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Ke An - One of the best experts on this subject based on the ideXlab platform.
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evaluation of triplet aromaticity by the indene isoindene isomerization Stabilization Energy method
European Journal of Organic Chemistry, 2014Co-Authors: Ke AnAbstract:Aromaticity, one of the most important concepts in chemistry, has attracted considerable interest from both experimentalists and theoreticians. According to Baird's rule, triplet annulenes with 4n π electrons are aromatic. However, the approach to evaluate the magnitude of the triplet aromaticity is less developed. Herein we apply the indene–isoindene isomerization Stabilization Energy (ISE) method to evaluate the aromaticity in the triplet state. The reliability of this approach can be demonstrated by the strong correlation of these indene–isoindene ISE values with nucleus-independent chemical shifts [NICS(1)zz] as well as methyl–methylene ISE values. Large [4n]annulenes have the tendency to be planar to achieve aromaticity in the T1 state. Steric effects play an important role in the stabilities of large [4n]annulene isomers.
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Evaluation of Triplet Aromaticity by the Indene–Isoindene Isomerization Stabilization Energy Method
European Journal of Organic Chemistry, 2014Co-Authors: Ke AnAbstract:Aromaticity, one of the most important concepts in chemistry, has attracted considerable interest from both experimentalists and theoreticians. According to Baird's rule, triplet annulenes with 4n π electrons are aromatic. However, the approach to evaluate the magnitude of the triplet aromaticity is less developed. Herein we apply the indene–isoindene isomerization Stabilization Energy (ISE) method to evaluate the aromaticity in the triplet state. The reliability of this approach can be demonstrated by the strong correlation of these indene–isoindene ISE values with nucleus-independent chemical shifts [NICS(1)zz] as well as methyl–methylene ISE values. Large [4n]annulenes have the tendency to be planar to achieve aromaticity in the T1 state. Steric effects play an important role in the stabilities of large [4n]annulene isomers.
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evaluation of triplet aromaticity by the isomerization Stabilization Energy
Organic Letters, 2013Co-Authors: Ke An, Paul Von Rague SchleyerAbstract:The many manifestations of aromaticity have long fascinated both experimentalists and theoreticians. Due to their degenerate half-filled MOs, triplet [n]annulenes with 4n π-electrons are also aromatic, but the degree of their Stabilization has been difficult to quantify. The isomerization Stabilization Energy (ISE) method has been applied to evaluate the triplet aromaticity. The reliability of this approach is indicated by the strong correlation of the ISE results with NICS(1)zz, a magnetic indicator of triplet state aromaticity.
Pavel Hobza - One of the best experts on this subject based on the ideXlab platform.
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The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies
Collection of Czechoslovak Chemical Communications, 2020Co-Authors: Jan Řezáč, Pavel Hobza, Karel Berka, Dominik Horinek, Jiří VondrášekAbstract:The Stabilization energies of Glu-Lys salt bridges are calculated at the CCSD(T) complete basis set limit to provide a reasonable description of the strength of the ion-pair bond in the gas phase. The effect of the environment (protein with ε = 4 and water with ε = 80) on the Stabilization Energy was introduced via a modification of the quantum chemical DFT Energy, for which the COSMO methodology was adopted. The other (standard) approach was based on incorporating a dielectric constant into the Coulomb electrostatic term of the Amber empirical potential function and utilizing the generalized Born model implemented in the Amber program. The environment affects the Stabilization Energy of the salt bridge dramatically: The protein reduces the Energy to less than one half of the original value, whereas water sometimes changes Stabilization to deStabilization. Both theoretical procedures, based on completely different theoretical backgrounds, yield very similar results, which strongly support their validity. An ion pair is converted to an ion-neutral pair when its pH is changed. This transformation is connected with a strong reduction of the Stabilization Energy regardless of the environment. The substantial differences in the Stabilization energies of ion pairs and ion-neutral pairs contradict the negligible changes of free Energy detected experimentally. Evidently, the contribution of formation and hydration entropy is significant and compensates for the large Stabilization energies.
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The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio , DFT and Empirical Potential Studies
Collection of Czechoslovak Chemical Communications, 2020Co-Authors: Jan Řezáč, Pavel Hobza, Karel Berka, Dominik Horinek, Jiří VondrášekAbstract:The Stabilization energies of Glu-Lys salt bridges are calculated at the CCSD(T) complete basis set limit to provide a reasonable description of the strength of the ion-pair bond in the gas phase. The effect of the environment (protein with e = 4 and water with e = 80) on the Stabilization Energy was introduced via a modification of the quantum chemical DFT Energy, for which the COSMO methodology was adopted. The other (standard) approach was based on incorporating a dielectric constant into the Coulomb electrostatic term of the Amber empirical potential function and utilizing the generalized Born model implemented in the Amber program. The environment affects the Stabilization Energy of the salt bridge dramatically: The protein reduces the Energy to less than one half of the original value, whereas water sometimes changes Stabilization to deStabilization. Both theoretical procedures, based on completely different theoretical backgrounds, yield very similar results, which strongly support their validity. An ion pair is converted to an ion-neutral pair when its pH is changed. This transformation is connected with a strong reduction of the Stabilization Energy regardless of the environment. The substantial differences in the Stabilization energies of ion pairs and ion-neutral pairs contradict the negligible changes of free Energy detected experimentally. Evidently, the contribution of formation and hydration entropy is significant and compensates for the large Stabilization energies.
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The World of Non-Covalent Interactions: 2006
Collection of Czechoslovak Chemical Communications, 2020Co-Authors: Pavel Hobza, Rudolf Zahradník, Klaus Müller-dethlefsAbstract:The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, Stabilization Energy, potential and free Energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.
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unexpectedly strong Energy Stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues correlated ab initio quantum chemical calculations
Journal of the American Chemical Society, 2005Co-Authors: Jiří Vondrášek, Lada Bendova, Pavel HobzaAbstract:The formation of a hydrophobic core of globular proteins is believed to be the consequence of exterior hydrophobic forces of entropic nature. This, together with the low occurrence of hydrogen bonds in the protein core, leads to the opinion that the Energy contribution of core formation to protein folding and stability is negligible. We show that Stabilization inside the hydrophobic core of a small protein, rubredoxin, determined by means of high-level correlated ab initio calculations (complete basis set limit of MP2 Stabilization Energy + CCSD(T) correction term), amounted to ∼50 kcal/mol. These results clearly demonstrate strong attraction inside a hydrophobic core. This finding may lead to substantial changes in the current view of protein folding. We also point out the inability of the DFT/B3LYP method to describe a strong attraction between studied amino acids.
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Abinitio second‐ and fourth‐order Mo/ller–Plesset study on structure, Stabilization Energy, and stretching vibration of benzene⋅⋅⋅X (X=He,Ne,Ar,Kr,Xe) van der Waals molecules
Journal of Chemical Physics, 1992Co-Authors: Pavel Hobza, Heinrich L. Selzle, Ota Bludský, Edward W. SchlagAbstract:The C6v structure of benzene⋅⋅⋅X (X=He, Ne, Ar, Kr, Xe) complexes was investigated with second‐order Mo/ller–Plesset (MP2) theory; for the benzene⋅⋅⋅He the whole potential‐Energy surface (PES) was also studied. The Stabilization Energy of the benzene⋅⋅⋅He was also determined at the fourth‐order Mo/ller–Plesset (MP4) level; the respective MP4 Stabilization Energy is almost identical with MP2 Stabilization Energy which is due to the compensation of MP3 and MP4 contributions. The ab initio MP2 intermolecular distances agree nicely for all the complexes studied with the experimental value. While the Stabilization Energy of benzene⋅⋅⋅He and benzene⋅⋅⋅Ne (67 cm−1; 99 cm−1) is considerably smaller than that of benzene⋅⋅⋅Ar (429 cm−1), the intersystem distance differs less (3.32 A, 3.50 A, 3.53 A). The Stabilization energies and intersystem distances for benzene⋅⋅⋅Kr and benzene⋅⋅⋅Xe are 485 and 601 cm−1 and 3.71 and 3.89 A, respectively. The PES of benzene⋅⋅⋅He differs from that of benzene⋅⋅⋅Ar and can be charac...
Paul Von Rague Schleyer - One of the best experts on this subject based on the ideXlab platform.
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evaluation of triplet aromaticity by the isomerization Stabilization Energy
Organic Letters, 2013Co-Authors: Ke An, Paul Von Rague SchleyerAbstract:The many manifestations of aromaticity have long fascinated both experimentalists and theoreticians. Due to their degenerate half-filled MOs, triplet [n]annulenes with 4n π-electrons are also aromatic, but the degree of their Stabilization has been difficult to quantify. The isomerization Stabilization Energy (ISE) method has been applied to evaluate the triplet aromaticity. The reliability of this approach is indicated by the strong correlation of the ISE results with NICS(1)zz, a magnetic indicator of triplet state aromaticity.
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On the Advantages of Hydrocarbon Radical Stabilization Energies Based on R−H Bond Dissociation Energies
Journal of Organic Chemistry, 2011Co-Authors: Matthew D. Wodrich, W. Chad Mckee, Paul Von Rague SchleyerAbstract:Hydrocarbon radical Stabilization Energy (RSE) estimates based on the differences in R−H vs CH3−H bond dissociation energies have inherent advantages over RSEs based on R−CH3 vs CH3−CH3, as well as R−R vs CH3−CH3 comparisons, since the R−CH3 and R−R reference systems are prone to unbalanced contaminating intramolecular interactions involving the R groups. When the effects of steric crowding, branching, protobranching, conjugation, and hyperconjugation are taken into account, R−CH3 and R−R based RSE values are nearly identical to R−H RSEs. Corrections for electronegativity differences between H and R are not needed to achieve agreement.
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on the aromatic Stabilization Energy of the 4n π electron pyrene
Molecular Physics, 2009Co-Authors: Judy I Wu, Michal A Dobrowolski, Michal K Cyranski, B L Merner, Graham J Bodwell, Y Mo, Paul Von Rague SchleyerAbstract:The aromatic Stabilization Energy (ASE) of pyrene, evaluated with both isodesmic equation and ab initio valence bond (VB) theory-based block localized wavefunction (BLW) methods, gives consistent results (ca 74 kcal/mol). Biphenyl, phenanthrene and benzene, evaluated similarly, all have essentially the same ASEs per ring carbon. The aromaticity of pyrene is not diminished because of its 4n π electron count.
Jiří Vondrášek - One of the best experts on this subject based on the ideXlab platform.
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The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies
Collection of Czechoslovak Chemical Communications, 2020Co-Authors: Jan Řezáč, Pavel Hobza, Karel Berka, Dominik Horinek, Jiří VondrášekAbstract:The Stabilization energies of Glu-Lys salt bridges are calculated at the CCSD(T) complete basis set limit to provide a reasonable description of the strength of the ion-pair bond in the gas phase. The effect of the environment (protein with ε = 4 and water with ε = 80) on the Stabilization Energy was introduced via a modification of the quantum chemical DFT Energy, for which the COSMO methodology was adopted. The other (standard) approach was based on incorporating a dielectric constant into the Coulomb electrostatic term of the Amber empirical potential function and utilizing the generalized Born model implemented in the Amber program. The environment affects the Stabilization Energy of the salt bridge dramatically: The protein reduces the Energy to less than one half of the original value, whereas water sometimes changes Stabilization to deStabilization. Both theoretical procedures, based on completely different theoretical backgrounds, yield very similar results, which strongly support their validity. An ion pair is converted to an ion-neutral pair when its pH is changed. This transformation is connected with a strong reduction of the Stabilization Energy regardless of the environment. The substantial differences in the Stabilization energies of ion pairs and ion-neutral pairs contradict the negligible changes of free Energy detected experimentally. Evidently, the contribution of formation and hydration entropy is significant and compensates for the large Stabilization energies.
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The Stabilization Energy of the GLU-LYS Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio , DFT and Empirical Potential Studies
Collection of Czechoslovak Chemical Communications, 2020Co-Authors: Jan Řezáč, Pavel Hobza, Karel Berka, Dominik Horinek, Jiří VondrášekAbstract:The Stabilization energies of Glu-Lys salt bridges are calculated at the CCSD(T) complete basis set limit to provide a reasonable description of the strength of the ion-pair bond in the gas phase. The effect of the environment (protein with e = 4 and water with e = 80) on the Stabilization Energy was introduced via a modification of the quantum chemical DFT Energy, for which the COSMO methodology was adopted. The other (standard) approach was based on incorporating a dielectric constant into the Coulomb electrostatic term of the Amber empirical potential function and utilizing the generalized Born model implemented in the Amber program. The environment affects the Stabilization Energy of the salt bridge dramatically: The protein reduces the Energy to less than one half of the original value, whereas water sometimes changes Stabilization to deStabilization. Both theoretical procedures, based on completely different theoretical backgrounds, yield very similar results, which strongly support their validity. An ion pair is converted to an ion-neutral pair when its pH is changed. This transformation is connected with a strong reduction of the Stabilization Energy regardless of the environment. The substantial differences in the Stabilization energies of ion pairs and ion-neutral pairs contradict the negligible changes of free Energy detected experimentally. Evidently, the contribution of formation and hydration entropy is significant and compensates for the large Stabilization energies.
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unexpectedly strong Energy Stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues correlated ab initio quantum chemical calculations
Journal of the American Chemical Society, 2005Co-Authors: Jiří Vondrášek, Lada Bendova, Pavel HobzaAbstract:The formation of a hydrophobic core of globular proteins is believed to be the consequence of exterior hydrophobic forces of entropic nature. This, together with the low occurrence of hydrogen bonds in the protein core, leads to the opinion that the Energy contribution of core formation to protein folding and stability is negligible. We show that Stabilization inside the hydrophobic core of a small protein, rubredoxin, determined by means of high-level correlated ab initio calculations (complete basis set limit of MP2 Stabilization Energy + CCSD(T) correction term), amounted to ∼50 kcal/mol. These results clearly demonstrate strong attraction inside a hydrophobic core. This finding may lead to substantial changes in the current view of protein folding. We also point out the inability of the DFT/B3LYP method to describe a strong attraction between studied amino acids.
Anthony K Cheetham - One of the best experts on this subject based on the ideXlab platform.
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influence of ligand field Stabilization Energy on the elastic properties of multiferroic mofs with the perovskite architecture
Dalton Transactions, 2012Co-Authors: Prashant K Jain, Anthony K CheethamAbstract:We report the mechanical properties of four isostructural metal–organic frameworks (MOFs) that adopt the ABX3 perovskite topology: [(CH3)2NH2]M(HCOO)3, where M = divalent Mn, Co, Ni, and Zn. Their Young's moduli were measured via single-crystal nanoindentation. We show that the mechanical stability of such isostructural frameworks with octahedral coordination increases with greater ligand field Stabilization Energy (LFSE).
