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18 pages, 3729 KiB

Open AccessArticle

Structure and Bonding Patterns in C₅H₄ Isomers: Pyramidane, Planar Tetracoordinate Carbon, and Spiro Molecules

by Sayon Satpati, Tarun Roy, Sandip Giri, Anakuthil Anoop, Venkatesan S. Thimmakondu and Subhas Ghosal

Atoms 2023, 11(6), 96; https://doi.org/10.3390/atoms11060096 - 10 Jun 2023

Cited by 3 | Viewed by 3632

Abstract

We have theoretically investigated nine unusual isomers of the molecular formula C₅H₄ using coupled cluster (CC) and density functional theory (DFT) methods. These molecules possess non-classical structures consisting of two pyramidanes, three planar tetracoordinate carbon (ptC), and four [...] Read more.

We have theoretically investigated nine unusual isomers of the molecular formula C₅H₄ using coupled cluster (CC) and density functional theory (DFT) methods. These molecules possess non-classical structures consisting of two pyramidanes, three planar tetracoordinate carbon (ptC), and four spiro types of isomers. Both the pyramidanes (tetracyclo-[2.1.0.0^1,3.0^2,5]pentane; py-1 and tricyclo-[2.1.0.0^2,5]pentan-3-ylidene; py-2) are minima on the potential energy surface (PES) of C₅H₄. Among the three isomers containing ptC, (SP4)-spiro [2.2]pent-1-yne (ptC-2) is a minimum, whereas isomer, (SP4)-spiro [2.2]pent-1,4-diene (ptC-1) is a fourth-order saddle point, and (SP4)-sprio[2.2]pent-1,4-diylidene (ptC-3) is a transition state. The corresponding spiro isomers spiro[2.2]pent-1,4-diene (spiro-1), sprio[2.2]pent-1,4-diylidene (spiro-3) and spiro[2.2]pent-4-en-1-ylidene (spiro-4) are local minima, except spiro[2.2]pent-1-yne (spiro-2), which is a second-order saddle point. All relative energies are calculated with respect to the global minimum (pent-1,3-diyne; 1) at the CCSD(T)/cc-pVTZ level of theory. Quantum chemical calculations have been performed to analyze the bonding and topological configurations for all these nine isomers at the B3LYP/6-311+G(d,p) level of theory for a better understanding of their corresponding electronic structures. ptC-2 was found to be thermodynamically more stable than its corresponding spiro counterpart (spiro-2) and possesses a high dipole moment (μ = 4.64 D). The stability of the ptC structures with their higher spin states has been discussed. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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10 pages, 2734 KiB

Open AccessCommunication

Searching for Systems with Planar Hexacoordinate Carbons

by Diego Inostroza, Luis Leyva-Parra, Osvaldo Yañez, José Solar-Encinas, Alejandro Vásquez-Espinal, Maria Luisa Valenzuela and William Tiznado

Atoms 2023, 11(3), 56; https://doi.org/10.3390/atoms11030056 - 13 Mar 2023

Cited by 2 | Viewed by 2172

Abstract

Here, we present evidence that the D_2h M₂C₅^0/2+ (M = Li-K, Be-Ca, Al-In, and Zn) species comprises planar hexacoordinate carbon (phC) structures that exhibit four covalent and two electrostatic interactions. These findings have been made possible using evolutionary [...] Read more.

Here, we present evidence that the D_2h M₂C₅^0/2+ (M = Li-K, Be-Ca, Al-In, and Zn) species comprises planar hexacoordinate carbon (phC) structures that exhibit four covalent and two electrostatic interactions. These findings have been made possible using evolutionary methods for exploring the potential energy surface (AUTOMATON program) and the Interacting Quantum Atoms (IQA) methodology, which support the observed bonding interactions. It is worth noting, however, that these structures are not the global minimum. Nonetheless, incorporating two cyclopentadienyl anion ligands (Cp) into the CaC₅²⁺ system has enhanced the relative stability of the phC isomer. Moreover, cycloparaphenylene ([8]CPP) provides system protection and kinetic stability. These results indicate that using appropriate ligands presents a promising approach for expanding the chemistry of phC species. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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15 pages, 6216 KiB

Open AccessArticle

Al₂C₄H₂ Isomers with the Planar Tetracoordinate Carbon (ptC)/Aluminum (ptAl)

by Abdul Hamid Malhan, Sony Sobinson, Nisha Job, Shilpa Shajan, Surya Prakash Mohanty, Venkatesan S. Thimmakondu and Krishnan Thirumoorthy

Atoms 2022, 10(4), 112; https://doi.org/10.3390/atoms10040112 - 11 Oct 2022

Cited by 4 | Viewed by 2106

Abstract

Forty-one isomers of Al₂C₄H₂ that lie within 50 kcal mol⁻¹ are theoretically identified in this work using density functional theory. Among these, isomers 3 and 14 contain a planar tetracoordinate carbon (ptC) atom that lies at 3.3 [...] Read more.

Forty-one isomers of Al₂C₄H₂ that lie within 50 kcal mol⁻¹ are theoretically identified in this work using density functional theory. Among these, isomers 3 and 14 contain a planar tetracoordinate carbon (ptC) atom that lies at 3.3 and 16.9 kcal mol⁻¹, respectively, and are above the global minimum geometry 1 at the ωB97XD/6-311++G(2d,2p) level of theory. The other ten isomers that also contain unique bonding features are isomers 4, 18, 20, 21, 22, 27, 28, 31, 34, and 40. Out of these isomers, 4, 18, 20, 22, 27, 28, and 34 contain planar tetracoordinate aluminum (ptAl) whereas isomers 31 and 40 contain both ptC and ptAl atoms. Chemical bonding characteristic features are thoroughly analyzed for all these eleven isomers with various bonding and topological quantum chemical tools, such as NBO, AdNDP, WBI, and ELF, except isomer 27 due to the observed elongated Al-Al bond length. The current results indicate that ptC isomer 3 is more stable than other isomers because electron delocalization is more prevalent and it also has double aromaticity as observed from the ELF, NICS, and AdNDP analysis. Further, the structural stability of these isomers is investigated through ab initio molecular dynamics (AIMD) simulation. Isomer 21 shows the planar pentacoordinate aluminum but it is observed as a kinetically unstable geometry from AIMD and, further, one could notice that it isomerizes to isomer 12. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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12 pages, 3387 KiB

Open AccessEditor’s ChoiceArticle

Persistent Planar Tetracoordinate Carbon in Global Minima Structures of Silicon-Carbon Clusters

by Luis Leyva-Parra, Diego Inostroza, Osvaldo Yañez, Julio César Cruz, Jorge Garza, Víctor García and William Tiznado

Atoms 2022, 10(1), 27; https://doi.org/10.3390/atoms10010027 - 28 Feb 2022

Cited by 12 | Viewed by 3501

Abstract

Recently, we reported a series of global minima whose structures consist of carbon rings decorated with heavier group 14 elements. Interestingly, these structures feature planar tetracoordinate carbons (ptCs) and result from the replacement of five or six protons (H⁺) from the [...] Read more.

Recently, we reported a series of global minima whose structures consist of carbon rings decorated with heavier group 14 elements. Interestingly, these structures feature planar tetracoordinate carbons (ptCs) and result from the replacement of five or six protons (H⁺) from the cyclopentadienyl anion (C₅H₅⁻) or the pentalene dianion (C₈H₆²⁻) by three or four E²⁺ dications (E = Si–Pb), respectively. The silicon derivatives of these series are the Si₃C₅ and Si₄C₈ clusters. Here we show that ptC persists in some clusters with an equivalent number of C and Si atoms, i.e., Si₅C₅, Si₈C₈, and Si₉C₉. In all these species, the ptC is embedded in a pentagonal C₅ ring and participates in a three-center, two-electron (3c-2e) Si-ptC-Si σ-bond. Furthermore, these clusters are π-aromatic species according to chemical bonding analysis and magnetic criteria. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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11 pages, 1245 KiB

Open AccessArticle

Exploring the Excited-State Nonadiabatic Effects in the Semisaturated Planar Tetracoordinated Carbon Molecule C₇H₄

by Chithra Mohan Jayakumari, Probal Nag, Sai Vamsi Krishna Isukapalli and Sivaranjana Reddy Vennapusa

Atoms 2022, 10(1), 10; https://doi.org/10.3390/atoms10010010 - 19 Jan 2022

Cited by 2 | Viewed by 2395

Abstract

We theoretically study the nonadiabatic relaxation dynamics of low-lying singlet excited-states of semisaturated planar tetracoordinated carbon molecule, C

_{7}

H

_{4}

. This molecule possesses a stable C

_{2 v}

ground-state equilibrium geometry. The three low-lying singlet states, S

_{1}

, S

_{2}

[...] Read more.

We theoretically study the nonadiabatic relaxation dynamics of low-lying singlet excited-states of semisaturated planar tetracoordinated carbon molecule, C

_{7}

H

_{4}

. This molecule possesses a stable C

_{2 v}

ground-state equilibrium geometry. The three low-lying singlet states, S

_{1}

, S

_{2}

and S

_{3}

, lie in the energy gap of about 1.2 eV. The potential energy surfaces constructed within the quadratic vibronic coupling formalism reveal multiple conical intersections in the Franck-Condon region. Upon photoexcitation to S

_{3}

, the wavepacket decays rapidly to lower states via these conical intersections. We also observe the wavepacket transfer to S

_{3}

during the initial wavepacket evolution on lower states, suggesting the nonadiabatic behavior of photoexcited planar C

_{7}

H

_{4}

. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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21 pages, 10014 KiB

Open AccessArticle

BAl₄Mg^−/0/+: Global Minima with a Planar Tetracoordinate or Hypercoordinate Boron Atom

by Maya Khatun, Saikat Roy, Sandip Giri, Sasanka Sankhar Reddy CH, Anakuthil Anoop and Venkatesan S. Thimmakondu

Atoms 2021, 9(4), 89; https://doi.org/10.3390/atoms9040089 - 27 Oct 2021

Cited by 7 | Viewed by 3956

Abstract

We have explored the chemical space of BAl

_{4}

Mg

^{- / 0 / +}

for the first time and theoretically characterized several isomers with interesting bonding patterns. We have used chemical intuition and a cluster building method based on the tabu-search algorithm [...] Read more.

We have explored the chemical space of BAl

_{4}

Mg

^{- / 0 / +}

for the first time and theoretically characterized several isomers with interesting bonding patterns. We have used chemical intuition and a cluster building method based on the tabu-search algorithm implemented in the Python program for aggregation and reaction (PyAR) to obtain the maximum number of possible stationary points. The global minimum geometries for the anion (1a) and cation (1c) contain a planar tetracoordinate boron (ptB) atom, whereas the global minimum geometry for the neutral (1n) exhibits a planar pentacoordinate boron (ppB) atom. The low-lying isomers of the anion (2a) and cation (3c) also contain a ppB atom. The low-lying isomer of the neutral (2n) exhibits a ptB atom. Ab initio molecular dynamics simulations carried out at 298 K for 2000 fs suggest that all isomers are kinetically stable, except the cation 3c. Simulations carried out at low temperatures (100 and 200 K) for 2000 fs predict that even 3c is kinetically stable, which contains a ppB atom. Various bonding analyses (NBO, AdNDP, AIM, etc.) are carried out for these six different geometries of BAl

_{4}

Mg

^{- / 0 / +}

to understand the bonding patterns. Based on these results, we conclude that ptB/ppB scenarios are prevalent in these systems. Compared to the carbon counter-part, CAl

_{4}

Mg

^{-}

, here the anion (BAl

_{4}

Mg

^{-}

) obeys the 18 valence electron rule, as B has one electron fewer than C. However, the neutral and cation species break the rule with 17 and 16 valence electrons, respectively. The electron affinity (EA) of BAl

_{4}

Mg is slightly higher (2.15 eV) than the electron affinity of CAl

_{4}

Mg (2.05 eV). Based on the EA value, it is believed that these molecules can be identified in the gas phase. All the ptB/ppB isomers exhibit

π

/

σ

double aromaticity. Energy decomposition analysis predicts that the interaction between BAl

_{4}^{- / 0 / +}

and Mg is ionic in all these six systems. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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10 pages, 9142 KiB

Open AccessFeature PaperArticle

Stereomutation in Tetracoordinate Centers via Stabilization of Planar Tetracoordinated Systems

by Komal Yadav, Upakarasamy Lourderaj and U. Deva Priyakumar

Atoms 2021, 9(4), 79; https://doi.org/10.3390/atoms9040079 - 14 Oct 2021

Cited by 3 | Viewed by 2067

Abstract

The quest for stabilizing planar forms of tetracoordinate carbon started five decades ago and intends to achieve interconversion between [R]- and [S]-stereoisomers without breaking covalent bonds. Several strategies are successful in making the planar tetracoordinate form a minimum on [...] Read more.

The quest for stabilizing planar forms of tetracoordinate carbon started five decades ago and intends to achieve interconversion between [R]- and [S]-stereoisomers without breaking covalent bonds. Several strategies are successful in making the planar tetracoordinate form a minimum on its potential energy surface. However, the first examples of systems where stereomutation is possible were reported only recently. In this study, the possibility of neutral and dications of simple hydrocarbons (cyclopentane, cyclopentene, spiropentane, and spiropentadiene) and their counterparts with the central carbon atom replaced by elements from groups 13, 14, and 15 are explored using ab initio MP2 calculations. The energy difference between the tetrahedral and planar forms decreases from row II to row III or IV substituents. Additionally, aromaticity involving the delocalization of the lone pair on the central atom appears to help in further stabilizing the planar form compared to the tetrahedral form, especially for the row II substituents. We identified 11 systems where the tetrahedral state is a minimum on the potential energy surface, and the planar form is a transition state corresponding to stereomutation. Interestingly, the planar structures of three systems were found to be minimum, and the corresponding tetrahedral states were transition states. The energy profiles corresponding to such transitions involving both planar and tetrahedral states without the breaking of covalent bonds were examined. The systems showcased in this study and research in this direction are expected to realize molecules that experimentally exhibit stereomutation. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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15 pages, 84547 KiB

Open AccessArticle

In Silico Studies on Selected Neutral Molecules, CGa₂Ge₂, CAlGaGe₂, and CSiGa₂Ge Containing Planar Tetracoordinate Carbon

by Prasenjit Das and Pratim Kumar Chattaraj

Atoms 2021, 9(3), 65; https://doi.org/10.3390/atoms9030065 - 10 Sep 2021

Cited by 16 | Viewed by 3471

Abstract

Density functional theory (DFT) was used to study the structure, stability, and bonding in some selected neutral pentaatomic systems, viz., CGa₂Ge₂, CAlGaGe₂, and CSiGa₂Ge containing planar tetracoordinate carbon. The systems are kinetically stable, as [...] Read more.

Density functional theory (DFT) was used to study the structure, stability, and bonding in some selected neutral pentaatomic systems, viz., CGa₂Ge₂, CAlGaGe₂, and CSiGa₂Ge containing planar tetracoordinate carbon. The systems are kinetically stable, as predicted from the ab initio molecular dynamics simulations. The natural bond orbital (NBO) analysis showed that strong electron donation occurs to the central planar carbon atom by the peripheral atoms in all the studied systems. From the nucleus independent chemical shift (NICS) analysis, it is shown that the systems possess both σ- and π- aromaticity. The presence of 18 valence electrons in these systems, in their neutral form, appears to be important for their stability with planar geometries rather than tetrahedral structures. The nature of bonding is understood through the adaptive natural density partitioning analysis (AdNDP), quantum theory of atoms in molecules (QTAIM) analysis, and also via Wiberg bond index (WBI) and electron localization function (ELF). Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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14 pages, 8961 KiB

Open AccessEditor’s ChoiceArticle

CAl₄Mg^0/−: Global Minima with a Planar Tetracoordinate Carbon Atom

by Nisha Job, Maya Khatun, Krishnan Thirumoorthy, Sasanka Sankhar Reddy CH, Vijayanand Chandrasekaran, Anakuthil Anoop and Venkatesan S. Thimmakondu

Atoms 2021, 9(2), 24; https://doi.org/10.3390/atoms9020024 - 9 Apr 2021

Cited by 18 | Viewed by 5399

Abstract

Isomers of CAl₄Mg and CAl₄Mg⁻ have been theoretically characterized for the first time. The most stable isomer for both the neutral and anion contain a planar tetracoordinate carbon (ptC) atom. Unlike the isovalent CAl₄Be case, which [...] Read more.

Isomers of CAl₄Mg and CAl₄Mg⁻ have been theoretically characterized for the first time. The most stable isomer for both the neutral and anion contain a planar tetracoordinate carbon (ptC) atom. Unlike the isovalent CAl₄Be case, which contains a planar pentacoordinate carbon atom as the global minimum geometry, replacing beryllium with magnesium makes the ptC isomer the global minimum due to increased ionic radii of magnesium. However, it is relatively easier to conduct experimental studies for CAl₄Mg^0/− as beryllium is toxic. While the neutral molecule containing the ptC atom follows the 18 valence electron rule, the anion breaks the rule with 19 valence electrons. The electron affinity of CAl₄Mg is in the range of 1.96–2.05 eV. Both the global minima exhibit π/σ double aromaticity. Ab initio molecular dynamics simulations were carried out for both the global minima at 298 K for 10 ps to confirm their kinetic stability. Full article

(This article belongs to the Special Issue Planar Tetracoordinate Carbon—Fifty Years and Beyond)

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