Transition between [<i>R</i>]- and [<i>S</i>]-stereoisomers without bond breaking

Raghunathan, Shampa; Yadav, Komal; Rojisha, Vallyanga Chalil; Jaganade, Tanashree; Prathyusha, V.; Bikkina, Swetha; Lourderaj, Upakarasamy

doi:10.1039/d0cp02918a

Cited by 12 publications

(11 citation statements)

References 64 publications

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“…Many studies are devoted to the consideration of transitions from tetrahedral to planar electron configurations. Planar intermediates are critical determinants of the racemization barrier and rate of racemization [63]. Free AAs and peptides/protein-incorporated AAs are characterized by significantly different rates of spontaneous reactions.…”

Section: Three Major Sources Of D-aas In Mammals Are Intrinsic Racemization (Enzymatic and Spontaneous) Diet And Gut Microbiotamentioning

confidence: 99%

“…Free AAs and peptides/protein-incorporated AAs are characterized by significantly different rates of spontaneous reactions. Due to the complexity of three-dimensional structure of globular proteins and the presence of many functional groups, susceptibility to spontaneous or enzyme-dependent stereo-chemical modifications is much higher for peptides and proteins than for free AAs [63]. Therefore, future research in this field will enormously contribute to understanding the molecular mechanism of protein misfolding, aggregation, disfunction, degradation, and aging.…”

Section: Three Major Sources Of D-aas In Mammals Are Intrinsic Racemization (Enzymatic and Spontaneous) Diet And Gut Microbiotamentioning

confidence: 99%

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Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive, and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

Dyakin¹,

Dyakina‐Fagnano²,

McIntire³

et al. 2021

Preprint

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In humans, age-associated degrading changes are observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psy-chological abilities, and memory. Cross talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, ge-nome, 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 chirali-ty, 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 re-lated to irreversible PTMs SP has been associated with the nontrivial interplay between poor so-matic and mental 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 un-der-appreciated hallmark of aging.

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Section: Three Major Sources Of D-aas In Mammals Are Intrinsic Racemization (Enzymatic and Spontaneous) Diet And Gut Microbiotamentioning

confidence: 99%

Section: Three Major Sources Of D-aas In Mammals Are Intrinsic Racemization (Enzymatic and Spontaneous) Diet And Gut Microbiotamentioning

confidence: 99%

Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive, and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

Dyakin¹,

Dyakina‐Fagnano²,

McIntire³

et al. 2021

Preprint

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“…The concept of molecules with a planar tetracoordinate carbon (ptC) [ 1,2 ] atom is an inspiration to all chemists [ 3–15 ] despite it breaking one of the fundamental paradigms of organic chemistry—that is, tetrahedral tetracoordinate carbon. [ 16,17 ] Experimental and theoretical confirmation of pentaatomic ptC species (CAl

_{4}^{-}

, CAl 3 Si −/0 , CAl 3 Ge −/0 , CAl

_{4}^{2 -}

, etc.,) [ 18–21 ] has provided some momentum in the search of these molecules in the gas phase.…”

Section: Introductionmentioning

confidence: 99%

Flat crown ethers with planar tetracoordinate carbon atoms

Thirumoorthy

Thimmakondu

2020

Int J of Quantum Chemistry

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Novel flat crown ether molecules have been characterized in silico using DFT hybrid and hybrid-meta functionals. Monomer units of Si2C3 with a planar tetracoordinate carbon atom have been used as building blocks. Alkali (Li+, Na+, K+, Rb+, and Cs+) and alkaline-earth (Ca2+, Sr2+, and Ba2+) metals, and uranyl (UO2+ 2) ion selective complexes have also been theoretically identified. The high symmetry and higher structural rigidity of the host molecules may likely to impart higher selectivity in chelation. Theoretical binding energies have been computed and experimental studies are invited. File list (2) download file view on ChemRxiv fce.pdf (39.20 MiB) download file view on ChemRxiv si-flat-crown-ether.pdf (5.79 MiB)

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“…[3][4][5][6][7][8][9][10] but also to other elements such as B [11][12][13][14][15][16][17], Al [18,19], N [20][21][22], P [23], O [24], and lately even to the F atom [25]. There are two main reasons why experimentalists [5,6,[26][27][28][29][30][31][32][33] and theoreticians [2,[34][35][36][37][38][39][40][41][42][43] have put a great deal of effort into studying these special class of molecules: (i) ptC is a fundamental deviation from the conventional ideas of tetrahedral tetracoordinate carbon [44,45]; (ii) no two structural isomers behave in the same way chemically. Thus, making this new class of molecules enhances our existing understanding about chemical bonding, and one could potentially make new materials.…”

Section: Introductionmentioning

confidence: 99%

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

Khatun

Roy

Giri

et al. 2021

Atoms

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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.

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Transition between [R]- and [S]-stereoisomers without bond breaking

Abstract:
First examples of racemization of tetrahedral tetracoordinated centers via a planar transition state or an intermediate structure.

Cited by 12 publications

References 64 publications

Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive, and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive, and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

Flat crown ethers with planar tetracoordinate carbon atoms

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

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Transition between [R]- and [S]-stereoisomers without bond breaking

Abstract: First examples of racemization of tetrahedral tetracoordinated centers via a planar transition state or an intermediate structure.

Cited by 12 publications

References 64 publications

Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive, and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

Fundamental Clock of Biological Aging: Convergence of Molecular, Neurodegenerative, Cognitive, and Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology

Flat crown ethers with planar tetracoordinate carbon atoms

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

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Product

Resources

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Abstract:
First examples of racemization of tetrahedral tetracoordinated centers via a planar transition state or an intermediate structure.