TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples.

In cancer genomics, variant calling has advanced, but traditional mean accuracy evaluations are inadequate for biomarkers like tumor mutation burden, which vary significantly across samples, affecting immunotherapy patient selection and threshold settings. In this study, we introduce TMBstable, an innovative method that dynamically selects optimal variant calling strategies for specific genomic regions using a meta-learning framework, distinguishing it from traditional callers with uniform sample-wide strategies. The process begins with segmenting the sample into windows and extracting meta-features for clustering, followed by using a pre-trained meta-model to select suitable algorithms for each cluster, thereby addressing strategy-sample mismatches, reducing performance fluctuations and ensuring consistent performance across various samples. We evaluated TMBstable using both simulated and real non-small cell lung cancer and nasopharyngeal carcinoma samples, comparing it with advanced callers. The assessment, focusing on stability measures, such as the variance and coefficient of variation in false positive rate, false negative rate, precision and recall, involved 300 simulated and 106 real tumor samples. Benchmark results showed TMBstable's superior stability with the lowest variance and coefficient of variation across performance metrics, highlighting its effectiveness in analyzing the counting-based biomarker. The TMBstable algorithm can be accessed at https://github.com/hello-json/TMBstable for academic usage only.

Integrated mRNA and miRNA analysis reveals the regulatory network of oxidative stress and inflammation in Coilia nasus brains during air exposure and salinity mitigation.

BACKGROUND: Air exposure is an inevitable source of stress that leads to significant mortality in Coilia nasus. Our previous research demonstrated that adding 10‰ NaCl to aquatic water could enhance survival rates, albeit the molecular mechanisms involved in air exposure and salinity mitigation remained unclear. Conversely, salinity mitigation resulted in decreased plasma glucose levels and improved antioxidative activity. To shed light on this phenomenon, we characterized the transcriptomic changes in the C. nasus brain upon air exposure and salinity mitigation by integrated miRNA-mRNA analysis. RESULTS: The plasma glucose level was elevated during air exposure, whereas it decreased during salinity mitigation. Antioxidant activity was suppressed during air exposure, but was enhanced during salinity mitigation. A total of 629 differentially expressed miRNAs (DEMs) and 791 differentially expressed genes (DEGs) were detected during air exposure, while 429 DEMs and 1016 DEGs were identified during salinity mitigation. GO analysis revealed that the target genes of DEMs and DEGs were enriched in biological process and cellular component during air exposure and salinity mitigation. KEGG analysis revealed that the target genes of DEMs and DEGs were enriched in metabolism. Integrated analysis showed that 24 and 36 predicted miRNA-mRNA regulatory pairs participating in regulating glucose metabolism, Ca2+ transport, inflammation, and oxidative stress. Interestingly, most of these miRNAs were novel miRNAs. CONCLUSION: In this study, substantial miRNA-mRNA regulation pairs were predicted via integrated analysis of small RNA sequencing and RNA-Seq. Based on predicted miRNA-mRNA regulation and potential function of DEGs, miRNA-mRNA regulatory network involved in glucose metabolism and Ca2+ transport, inflammation, and oxidative stress in C. nasus brain during air exposure and salinity mitigation. They regulated the increased/decreased plasma glucose and inhibited/promoted antioxidant activity during air exposure and salinity mitigation. Our findings would propose novel insights to the mechanisms underlying fish responses to air exposure and salinity mitigation.

PEcnv: accurate and efficient detection of copy number variations of various lengths.

Copy number variation (CNV) is a class of key biomarkers in many complex traits and diseases. Detecting CNV from sequencing data is a substantial bioinformatics problem and a standard requirement in clinical practice. Although many proposed CNV detection approaches exist, the core statistical model at their foundation is weakened by two critical computational issues: (i) identifying the optimal setting on the sliding window and (ii) correcting for bias and noise. We designed a statistical process model to overcome these limitations by calculating regional read depths via an exponentially weighted moving average strategy. A one-run detection of CNVs of various lengths is then achieved by a dynamic sliding window, whose size is self-adopted according to the weighted averages. We also designed a novel bias/noise reduction model, accompanied by the moving average, which can handle complicated patterns and extend training data. This model, called PEcnv, accurately detects CNVs ranging from kb-scale to chromosome-arm level. The model performance was validated with simulation samples and real samples. Comparative analysis showed that PEcnv outperforms current popular approaches. Notably, PEcnv provided considerable advantages in detecting small CNVs (1 kb-1 Mb) in panel sequencing data. Thus, PEcnv fills the gap left by existing methods focusing on large CNVs. PEcnv may have broad applications in clinical testing where panel sequencing is the dominant strategy. Availability and implementation: Source code is freely available at https://github.com/Sherwin-xjtu/PEcnv.

Multiple Bonding in AeN- (Ae=Ca, Sr, Ba).

Quantum chemical calculations using ab initio methods at the MRCI+Q(8,9)/def2-QZVPPD and CCSD(T)/def2-QZVPPD levels as well as using density functional theory are reported for the diatomic molecules AeN- (Ae=Ca, Sr, Ba). The anions CaN- and SrN- have electronic triplet (3Π) ground states with nearly identical bond dissociation energies De ~57 kcal/mol calculated at the MRCI+Q(8,9)/def2-QZVPPD level. In contrast, the heavier homologue BaN- has a singlet (1Σ+) ground state, which is only 1.1 kcal/mol below the triplet (3Σ-) state. The computed bond dissociation energy of (1Σ+) BaN- is 68.4 kcal/mol. The calculations at the CCSD(T)-full/def2-QZVPPD and BP86-D3(BJ)/def2-QZVPPD levels are in reasonable agreement with the MRCI+Q(8,9)/def2-QZVPPD data, except for the singlet (1Σ+) state, which has a large multireference character. The calculated atomic partial charges given by the CM5, Voronoi and Hirshfeld methods suggest small to medium-sized Ae←N- charge donation for most electronic states. In contrast, the NBO method predicts for all species medium to large Ae→N- electronic charge donation, which is due to the neglect of the (n)p AOs of Ae atoms as genuine valence orbitals. Neither the bond orders nor the bond lengths correlate with the bond dissociation energies. The EDA-NOCV calculations show that the heavier alkaline earth atoms Ca, Sr, Ba use their (n)s and (n-1)d orbitals for covalent bonding.

Analysis of the Unusual Chemical Bonds and Dipole Moments of AeF- (Ae=Be-Ba): A Lesson in Covalent Bonding.

Quantum chemical calculations of the anions AeF- (Ae=Be-Ba) have been carried out using ab initio methods at the CCSD(T)/def2-TZVPP level and density functional theory employing BP86 with various basis sets. The detailed bonding analyses using different charge- and energy partitioning methods show that the molecules possess three distinctively different dative bonds in the lighter species with Ae=Be, Mg and four dative bonds when Ae=Ca, Sr, Ba. The occupied 2p atomic orbitals (AOs) and to a lesser degree the occupied 2s AO of F- donate electronic charge into the vacant spx(σ) and p(π) orbitals of Be and Mg which leads to a triple bond Ae F-. The heavier Ae atoms Ca, Sr, Ba use their vacant (n-1)d AOs as acceptor orbitals which enables them to form a second σ donor bond with F- that leads to quadruply bonded Ae F- (Ae=Ca-Ba). The presentation of molecular orbitals or charge distribution using only one isodensity value may give misleading information about the overall nature of the orbital or charge distribution. Better insights are given by contour line diagrams. The ELF calculations provide monosynaptic and disynaptic basins of AeF- which nicely agree with the analysis of the occupied molecular orbitals and with the charge density difference maps. A particular feature of the covalent bonds in AeF- concerns the inductive interaction of F- with the soft valence electrons in the (n)s valence orbitals of Ae. The polarization of the (n)s2 electrons induces a (n)spx hybridized lone-pair orbital at atom Ae, which yields a large dipole moment with the negative end at Ae. The concomitant formation of a vacant (n)spx AO of atom Ae, which overlaps with the occupied 2p(σ) AO of F-, leads to a strong covalent σ bond.

MB16 - (M=Sc, Y, La): Perfect Bowl-Like Boron Clusters.

The introduction of transition-metal doping has engendered a remarkable array of unprecedented boron motifs characterized by distinctive geometries and bonding, particularly those heretofore unobserved in pure boron clusters. In this study, we present a perfect (no defects) boron framework manifesting an inherently high-symmetry, bowl-like architecture, denoted as MB16 - (M=Sc, Y, La). In MB16 -, the B16 is coordinated to M atoms along the C5v-symmetry axis. The bowl-shaped MB16 - structure is predicted to be the lowest-energy structure with superior stability, owing to its concentric (2 π+10 π) dual π aromaticity. Notably, the C5v-symmetry bowl-like B16 - is profoundly stabilized through the doping of an M atom, facilitated by strong d-pπ interactions between M and boron motifs, in conjunction with additional electrostatic stabilization by an electron transfer from M to the boron motifs. This concerted interplay of covalent and electrostatic interactions between M and bowl-like B16 renders MB16 - a species of exceptional thermodynamic stability, thus making it a viable candidate for gas-phase experimental detection.

Transition Metal Behavior of Heavier Alkaline Earth Elements in Doped Monocyclic and Tubular Boron Clusters.

Quantum chemical calculations are carried out to design highly symmetric-doped boron clusters by employing the transition metal behavior of heavier alkaline earth (Ae = Ca, Sr, and Ba) metals. Following an electron counting rule, a set of monocyclic and tubular boron clusters capped by two heavier Ae metals were tested, which leads to the highly symmetric Ae2B8, Ae2B18, and Ae2B30 clusters as true minima on the potential energy surface having a monocyclic ring, two-ring tubular, and three-ring tubular boron motifs, respectively. Then, a thorough global minimum (GM) structural search reveals that a monocyclic B8 ring capped with two Ae atoms is indeed a GM for Ca2B8 and Ba2B8, while for Sr2B8 it is a low-lying isomer. Similarly, the present search also unambiguously shows the most stable isomers of Ae2B18 and Ae2B30 to be highly symmetric two- and three-ring tubular boron motifs, respectively, capped with two Ae atoms on each side of the tube. In these Ae-doped boron clusters, in addition to the electrostatic interactions, a substantial covalent interaction, specifically the bonding occurring between (n - 1)d orbitals of Ae and delocalized orbitals of boron motifs, provides the essential driving force behind their highly symmetrical structures and overall stability.

BeM(CO)3- (M = Co, Rh, Ir) and BeM(CO)3 (M = Ni, Pd, Pt): Triply bonded terminal beryllium in zero oxidation state.

We perform detailed potential energy surface explorations of BeM(CO)3- (M = Co, Rh, Ir) and BeM(CO)3 (M = Ni, Pd, Pt) using both single-reference and multireference-based methods. The present results at the CASPT2(12,12)/def2-QZVPD//M06-D3/def2-TZVPPD level reveal that the global minimum of BeM(CO)3- (M = Co, Rh, Ir) and BePt(CO)3 is a C3v symmetric structure with an 1A1 electronic state, where Be is located in a terminal position bonded to M along the center axis. For other cases, the C3v symmetric structure is a low-lying local minimum. Although the present complexes are isoelectronic with the recently reported BFe(CO)3- complex having a B-Fe quadruple bond, radial orbital-energy slope (ROS) analysis reveals that the highest occupied molecular orbital (HOMO) in the title complexes is slightly antibonding in nature, which bars a quadruple bonding assignment. Similar weak antibonding nature of HOMO in the previously reported BeM(CO)4 (M = Ru, Os) complexes is also noted in ROS analysis. The bonding analysis through energy decomposition analysis in combination with the natural orbital for chemical valence shows that the bonding between Be and M(CO)3q (q = -1 for M = Co, Rh, Ir and q = 0 for M = Ni, Pd, Pt) can be best described as Be in the ground state (1S) interacting with M(CO)30/- via dative bonds. The Be(spσ) → M(CO)3q σ-donation and the complementary Be(spσ) ← M(CO)3q σ-back donation make the overall σ bond, which is accompanied by two weak Be(pπ) ← M(CO)3q π-bonds. These complexes represent triply bonded terminal beryllium in an unusual zero oxidation state.

Preparation and functional properties of rice bran globulin-chitooligosaccharide-quercetin-resveratrol covalent complex.

BACKGROUND: As the major protein (approximately 36%) in rice bran, globulin exhibits excellent foaming and emulsifying properties, endowing its useful application as a foaming and emulsifying agent in the food industry. However, the low water solubility restricts its commercial potential in industrial applications. The present study aimed to improve this protein's processing and functional properties. RESULTS: A novel covalent complex was fabricated by a combination of the Maillard reaction and alkaline oxidation using rice bran globulin (RBG), chitooligosaccharide (C), quercetin (Que) and resveratrol (Res). The Maillard reaction improved the solubility, emulsifying and foaming properties of RBG. The resultant glycosylated protein was covalently bonded with quercetin and resveratrol to form a (RBG-C)-Que-Res complex. (RBG-C)-Que-Res exhibited higher thermal stability and antioxidant ability than the native protein, binary globulin-chitooligosaccharide or ternary globulin-chitooligosaccharide-polyphenol (only containing quercetin or resveratrol) conjugates. (RBG-C)-Que-Res exerted better cytoprotection against the generation of malondialdehyde and reactive oxygen species in HepG2 cells, which was associated with increased activities of antioxidative enzymes superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) through upregulated genes SOD1, CAT, GPX1 (i.e. gene for glutathione peroxidase-1), GCLM (i.e. gene for glutamate cysteine ligase modifier subunit), SLC1A11 (i.e. gene for solute carrier family 7, member 11) and SRXN1 (i.e. gene for sulfiredoxin-1). The anti-apoptotic effect of (RBG-C)-Que-Res was confirmed by the downregulation of caspase-3 and p53 and the upregulation of B-cell lymphoma-2 gene expression. CONCLUSION: The present study highlights the potential of (RBG-C)-Que-Res conjugates as functional ingredients in healthy foods. © 2024 Society of Chemical Industry.

Two-layer molecular rotors: A zinc dimer rotating over planar hypercoordinate motifs.

Multi-layer molecular rotors represent a class of unique combination of topology and bonding, featuring a barrier-free rotation of one layer with respect to other layers. This emerging fluxional behavior has been found in a few doped boron clusters. Herein, we strongly enrich this intriguing family followed by an effective design strategy, summarized as essential factors: i) considerable electrostatic interactions originated from a strong charge transfer between layers; ii) the absence of strong covalent bonds between layers; and iii) fully delocalized σ/π electrons from at least one layer. We found that planar hypercoordinate motifs consisting of monocyclic boron rings and metals with σ + π dual aromaticity can be regarded as one promising layer, which can support the suspended X2 (X = Zn, Cd, Hg) dimers. By detailed investigations of thermodynamic and kinetic stabilities of 60 species, eventually, MB7 X2 - and MB8 X2 (X = Zn, Cd; M = Be, Ru, Os; Be works only for Zn-based cases) clusters were verified to be the global-minimum two-layer molecular rotors. Especially, their electronic structure analyses vividly confirm the practicability of the electronic structure requirements mentioned above for designing multi-layer molecular rotors.

Bonding situations in tricoordinated beryllium phenyl complexes.

The bonding situation in the tricoordinated beryllium phenyl complexes [BePh3 ]- , [(pyridine)BePh2 ] and [(trimethylsilyl-N-heterocyclic imine)BePh2 ] is investigated experimentally and computationally. Comparison of the NMR spectroscopic properties of these complexes and of their structural parameters, which were determined by single crystal X-ray diffraction experiments, indicates the presence of π-interactions. Topology analysis of the electron density reveals elliptical electron density distributions at the bond critical points and the double bond character of the beryllium-element bonds is verified by energy decomposition analysis with the combination of natural orbital for chemical valence. The present beryllium-element bonds are highly polarized and the ligands around the central atom have a strong influence on the degree of π-delocalization. These results are compared to related triarylboranes.

Quest of Quadruple Bonding Between Two Main-Group Atoms in AeB- and AeC (Ae=Ca, Sr, Ba) and the Role of d Orbitals of Heavier Alkaline-Earth Atoms in Covalent Interactions.

Quantum chemical calculations using ab initio methods at the MRCI+Q(6,8)/def2-QZVPP and CCSD(T)/def2-QZVPP levels as well as density functional theory are reported for the diatomic molecules AeB- and isoelectronic AeC (Ae=Ca, Sr, Ba). The boride anions AeB- have an electronic triplet (3 Σ- ) ground state. The quintet (5 Σ- ) state is 5.8-12.3 kcal/mol higher in energy and the singlet (1 Δ) state is 13.1-15.3 kcal/mol above the triplet. The isoelectronic AeC molecules are also predicted to have a low-lying triplet (3 Σ- ) state but the quintet (5 Σ- ) state is only 2.2 kcal/mol (SrC) and 2.9 kcal/mol (CaC) above the triplet state. The triplet (3 Σ- ) and quintet (5 Σ- ) states of BaC are nearly isoenergetic. All systems have rather strong bonds. The calculated bond dissociation energies of the triplet (3 Σ- ) state are between De =38.3-41.7 kcal/mol for AeB- and De =49.4-57.5 kcal/mol for AeC. The barium species have always the strongest bonds whereas the calcium and strontium compounds have similar BDEs. The bonding analysis indicates that there is little charge migration in AeB- in the direction Ae→B- where the alkaline earth atoms carry positive charges between 0.09 e-0.22 e. The positive charges at the Ae atoms are much larger in AeC where the charge migration Ae→C is between 0.90 e-0.91 e. A detailed analysis of the interatomic interactions with the EDA-NOCV method shows that all diatomic species AeB- and AeC are built from dative interactions between Ae (1 S, ns2 ) and B- or C (3 P, 2 s2 2pπ 1 2pπ' 1 ). The eventually formed bonds in AeC are better described in terms of interactions between the ions Ae+ (2 S, ns1 )+C- (4 S, 2 s2 2pπ 1 2pπ' 1 2pσ 1 ). Inspection of the orbital interactions suggests that the alkaline earth atoms Ca, Sr, Ba use mainly their (n-1)d AOs besides the (n)s AOs for the covalent bonds. This creates a second energetically low-lying σ-bonding MO in the molecules, which feature valence orbitals with the order ϕ1 (σ-bonding)<ϕ2 (σ-bonding)<ϕ3 (degenerate π-bonding). All four occupied valence MOs of AeB- and AeC are bonding orbitals. Since the degenerate π orbitals ϕ3 are only singly occupied, the formal bond order is three.

Global Planar Tetra-, Penta- and Hexa-coordinate Silicon Clusters Constructed by Decorating SiO3 with Alkali Metals.

The achievement of the rule-breaking planar hypercoordinate motifs (carbon and other elements) is mainly attributed to a practical electronic stabilization mechanism, where the bonding of the central atom pz π electrons is a crucial issue. We have demonstrated that strong multiple bonds between the central atom and partial ligands can be an effective approach to explore stable planar hypercoordinate species. A set of planar tetra-, penta- and hexa-coordinate silicon clusters were herein found to be the lowest-energy structure, which can be viewed as decorating SiO3 by alkali metals in the MSiO3 - , M2 SiO3 and M3 SiO3 + (M=Li, Na) clusters. The strong charge transfer from M atoms to SiO3 effectively results in [M]+ SiO3 2- , [M2 ]2+ SiO3 2- and [M3 ]3+ SiO3 2- salt complexes, where the Si-O multiple bonding and structural integrity of the Benz-like SiO3 framework is maintained better than the corresponding SiO3 2- motifs. The bonding between M atoms and SiO3 motif is best described as M+ forming a few dative interactions by employing its vacant s, p, and high-lying d orbitals. These considerable M←SiO3 interactions and Si-O multiple bonding give rise to the highly stable planar hypercoordinate silicon clusters.

Three-Dimensional Neodymium Metal-Organic Framework for Catalyzing the Cyanosilylation of Aldehyde and the Synthesis of 2,3-Dihydroquinazolin-4(1H)-one Derivatives.

In this work, a novel 3D lanthanide metal-organic framework (Ln-MOF) Nd-cdip (H4cdip = 5,5'-carbonyldiisophthalic acid) was successfully synthesized, which could be used as an efficient heterogeneous catalyst for cyanosilylation and the synthesis of 2,3-dihydroquinazolin-4(1H)-one derivatives at room temperature based on the Lewis acid sites in the channels of the MOF. Moreover, Nd-cdip had an excellent turnover number (500) for catalyzing cyanosilylation in no solvent condition. Nd-cdip could be reused in both of the above-mentioned reactions at least five times without a significant decrease in yield. The possible mechanism of cyanosilylation catalyzed by Nd-cdip was studied by using the luminescence properties of Tb-cdip, which has the same structure and functions as Nd-cdip. Furthermore, both reactions catalyzed by Nd-cdip were fitted to zero-order dynamics.

Interactions between Phosphorus Enrichment and Nitrification Accelerate Relative Nitrogen Deficiency during Cyanobacterial Blooms in a Large Shallow Eutrophic Lake.

Regime shifts between nitrogen (N) and phosphorus (P) limitation, which trigger cyanobacterial succession, occur in shallow eutrophic lakes seasonally. However, the underlying mechanism is not yet fully illustrated. We provide a novel insight to address this from interactions between sediment P and nitrification through monthly field investigations including 204 samples and microcosm experiments in Lake Chaohu. Total N to P mass ratios (TN/TP) varied significantly across seasons especially during algal bloom in summer, with the average value being 26.1 in June and descending to 7.8 in September gradually, triggering dominant cyanobacterial succession from Microcystis to Dolichospermum. The regulation effect of sediment N/P on water column TN/TP was stronger in summer than in other seasons. Iron-bound P and alkaline phosphatase activity in sediment, rather than ammonium, contributed to the higher part of nitrification. Furthermore, our microcosm experiments confirmed that soluble active P and enzymatic hydrolysis of organic P, accumulating during algal bloom, fueled nitrifiers and nitrification in sediments. These processes promoted lake N removal and led to relative N deficiency in turn. Our results highlight that N and P cycles do not exist independently but rather interact with each other during lake eutrophication, supporting the dual N and P reduction program to mitigate eutrophication in shallow eutrophic lakes.

Mimicking the C2 molecule: M2B2 and M3B2+ clusters (M = Li, Na) and the reactivity of the N-heterocyclic carbene bound Li2B2 complex.

C2 has attracted considerable attention from the scientific community for its debatable bonding situation. Herein, we show that the global minima of M2B2 and M3B2+ (M = Li, Na) possess similar covalent bonding patterns to C2. Because of strong charge transfer from M2/M3 to B2 dimer, they can be better described as [M2]2+[B2]2- and [M3]3+[B2]2- salt complexes with the B22- core surrounded perpendicularly by two and three M+ atoms, respectively. The energy decomposition analyses in combination with the natural orbital for chemical valence theory give four bonding components in C2, M2B2, and M3B2+ clusters. However, the fourth component does not arise from a bonding interaction but from polarization/hybridization. Considering the effect of Pauli repulsion in σ-space, the attractive covalent interaction in these molecules mainly comes from the two π-bonds. We further presented stable N-heterocyclic carbene (NHC) and triphenylphosphine (PPh3) ligands bound Li2B2(NHC)2 and Li2B2(PPh3)2 complexes. A comparative study of reactivity towards L = CO2, CO, and N2 between Li2B2(NHC)2 and B2(NHC)2 is also performed. L-Li2B2(NHC)2 is highly stable against L dissociation at room temperature for L = CO2 and CO, and the stability is markedly higher than that in L-B2(NHC)2. The larger B2→L π-backdonation in L-Li2B2(NHC)2 also makes L more activated than in L-B2(NHC)2.

Rotational energy transfer in the collision of N2O with He atom.

The quantum state-to-state rotationally inelastic quenching of N2O by colliding with a He atom is studied on an ab initio potential energy surface with N2O lying on its vibrational ground state. The cross sections for collision energies from 10-6-100 cm-1 and rate constants from 10-5-10 K are calculated employing the fully converged quantum close-coupling method for the quenching of the j = 1-6 rotational states of N2O. Numerous van der Waals shapes or Feshbach resonances are observed; the cross sections of different channels are found to follow the Wigner scaling law in the cold threshold regime and may intersect with each other. In order to interpret the mechanism and estimate the cross sections of the rotational energy transfer, we propose a minimal classical model of collision between an asymmetric double-shell ellipsoid and a point particle. The classical model reproduces the quantum scattering results and points out the attractive interactions and the potential asymmetry can affect the collision process. The resulting insights are expected to expand our interpretations of inelastic scattering and energy transfer in molecular collisions.

Clusters and bulky Lewis acid protected complexes with planar hexacoordinate beryllium and magnesium.

Planar hexacoordination (ph) is only rarely reported in the literature. So far, only a few neutral and cationic molecules possessing phE (E = C, Si, B, Al, Ga) in the most stable isomer are predicted theoretically. Present electronic structure calculations report hitherto unknown anionic planar hexcoordinate beryllium and magnesium, phBe/Mg, as the most stable isomer. Global minimum searches show that the lowest energy structure of BeC6M3- (M = Al, Ga) and MgC6M3- (M = Ga, In, Tl) is the D3h symmetric phBe/Mg clusters, where beryllium/magnesium is covalently bonded with six carbon centers and M is located in a bridging position between two carbon centers. These global minimum phBe/Mg clusters are highly kinetically stable against isomerization, facilitating the experimental confirmation by photoelectron spectroscopy. Noteworthy is the fact that the phBe/Mg center is linked with carbon centers through three 7c-2e delocalized σ bonds and three 7c-2e π bonds, making the cluster double aromatic (σ + π) in nature. The bonding between the Be/Mg and outer ring moiety can be best expressed as an electron-sharing σ-bond between the s orbital of Be+/Mg+ and C6M32- followed by three dative interactions involving empty pπ and two in-plane p orbitals of Be/Mg. Furthermore, Lewis basic M centers of the title clusters can be passivated through the complexation with bulky Lewis acid, 9-boratriptycene, lowering the overall reactivity of the cluster, which can eventually open up the possibility of their large-scale syntheses.

B7 Be6 B7 : A Boron-Beryllium Sandwich Complex.

Planar boron clusters have often been regarded as "π-analogous" to aromatic arenes because of their similar delocalized π-bonding. However, unlike arenes such as C5 H5 - and C6 H6 , boron clusters have not previously shown the ability to form sandwich complexes. In this study, we present the first sandwich complex involving beryllium and boron, B7 Be6 B7 . The global minimum of this combination adopts a unique architecture having a D6h geometry, featuring an unprecedented monocyclic Be6 ring sandwiched between two quasi-planar B7 motifs. The thermochemical and kinetic stability of B7 Be6 B7 can be attributed to strong electrostatic and covalent interactions between the fragments. Chemical bonding analysis shows that B7 Be6 B7 can be considered as a [B7 ]3- [Be6 ]6+ [B7 ]3- complex. Moreover, there is a significant electron delocalization within this cluster, supported by the local diatropic contributions of the B7 and Be6 fragments.

Quantification of quetiapine fumarate based on electrochemical analysis by reduced graphene oxide modified nano-silica functionalized with polydopamine and gold nanostars: A novel pharmaceutical analysis strategy.

Quetiapine fumarate (QF) is an antipsychotic drug that has been most widely prescribed as an antipsychotic. In this regard, sensitive recognition of QF in bodily fluids must be done accurately. In this work, an electrochemical sensor for QF detection was fabricated, using GNSs-PDA@SiO2 modified rGO stabilized on glassy carbon electrode. According to the electrical nature of gold nanoparticles (GNPs), polydopamine (PDA), and its composition with nano-silica, the proposed hybrid material is able to enhance the electro-oxidation signals of QF toward its sensitive detection in complex biological media. The morphology of synthesized polymeric nanocomposites and various surfaces of electrodes were investigated using Field Emission Scanning Electron Microscopy and Energy-Dispersive X-Ray Spectroscopy methods. Using the square wave voltammetry technique, the fabricated electrochemical sensor could detect QF in the linear range of 500 µM to 3 mM, which low limit of quantification was obtained as 500 µM, indicating the sensor's appropriate sensitivity. For the first time, the application of novel hybrid material (GNSs-PDA@SiO2 ) for pharmaceutical analysis in human plasma was studied using electrochemical sensor technology. Based on the obtained analytical results, engineered nano-surface led to entrapment and oxidation of QF in real samples. So, a novel and efficient method for the analysis of QF was designed and validated, which opens a new horizon for pharmaceutical analysis and therapeutic drug monitoring.