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Jaan Laane - One of the best experts on this subject based on the ideXlab platform.
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theoretical calculations and vibrational potential energy surface of 4 silaspiro 3 3 heptane
Journal of Chemical Physics, 2014Co-Authors: Esther J. Ocola, Niklas Meinander, Cross Medders, Jaan LaaneAbstract:Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x14 + x24) – b(x12 + x22) + cx12x22, where x1 and x2 are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing Pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.
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two dimensional vibrational potential energy surface for the ring bending and twisting of 1 3 oxathiolane evidence for the anomeric effect resulting from o ch2 s linkages
Journal of Chemical Physics, 1994Co-Authors: S J Leibowitz, Jaan LaaneAbstract:The far‐infrared spectra of 1,3‐oxathiolane and its 2,2‐d2 isotopomer have been analyzed in terms of a two‐dimensional vibrational potential energy surface expressed as a function of ring‐bending and ring‐twisting coordinates. The barrier to planarity was determined to be 2289±200 cm−1 while the barrier to Pseudorotation, representing the energy difference between the lowest energy twisted form and the highest energy bent form, was found to be 570±20 cm−1. The barrier to planarity is about 500 cm−1 higher than that of cyclopentane, and this is attributed to the anomeric effect resulting from the –O–CH2–S– linkage which tends to twist the molecule out of the planar configuration.
Toshiyasu Suzuki - One of the best experts on this subject based on the ideXlab platform.
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tetrabenzo 8 circulene aromatic saddles from negatively curved graphene
Journal of the American Chemical Society, 2013Co-Authors: Youichi Sakamoto, Toshiyasu SuzukiAbstract:An aromatic saddle was designed from the hypothetical three-dimensional graphene with the negative Gaussian curvature (Schwarzite P192). Two aromatic saddles, tetrabenzo[8]circulene (TB8C) and its octamethyl derivative OM-TB8C, were synthesized by the Scholl reaction of cyclic octaphenylene precursors. The structure of TB8C greatly deviates from planarity, and the deep saddle shape was confirmed by single-crystal X-ray crystallography. There are two conformers with the S4 symmetry, which are twisted compared to the DFT structure (D2d). The theoretical studies propose that the interconversion of TB8C via the planar transition state (125 kcal mol–1) is not possible. However, the Pseudorotation leads to a low-energy tub-to-tub inversion via the nonplanar transition state (7.3 kcal mol–1). The ground-state structure of TB8C in solution is quite different from the X-ray structure because of the crystal-packing force and low-energy Pseudorotation. OM-TB8C is a good electron donor and works as the p-type semicon...
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Tetrabenzo[8]circulene: Aromatic Saddles from Negatively Curved Graphene
2013Co-Authors: Youichi Sakamoto, Toshiyasu SuzukiAbstract:An aromatic saddle was designed from the hypothetical three-dimensional graphene with the negative Gaussian curvature (Schwarzite P192). Two aromatic saddles, tetrabenzo[8]circulene (TB8C) and its octamethyl derivative OM-TB8C, were synthesized by the Scholl reaction of cyclic octaphenylene precursors. The structure of TB8C greatly deviates from planarity, and the deep saddle shape was confirmed by single-crystal X-ray crystallography. There are two conformers with the S4 symmetry, which are twisted compared to the DFT structure (D2d). The theoretical studies propose that the interconversion of TB8C via the planar transition state (125 kcal mol–1) is not possible. However, the Pseudorotation leads to a low-energy tub-to-tub inversion via the nonplanar transition state (7.3 kcal mol–1). The ground-state structure of TB8C in solution is quite different from the X-ray structure because of the crystal-packing force and low-energy Pseudorotation. OM-TB8C is a good electron donor and works as the p-type semiconductor
Ayan Datta - One of the best experts on this subject based on the ideXlab platform.
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can arsenates replace phosphates in natural biochemical processes a computational study
Journal of Physical Chemistry B, 2013Co-Authors: A K Jissy, Ayan DattaAbstract:A bacterial strain, GFAJ-1 was recently proposed to be substituting arsenic for phosphorus to sustain its growth. We have performed theoretical calculations for analyzing this controversial hypothesis by examining the addition of phosphate to ribose and glucose. Dispersion corrected Density Functional Theory (DFT) calculations in small molecules and QM/MM calculations on clusters derived from crystal structure are performed on structures involved in phosphorylation, considering both phosphates and arsenates. The exothermicity as well as the activation barriers for phosphate and arsenate transfer were examined. Quantum mechanical studies reveal that the relative stability of the products decrease marginally with successive substitution of P with As. However, simultaneously, the transition state barriers decrease with P replacement. This indicates that, kinetically, addition of As is more facile. Pseudorotation barriers for the pentavalent intermediates formed during the nucleophilic attack are also analyze...
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Can Arsenates Replace Phosphates in Natural Biochemical Processes? A Computational Study
2013Co-Authors: A K Jissy, Ayan DattaAbstract:A bacterial strain, GFAJ-1 was recently proposed to be substituting arsenic for phosphorus to sustain its growth. We have performed theoretical calculations for analyzing this controversial hypothesis by examining the addition of phosphate to ribose and glucose. Dispersion corrected Density Functional Theory (DFT) calculations in small molecules and QM/MM calculations on clusters derived from crystal structure are performed on structures involved in phosphorylation, considering both phosphates and arsenates. The exothermicity as well as the activation barriers for phosphate and arsenate transfer were examined. Quantum mechanical studies reveal that the relative stability of the products decrease marginally with successive substitution of P with As. However, simultaneously, the transition state barriers decrease with P replacement. This indicates that, kinetically, addition of As is more facile. Pseudorotation barriers for the pentavalent intermediates formed during the nucleophilic attack are also analyzed. A monotonic increase in barriers is observed for Pseudorotation with the successive replacement of phosphorus with arsenic in methyl-DHP. A glucokinase crystal structure was chosen to construct a model system for QM/MM calculations. Free energy of the reaction (ΔG) reduces by less than 2.0 kcal/mol and the activation barrier (ΔG‡) decreases by ∼1 kcal/mol on arsenic incorporation. Thus, both DFT and QM/MM calculations show that arsenic can readily substitute phosphorus in key biomolecules. Secondary kinetic isotope effects for phosphorylation mechanism obtained by QM/MM calculations are also reported. The solvent kinetic isotopic effects (SKIE) for ATP and ATP (As) are calculated to be 5.81 and 4.73, respectively. A difference of ∼1.0 in SKIE suggests that it should be possible to experimentally determine the As–phosphorylation process
Youichi Sakamoto - One of the best experts on this subject based on the ideXlab platform.
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tetrabenzo 8 circulene aromatic saddles from negatively curved graphene
Journal of the American Chemical Society, 2013Co-Authors: Youichi Sakamoto, Toshiyasu SuzukiAbstract:An aromatic saddle was designed from the hypothetical three-dimensional graphene with the negative Gaussian curvature (Schwarzite P192). Two aromatic saddles, tetrabenzo[8]circulene (TB8C) and its octamethyl derivative OM-TB8C, were synthesized by the Scholl reaction of cyclic octaphenylene precursors. The structure of TB8C greatly deviates from planarity, and the deep saddle shape was confirmed by single-crystal X-ray crystallography. There are two conformers with the S4 symmetry, which are twisted compared to the DFT structure (D2d). The theoretical studies propose that the interconversion of TB8C via the planar transition state (125 kcal mol–1) is not possible. However, the Pseudorotation leads to a low-energy tub-to-tub inversion via the nonplanar transition state (7.3 kcal mol–1). The ground-state structure of TB8C in solution is quite different from the X-ray structure because of the crystal-packing force and low-energy Pseudorotation. OM-TB8C is a good electron donor and works as the p-type semicon...
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Tetrabenzo[8]circulene: Aromatic Saddles from Negatively Curved Graphene
2013Co-Authors: Youichi Sakamoto, Toshiyasu SuzukiAbstract:An aromatic saddle was designed from the hypothetical three-dimensional graphene with the negative Gaussian curvature (Schwarzite P192). Two aromatic saddles, tetrabenzo[8]circulene (TB8C) and its octamethyl derivative OM-TB8C, were synthesized by the Scholl reaction of cyclic octaphenylene precursors. The structure of TB8C greatly deviates from planarity, and the deep saddle shape was confirmed by single-crystal X-ray crystallography. There are two conformers with the S4 symmetry, which are twisted compared to the DFT structure (D2d). The theoretical studies propose that the interconversion of TB8C via the planar transition state (125 kcal mol–1) is not possible. However, the Pseudorotation leads to a low-energy tub-to-tub inversion via the nonplanar transition state (7.3 kcal mol–1). The ground-state structure of TB8C in solution is quite different from the X-ray structure because of the crystal-packing force and low-energy Pseudorotation. OM-TB8C is a good electron donor and works as the p-type semiconductor
Darrin M. York - One of the best experts on this subject based on the ideXlab platform.
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Pseudorotation barriers of biological oxyphosphoranes: a challenge for simulations of ribozyme catalysis
2014Co-Authors: Carlos Silva Lopez, Olalla Nieto Faza, Angel Rodriguez De Lera, Darrin M. YorkAbstract:Pseudorotation reactions of biologically relevant oxyphosphoranes were studied using density-functional and continuum solvation methods. A series of 16 Pseudorotation reactions involving acyclic and cyclic oxyphos-phoranes in neutral and monoanionic (singly deprotonated) forms were studied, in addition to Pseudorotation of PF5. The effect of solvent was treated using 3 different solvation models for comparison. The barri-ers to Pseudorotation ranged from 1.5 to 8.1 kcal/mol and were influenced systematically by charge state, apicophilicity of ligands, intramolecular hydrogen bonding, cyclic structure and solvation. Barriers to pseu-dorotation for monoanionic phosphoranes occur with the anionic oxo ligand as the pivotal atom, and are generally lower than for neutral phosphoranes. The OCH3 groups were observed to be more apicophilic than OH groups, and hence Pseudorotations that involve axial OCH3/equatorial OH exchange had higher reaction and activation free energy values. Solvent generally lowered barriers relative to the gas phase reactions. These results, together with isotope 18O exchange experiments, support the assertion that dianionic phosphoranes are not sufficiently long-lived to undergo Pseudorotation. Comparison of the density-functional results with those from several semiempirical quantum models highlight a challenge for new-generation hybrid quantum mechanical/molecular mechanical potentials for non-enzymatic and enzymatic phosphoryl transfer reactions: the reliable modeling of Pseudorotation processes. 1 Silva-Lopez et al. Pseudorotation barriers of biological oxyphosphoranes
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Pseudorotation of natural and chemically modified biological phosphoranes: implications for RNA catalysis∗∗
2014Co-Authors: Carlos Silva López, Olalla Nieto Faza, Brent A Gregersen, Xabier Lopez, Angel R De Lera, Darrin M. YorkAbstract:(Euskal Herriko Unibersitatea) for financial support. CSL and ONF are grateful for the fellowships provided by the Ministerio de Educacion Cultura y Deporte from the Spanish Government and for the kind invitation from DY to join his group. Biological phosphates form the anionic backbone linkage in DNA and RNA, and play a central role in the regulation of cellular processes including signaling, respiration, replication and translation.1 Consequently, the study of the chemistry of biological phosphates is an area of great importance.2–5 Of particular interest are the mechanisms for which RNA can catalyze fairly complicated reactions,6–8 such as the transphosphorylation and hydrolysis of phosphodiester bonds. A useful experimental strategy to probe the catalytic mechanisms of RNA enzymes is through the study of thio effects: changes in the reaction rate that occur upon substitution of key phosphate oxygen positions with sulfur.9, 10 Kinetic analysis of thio effects provides insight into the specific role these oxygen positions play in catalysis.11 Theoretical methods are powerful tools to aid the interpretation of kinetic data through characterization of the structure and energetics of transition states and intermediates along competing reaction paths.12 The dominant reaction path for transphosphorylation in RNA2 (Scheme 1) proceeds via an in-line attack of an activated 2 ’ hydroxyl group of the RNA sugar ring to the reactive phosphate to produce
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Pseudorotation of natural and chemically modified biological phosphoranes implications for rna catalysis
ChemPhysChem, 2004Co-Authors: Carlos Silva Lopez, Olalla Nieto Faza, Brent A Gregersen, Xabier Lopez, Angel R De Lera, Darrin M. YorkAbstract:Biological phosphates form the anionic backbone linkage in DNA and RNA and play a central role in the regulation of cellular processes including signaling, respiration, replication, and translation. Consequently, the study of the chemistry of biological phosphates is an area of great importance. Of particular interest are the mechanisms by which RNA can catalyze fairly complicated reactions such as the transphosphorylation and hydrolysis of phosphodiester bonds. A useful experimental strategy to probe the catalytic mechanisms of RNA enzymes is the study of thio effects: changes in the reaction rate that occur upon substitution of key phosphate oxygen atoms with sulfur atoms. Kinetic analysis of thio effects provides insight into the specific role that these oxygen positions play in catalysis. Theoretical methods are powerful tools to aid the interpretation of kinetic data through characterization of the structure and energetics of transition states and intermediates along competing reaction paths. The dominant reaction path for transphosphorylation in RNA (Scheme 1) proceeds via an in-line attack of an activated 2’-hydroxy group of the RNA sugar ring on the reactive phosphate group to produce a pentavalent phosphorane transition state or intermediate, followed by the cleavage of the P-O bond to produce a 2’,3’-cyclic phosphate. Experimental and theoretical data suggest a dianionic oxyphosphorane transphosphorylation intermediate is kinetically indistinguishable from a transition state and is too short-lived to undergo other processes such as protonation or Pseudorotation. As the pH is lowered, acid-catalyzed migration products begin to emerge, which result from Pseudorotation of a singly or doubly protonated phosphorane intermediate (Scheme 2). The ratio of products resulting from phosphate hydrolysis/ transphosphorylation and isomerization (migration) and their pH dependence involve a balance between the endoand exo-
