the asymmetric induction in the aldol addition. The contrasting stereochemical results of the tin(II)-mediated aldol reactions have been rationalized with the aid of density functional theory calculations (B3LYP/cc-pVDZ-PP). DFT calculations indicate that boat-shaped transition structures that allow the formation of a stabilizing hydrogen bond can account for the unusual anti,syn-stereoselectivity of the aldol addition to beta-protected 2,4-O-ethylidene-erythroses. In the addition to the "unprotected" 2,4-O-ethylidene-erythrose, the preference for chair-shaped transition structures in which the erythrose moiety is involved in a six-membered chelate ring is consistent with the experimentally observed syn,anti-stereochemical outcome. The preparative utility of the aldol-based approach was demonstrated by application in concise routes for the synthesis of glycosidase inhibitors 2,5-dideoxy-2,5-iminogalactitol and 2,5-dideoxy-2,5-imino-d-glucitol (DGADP and DGDP) and 3,4-dihydroxy-5-hydroxymethylprolines (2,5-dideoxy-2,5-imino-l-gulonic acid and 2,5-dideoxy-2,5-imino-l-galactonic acid) that may be useful for glycosidase and glycuronidase inhibition.

1,5-Anti Stereocontrol in the Boron-Mediated Aldol Reactions of β-Alkoxy Methyl Ketones: The Role of the Formyl Hydrogen Bond

The boron-mediated aldol reactions of certain types of beta-alkoxy methyl ketone show remarkably high levels of stereoinduction with achiral aldehydes, leading preferentially to 1,5-anti related stereocenters. Given the low levels of asymmetric induction usually observed in acetate aldol reactions, this is of great synthetic utility and has been used successfully in the total synthesis of a number of polyketide natural products. We have investigated the effects of the alkoxy protecting group (OMe, OPMB, PMP acetal, tetrahydropyran, and OTBS) present in the boron enolate on the level and sense of remote 1,5-stereoinduction, using density functional theory calculations (B3LYP/6-31G**). Our predictions of diastereoselectivity from comparison of the competing aldol transition structures are in excellent qualitative and quantitative agreement with experimentally reported values. We conclude that the boron aldol reactions of unsubstituted boron enolates proceed via boat-shaped transition structures in which a stabilizing formyl hydrogen bond exists between the alkoxy oxygen and the aldehyde proton. It is this interaction that leads to preferential formation of the 1,5-anti adduct, by minimizing steric interactions between the beta-alkyl group and one of the ligands on boron. In the case of silyl ethers, the preference for this internal hydrogen bond is not observed due to the size of the protecting group and the electron-poor oxygen atom that donates electron density into the adjacent silicon atom. We show that this stereochemical model is also applicable in rationalizing the 1,4-syn stereoselectivity of boron aldol reactions involving certain alpha-chiral methyl ketones. These detailed results may be summarized as a conformational diagram that can be used to predict the sense of stereoinduction.

Cation−π Interactions Stabilize the Structure of the Antimicrobial Peptide Indolicidin near Membranes: Molecular Dynamics Simulations

We implemented molecular dynamics simulations of the 13-residue antimicrobial peptide indolicidin (ILPWKWPWWPWRR-NH2) in dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles. In DPC, a persistent cation-pi interaction between TRP11 and ARG13 defined the structure of the peptide near the interface. A transient cation-pi interaction was also observed between TRP4 and the choline group on DPC lipids. We also implemented simulation of a mutant of indolicidin in the DPC micelle where TRP11 was replaced by ALA11. As a result of the mutation, the boat-shaped conformation is lost and the structure becomes significantly less defined. On the basis of this evidence, we argue that cation-pi interactions determine the experimentally measured, well-defined boat-shaped structure of indolicidin. In SDS, the lack of such interactions and the electrostatic binding of the terminal arginine residues to the sulfate groups leads to an extended peptide structure. To the best of our knowledge, this is the first time that a cation-pi interaction between peptide side chains has been shown to stabilize the structure of a small antimicrobial peptide. The simulations are in excellent agreement with available experimental measurements: the backbone of the peptide is more ordered in DPC than in SDS; the tryptophan side chains pack against the backbone in DPC and point away from the backbone in SDS; the rms fluctuation of the peptide backbone and peptide side chains is greater in SDS than in DPC; and the peptide backbone order parameters are higher in DPC than in SDS.

Cyclooctatetraene computational photo- and thermal chemistry: a reactivity model for conjugated hydrocarbons.

We use ab initio CASSCF and CASPT2 computations to construct the composite multistate relaxation path relevant to cycloocta-1,3,5,7-tetraene singlet photochemistry. The results show that an efficient population of the dark excited state (S(1)) takes place after ultrafast decay from the spectroscopic excited state (S(2)). A planar D(8)(h)-symmetric minimum represents the collecting point on S(1). Nonadiabatic transitions to S(0) appear to be controlled by two different tetraradical-type conical intersections, which are directly accessible from the S(1) minimum following specific excited-state reaction paths. The higher-energy conical intersection belongs to the same type of intersections previously documented in linear and cyclic conjugated hydrocarbons and features a triangular -(CH)(3)- kink. This point mediates both cis --> trans photoisomerization and cyclopropanation reactions. The lowest energy conical intersection has a boat-shaped structure. This intersection accounts for production of semibullvalene or for double-bond shifting. The mapping of both photochemical and thermal reaction paths (including also Cope rearrangements, valence isomerizations, ring inversions, and double-bond shifting) has allowed us to draw a comprehensive reactivity scheme for cyclooctatetraene, which rationalizes the experimental observations and documents the complex network of photochemical and thermal reaction path interconnections. The factors controlling the selection and accessibility of a number of conjugated hydrocarbon prototype conical intersections and ground-state relaxation channels are discussed.