1
|
Pentacoordinate Carbon Atoms in a Ferrocene Dication Derivative—[Fe(Si2-η5-C5H2)2]2+. CHEMISTRY 2022. [DOI: 10.3390/chemistry4040074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
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.
Collapse
|
2
|
Sigmund LM, Ehlert C, Gryn'ova G, Greb L. Stereoinversion of tetrahedral p-block element hydrides. J Chem Phys 2022; 156:194113. [PMID: 35597652 DOI: 10.1063/5.0090267] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The potential energy surfaces of 15 tetrahedral p-block element hydrides were screened on the multireference level. It was addressed whether stereoinversion competes against other reactions, such as reductive H2-elimination or hydride loss, and if so, along which pathway the stereomutation occurs. Importantly, stereoinversion transition structures for the ammonium cation (C4v) and the tetrahydridoborate anion (Cs) were identified for the first time. Revisiting methane's Cs symmetric inversion transition structure with the mHEAT+ protocol revealed an activation enthalpy for stereoinversion, in contrast to all earlier studies, which is 5 kJ mol-1 below the C-H bond dissociation enthalpy. Square planar structures were identified lowest in energy only for the inversion of AlH4 -, but a novel stepwise Cs-inversion was discovered for SiH4 or PH4 +. Overall, the present contribution delineates essentials of the potential energy surfaces of p-block element hydrides, while structure-energy relations offer design principles for the synthetically emerging field of structurally constrained compounds.
Collapse
Affiliation(s)
- Lukas M Sigmund
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Christopher Ehlert
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Ganna Gryn'ova
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany and Interdisciplinary Center for Scientific Computing (IWR), Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Lutz Greb
- Anorganische Chemie, Freie Universität Berlin, Fabeckstraße 34-36, 14195 Berlin, Germany
| |
Collapse
|
3
|
Karton A, Thimmakondu VS. From Molecules with a Planar Tetracoordinate Carbon to an Astronomically Known C 5H 2 Carbene. J Phys Chem A 2022; 126:2561-2568. [PMID: 35426667 PMCID: PMC9442649 DOI: 10.1021/acs.jpca.2c01261] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Ethynylcyclopropenylidene
(2), an isomer of C5H2, is a known
molecule in the laboratory and has
recently been identified in Taurus Molecular Cloud-1 (TMC-1). Using
high-level coupled-cluster methods up to the CCSDT(Q)/CBS level of
theory, it is shown that two isomers of C5H2 with a planar tetracoordinate carbon (ptC) atom, (SP-4)-spiro[2.2]pent-1,4-dien-1,4-diyl
(11) and (SP-4)-spiro[2.2]pent-1,4-dien-1,5-diyl (13), serve as the reactive intermediates for the formation
of 2. Here, a theoretical connection has been established
between molecules containing ptC atoms (11 and 13) and a molecule (2) that is present nearly
430 light years away, thus providing evidence for the existence of
ptC species in the interstellar medium. The reaction pathways connecting
the transition states and the reactants and products have been confirmed
by intrinsic reaction coordinate calculations at the CCSDT(Q)/CBS//B3LYP-D3BJ/cc-pVTZ
level. While isomer 11 is non-polar (μ = 0), isomers 2 and 13 are polar, with dipole moment values
of 3.52 and 5.17 Debye at the CCSD(T)/cc-pVTZ level. Therefore, 13 is also a suitable candidate for both laboratory and radioastronomical
studies.
Collapse
Affiliation(s)
- Amir Karton
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Venkatesan S Thimmakondu
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182-1030, USA
| |
Collapse
|
4
|
Tipker RM, Muldoon JA, Pham DH, Varga BR, Hughes RP, Glueck DS, Balaich GJ, Rheingold AL. Configurational Lability at Tetrahedral Phosphorus: syn/anti-Isomerization of a P-Stereogenic Phosphiranium Cation by Intramolecular Epimerization at Phosphorus. Angew Chem Int Ed Engl 2022; 61:e202110753. [PMID: 34755431 DOI: 10.1002/anie.202110753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Indexed: 11/05/2022]
Abstract
Tetrahedral main-group compounds are normally configurationally stable, but P-epimerization of the chiral phosphiranium cations syn- or anti-[Mes*P(Me)CH2 CHPh][OTf] (Mes*=2,4,6-(t-Bu)3 C6 H2 ) occurred under mild conditions at 60 °C in CD2 Cl2 , resulting in isomerization to give a syn-enriched equilibrium mixture. Ion exchange with excess [NBu4 ][Δ-TRISPHAT] (Δ-TRISPHAT=Δ-P(o-C6 Cl4 O2 )3 ) followed by chromatography on silica removed [NBu4 ][OTf] and gave mixtures of syn- and anti-[Mes*P(Me)CH2 CHPh][Δ-TRISPHAT]⋅x[NBu4 ][Δ-TRISPHAT]. NMR spectroscopy showed that isomerization proceeded with epimerization at P and retention at C. DFT calculations are consistent with a mechanism involving P-C cleavage to yield a hyperconjugation-stabilized carbocation, pyramidal inversion promoted by σ-interaction of the P lone pair with the neighboring β-carbocation, and ring closure with inversion of configuration at P.
Collapse
Affiliation(s)
- Ryan M Tipker
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
| | - Jake A Muldoon
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
| | - Daniel H Pham
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
| | - Balazs R Varga
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
| | - Russell P Hughes
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
| | - David S Glueck
- 6128 Burke Laboratory, Department of Chemistry, Dartmouth College, Hanover, NH, 03755, USA
| | - Gary J Balaich
- Department of Chemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Arnold L Rheingold
- Department of Chemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| |
Collapse
|
5
|
Tipker RM, Muldoon JA, Pham DH, Varga BR, Hughes RP, Glueck DS, Balaich GJ, Rheingold AL. Configurational Lability at Tetrahedral Phosphorus:
syn/anti
‐Isomerization of a P‐Stereogenic Phosphiranium Cation by Intramolecular Epimerization at Phosphorus. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ryan M. Tipker
- 6128 Burke Laboratory Department of Chemistry Dartmouth College Hanover NH 03755 USA
| | - Jake A. Muldoon
- 6128 Burke Laboratory Department of Chemistry Dartmouth College Hanover NH 03755 USA
| | - Daniel H. Pham
- 6128 Burke Laboratory Department of Chemistry Dartmouth College Hanover NH 03755 USA
| | - Balazs R. Varga
- 6128 Burke Laboratory Department of Chemistry Dartmouth College Hanover NH 03755 USA
| | - Russell P. Hughes
- 6128 Burke Laboratory Department of Chemistry Dartmouth College Hanover NH 03755 USA
| | - David S. Glueck
- 6128 Burke Laboratory Department of Chemistry Dartmouth College Hanover NH 03755 USA
| | - Gary J. Balaich
- Department of Chemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Arnold L. Rheingold
- Department of Chemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| |
Collapse
|
6
|
Dyakin VV, Dyakina-Fagnano NV, Mcintire LB, Uversky VN. Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology. Int J Mol Sci 2021; 23:ijms23010285. [PMID: 35008708 PMCID: PMC8745688 DOI: 10.3390/ijms23010285] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/24/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging related to irreversible PTMs SP has been associated with the nontrivial interplay between somatic (molecular aging) and mental (psychological aging) health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet underappreciated hallmark of aging. We provide the experimental arguments in support of the racemization theory of aging.
Collapse
Affiliation(s)
- Victor V. Dyakin
- The Nathan S. Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Bldg, 35, Bld. 35. Rom 201-C, Orangeburg, NY 10962, USA
- Correspondence: ; Tel.: +1-845-548-96-94; Fax: +1-845-398-5510
| | - Nuka V. Dyakina-Fagnano
- Child, Adolescent and Young Adult Psychiatry, 36 Franklin Turnpike, Waldwick, NJ 07463, USA;
| | - Laura B. Mcintire
- Department of Pathology and Cell Biology, Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA;
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA;
| |
Collapse
|
7
|
Abstract
We have explored the chemical space of BAl4Mg−/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 BAl4Mg−/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, CAl4Mg−, here the anion (BAl4Mg−) 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 BAl4Mg is slightly higher (2.15 eV) than the electron affinity of CAl4Mg (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 BAl4−/0/+ and Mg is ionic in all these six systems.
Collapse
|
8
|
Stereomutation in Tetracoordinate Centers via Stabilization of Planar Tetracoordinated Systems. ATOMS 2021. [DOI: 10.3390/atoms9040079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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 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.
Collapse
|
9
|
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 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 CAl4Mg0/− 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.
Collapse
|
10
|
Abstract
Dissociation pathways of the global minimum geometry of Si2C5H2 with a planar tetracoordinate carbon (ptC) atom, 2,7-disilatricyclo[4.1.0.01,3]hept-2,4,6-trien-2,7-diyl (1), have been theoretically investigated using density functional theory and coupled-cluster (CC) methods. Dissociation of Si-C bond connected to the ptC atom leads to the formation of 4,7-disilabicyclo[4.1.0]hept-1(6),4(5)-dien-2-yn-7-ylidene (4) through a single transition state. Dissociation of C-C bond connected to the ptC atom leads to an intermediate with two identical transition states and leads back to 1 itself. Simultaneous breaking of both Si-C and C-C bonds leads to an acyclic transition state, which forms an acyclic product, cis-1,7-disilahept-1,2,3,5,6-pentaen-1,7-diylidene (19). Overall, two different products, four transition states, and an intermediate have been identified at the B3LYP/6-311++G(2d,2p) level of theory. Intrinsic reaction coordinate calculations have also been done at the latter level to confirm the isomerization pathways. CC calculations have been done at the CCSD(T)/cc-pVTZ level of theory for all minima. Importantly, all reaction profiles for 1 are found be endothermic in Si2C5H2. These results are in stark contrast compared to the structurally similar and isovalent lowest-energy isomer of C7H2 with a ptC atom as the overall reaction profiles there have been found to be exothermic. The activation energies for Si-C, C-C, and Si-C/C-C breaking are found to be 30.51, 64.05, and 61.85 kcal mol−1, respectively. Thus, it is emphasized here that 1 is a kinetically stable molecule. However, it remains elusive in the laboratory to date. Therefore, energetic and spectroscopic parameters have been documented here, which may be of relevance to molecular spectroscopists in identifying this key anti-van’t-Hoff-Le Bel molecule.
Collapse
|