The planar pentacoordinate carbon (ppC) atom is theoretically established here in [XC7H2]2+ and [XSi2C5H2]2+, where X = Be and Mg, using density functional theory. Inclusion compounds with alkali and alkaline earth metal ions are identified with the monomer units of tricyclic C7H2 and Si2C5H2 isomers with a planar tetracoordinate carbon (ptC) atom. While all alkali and some alkaline earth metals (Ca2+, Sr2+, and Ba2+) stabilize the ptC isomer in both cases, Be2+ and Mg2+ ions form a bond directly with the ptC atom, thus making it a ppC atom. The theoretical binding energies computed at the PBE0-D3/def2-TZVP level of theory are ∼-9.68, -10.42, -5.85, and -5.47 eV for [BeC7H2]2+, [BeSi2C5H2]2+, [MgC7H2]2+, and [MgSi2C5H2]2+, respectively.

Planar pentacoordinate carbon in [XC7H2]2+ (X = Be and Mg) and its derivatives.

Here we show that substituting the ten protons in the dianion of a bispentalene derivative (C 18 H 102- ) by six Si 2+ dications produces a minimum energy structure with two planar tetracoordinate carbons (ptC). In Si 6 C 18 , the ptCs are embedded in the terminal C 5 pentagonal rings and participate in a three-center, two-electron (3c-2e) Si-ptC-Si σ- bond. Our exploration of the potential energy surface identiﬁes a triphenylene derivative as the putative global minimum. But robustness to Born-Oppenheimer molecular dynamics (BOMD) simulations at 900 and 1500 K supports bispentalene derivative kinetic stability. Chemical bonding analysis reveals ten delocalized π- bonds, which, according to H¨uckel’s 4n+2 π- electron rule


 Si
 6
 C
 18
 
 : A bispentalene derivative with two planar tetracoordinate carbons

Abstract The structure, stability, and intermolecular interactions in SO3-(H2O) n (n = 1 -7) clusters were investigated using density functional and wave functional methods. The putative global minimum shows the SO3molecule tends to be on the surface water clusters. The increase in the number of water molecules chalcogen bond distance between water molecules and SO3decreases, while the maximum number of water molecules coordinated to the SO3molecule remains at three. The calculated solvation energy increases with the increase in the number of water molecules and it does not saturate, which indicates that the addition of water molecules can add up to the existing water cluster network. The interaction energy between water molecules and SO3was less than the solvation energy conforming to the cluster forming of water molecules. The Gibbs free energy and entropy values decrease with the increase in cluster size, signifying the amount of water molecule decide the sequential hydration process. Thermochemistry data at various temperatures show that low-temperature regions found in the upper part of the troposphere favor hydration formation. Molecular electrostatic potentials (MESP) show reduced Vs,max value of π-hole on sulfur atom, and increased value on hydrogens of water molecules which results in the addition of water which leads to the sequential addition of water molecules to the water network. The quantum theory of atoms in molecules (QTAIM) shows the presence of S···O, O···H interactions between SO3and water molecules. Between water molecules O···H, H-bonding interactions were observed, and in larger clusters, O···O interaction was also noticed. QTAIM analysis shows the water–water HBs in these clusters are weak H-bond, while the SO3-water interaction can be classified as medium H-bonds which was further supported by the NCI and 2D RDG plots. 

The structure, stability, thermochemistry, and bonding in SO3-(H2O)n (n=1–7) clusters: a computational analysis

Here, five bonds to carbon through tri-coordination are theoretically established in the global minimum energy isomers of Al3C3− anion (1a) and Al3C3 neutral (1n) for the first time. Various isomers of Al3C3−/0 are theoretically identified using density functional theory at the PBE0-D3/def2-TZVP level. Chemical bonding features are thoroughly analyzed for these two isomers (1a and 1n) with different bonding and topological quantum chemical tools, such as adaptive natural density partitioning (AdNDP), Wiberg Bond Indices (WBIs), nucleus-independent chemical shifts (NICS), and atoms in molecules (AIM) analyses. The structure of isomer 1a is planar with C2v symmetry, whereas its neutral counterpart 1n is non-planar with C2 symmetry, in which its terminal aluminum atoms are out of the plane. The central allenic carbon atom of isomers 1a and 1n exhibits tri-coordination and thus makes it a case of five bonds to carbon, which is confirmed through their total bond order as observed in WBI. Both the isomers show σ- and π-aromaticity and are predicted with the NICS and AdNDP analyses. Further, the results of ab initio molecular dynamics simulations reveal their kinetic stability at room temperature; thus, they are experimentally viable systems.

/pdf/five-bonds-to-carbon-through-tri-coordination-in-al3c3-0-56hx0ueo.pdf

Five Bonds to Carbon through Tri-Coordination in 
Al3C3−/0

. – OBJECTIVE: Preeclampsia (PE) is a complex disease-causing multisystem damage. Many genes, environmental factors, and their interactions are involved in the development and progression of PE. The pathogenesis of PE is not fully understood, limiting the prevention and treatment of PE. The aim of this study was to investigate the effect of 4,4’-diiso-thiocyanato-stilbene-2,2’-disulfonic acid (DIDS), an ATP-binding cassette transporter A1 (ABCA1) blocker, on apoM mRNA and protein levels. PATIENTS AND METHODS: The role of liver X receptor α (LXRα) and ABCA1 in the pathogenesis of PE was investigated by opti - mizing the design of DIDS inhibition based on a deep learning model. RESULTS: The proportion of primipara in the research group, EOPE group, LOPE group, and controls was 59.82%, 65.85%, 56.34%, and 21.43%, respectively. The difference between the research group and the controls was statistical - ly significant ( p <0.01). In the clinical data, serum-free triiodothyronine (FT3), gestational age at delivery, high-density lipoprotein cholesterol (HDL-C), hemoglobin (HGB), albumin, and plate-let (PLT) in the research group were lower than those in the controls ( p <0.05). CONCLUSIONS: ABCA1 is considered to affect apoM mRNA expression, G/HDL-C may increase the risk of LOPE, and overweight or obesity, ab - normal glycemic regulation, and hypothyroidism are independent risk factors closely related to the pathogenesis of PE and its subgroups.

Mechanism of liver X receptor α and ATP binding cassette transporter A1 involved in preeclampsia using an optimized deep learning model

Though search algorithms are appropriate tools for identifying low-energy isomers, fixing several constraints seems to be a fundamental prerequisite to successfully running any structural search program. This causes some potential setbacks as far as identifying all possible isomers, close to the lowest-energy isomer, for any elemental composition. The number of explored candidates, the choice of method, basis set, and availability of CPU time needed to analyze the various initial test structures become necessary restrictions in resolving the issues of structural isomerism reasonably. While one could arrive at new structures through chemical intuition, reproducing or achieving those exact same structures requires increasing the number of variables in any given program, which causes further constraints in exploring the potential energy surface in a reasonable amount of time. Thus, it is emphasized here that an integrated approach between search algorithms and chemical intuition is necessary by taking the C12O2Mg2 system as an example. Our initial search through the AUTOMATON program yielded 1450 different geometries. However, through chemical intuition, we found eighteen new geometries within 40.0 kcal mol-1 at the PBE0-D3/def2-TZVP level. These results indirectly emphasize that an integrated approach between search algorithms and chemical intuition is necessary to further our knowledge in chemical space for any given elemental composition.

Why an integrated approach between search algorithms and chemical intuition is necessary?

Pentacoordinate carbon atoms are theoretically predicted here in a ferrocene dication derivative in the eclipsed-(1; C2v), gauche-(2; C2) and staggered-[Fe(Si2-η5-C5H2)2]2+(3; C2h) forms for the first time. Energetically, the relative energy gaps for 2 and 3 range from −3.06 to 16.74 and −2.78 to 40.34 kJ mol−1, respectively, when compared to the singlet electronic state of 1 at different levels. The planar tetracoordinate carbon (ptC) atom in the ligand Si2C5H2 becomes a pentacoordinate carbon upon complexation. The ligand with a ptC atom was predicted to be both a thermodynamically and kinetically stable molecule by some of us in our earlier theoretical works. Natural bond orbital and adaptive natural density partitioning analyses confirm the pentacoordinate nature of carbon in these three complexes (1–3). Although they are hypothetical at the moment, they support the idea of “hypercoordinate metallocenes” within organometallic chemistry. Moreover, ab initio molecular dynamics simulations carried out at 298 K temperature for 2000 fs suggest that these molecules are kinetically stable.

/pdf/pentacoordinate-carbon-atoms-in-a-ferrocene-dication-3as0vuul.pdf

Pentacoordinate Carbon Atoms in a Ferrocene Dication Derivative—[Fe(Si2-η5-C5H2)2]2+

Considering the recent findings of linear doublet (2Σ+) MgCnH isomers (n = 2, 4, and 6) in the evolved carbon star IRC+10216, various structural isomers of MgC3H and MgC3H+ are theoretically investigated here. For MgC3H, 11 doublet and 8 quartet stationary points ranging from 0.0 to 71.8 and 0.0 to 110.1 kcal mol–1, respectively, have been identified initially at the UωB97XD/6-311++G(2d,2p) level. To get accurate relative energies, further energy evaluations are carried out for all isomers with coupled cluster methods and thermochemical modules such as G3//B3LYP, G4MP2, and CBS-QB3 methods. Unlike the even series, where the global minima are linear molecules with a Mg atom at one end, in the case of MgC3H, the global minimum geometry turns out to be a cyclic isomer, 2-magnesabicyclo[1.1.0]but-1,3,4-triyl (1, C2v, 2A1). In addition, five low-lying isomers, magnesium-substituted cyclopropenylidene (2, Cs, 2A′), 1-magnesabut-2,3-dien-1-yl-4-ylidene (3, Cs, 2A″), 1-magnesabut-2-yn-1-yl-4-ylidene (4, Cs, 2A″), 2λ3-magnesabicyclo[1.1.0]but-1,3-diyl-4-ylidene (5, C2v;, 2A1), and 1-magnesabut-2,3-dien-2-yl-4-ylidene (6, C∞v, 2Σ+), were also identified. The doublet linear isomer of MgC3H, 1-magnesabutatrienyl (10, C∞v, 2Σ+) turns out to be a minimum but lies 54.1 kcal mol–1 above 1 at the ROCCSD(T)/cc-pVTZ level. The quartet (4Σ+) electronic state of 10 was also found to be a minimum, but it lies 8.0 kcal mol–1 above 1 at the same level. Among quartets, isomer 10 is the most stable molecule. The next quartet electronic state (of isomer 11) is 34.4 kcal mol–1 above 10, and all other quartet electronic states of other isomers are not energetically close to low-lying doublet isomers 2 to 6. Overall, the chemical space of MgC3H contains more cyclic isomers (1, 2, and 3) on the low-energy side unlike their even-numbered MgCnH counterparts (n = 2, 4, and 6). Though the quartet electronic state of 10 is linear, it is not the global minimum geometry on the MgC3H potential energy surface. Isomerization pathways among the low-lying isomers (doublets of 1–4 and a quartet of 10) reveal that these molecules are kinetically stable. For the cation, MgC3H+, the cyclic isomers (1+, 2+, and 3+) are on the low-energy side. The singlet linear isomer, 10+, is a fourth-order saddle point. The low-lying cations are quite polar, with dipole moment values of >7.00 D. The current theoretical data would be helpful to both laboratory astrophysicists and radioastronomers for further studies on the MgC3H0/+ isomers.

https://pubs.acs.org/doi/pdf/10.1021/acs.jpca.2c02220

Aland Sinjari

Papers

Why an integrated approach between search algorithms and chemical intuition is necessary?

Pentacoordinate Carbon Atoms in a Ferrocene Dication Derivative—[Fe(Si2-η5-C5H2)2]2+

Why Are MgC3H Isomers Missing in the Interstellar Medium?

Computational studies of mgc4h isomers