The Experts below are selected from a list of 1752 Experts worldwide ranked by ideXlab platform
Yukari Fujimoto - One of the best experts on this subject based on the ideXlab platform.
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Chemical Synthesis of d-glycero-d-manno-Heptose 1,7-Bisphosphate and Evaluation of Its Ability to Modulate NF-κB Activation
Organic letters, 2017Co-Authors: Shinsuke Inuki, Toshihiko Aiba, Shota Kawakami, Taishin Akiyama, Jun-ichiro Inoue, Yukari FujimotoAbstract:d-glycero-d-manno-Heptose 1,7-bisphosphate (HBP) is the precursor for heptose residues found in Gram-negative bacterial membrane surface glycoproteins and glycolipids. HBP β-Anomer was recently reported to be a pathogen-associated molecular pattern (PAMP) that regulates TIFA-dependent immunity. Herein, we report the chemical synthesis of HBP α- and β-Anomers, which highlights a C-7 carbon homologation via the Corey–Chaykovsky reaction, and the introduction of a phosphate group at the Anomeric position using the Mitsunobu reaction. Furthermore, NF-κB reporter assaying revealed that HBP β-Anomer activates the NF-κB signaling pathway.
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Chemical Synthesis of d-glycero-d-manno-Heptose 1,7-Bisphosphate and Evaluation of Its Ability to Modulate NF-κB Activation
2017Co-Authors: Shinsuke Inuki, Toshihiko Aiba, Shota Kawakami, Taishin Akiyama, Jun-ichiro Inoue, Yukari FujimotoAbstract:d-glycero-d-manno-Heptose 1,7-bisphosphate (HBP) is the precursor for heptose residues found in Gram-negative bacterial membrane surface glycoproteins and glycolipids. HBP β-Anomer was recently reported to be a pathogen-associated molecular pattern (PAMP) that regulates TIFA-dependent immunity. Herein, we report the chemical synthesis of HBP α- and β-Anomers, which highlights a C-7 carbon homologation via the Corey–Chaykovsky reaction, and the introduction of a phosphate group at the Anomeric position using the Mitsunobu reaction. Furthermore, NF-κB reporter assaying revealed that HBP β-Anomer activates the NF-κB signaling pathway
Frank A Momany - One of the best experts on this subject based on the ideXlab platform.
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b3lyp 6 311 g geometry optimization study of pentahydrates of α and β d glucopyranose
Carbohydrate Research, 2005Co-Authors: Frank A Momany, Michael Appell, J L Willett, Wayne B BosmaAbstract:Five water molecules were placed in 37 different configurations around alpha- and beta-D-glucopyranose in the gt, gg, and tg conformational states, and the glucose-water complexes were geometry optimized using density functionals at the B3LYP/6-311++G** level of theory. The five water molecules were organized in space and energy minimized using an empirical potential, AMB02C, and then further geometry optimized using DFT algorithms to minimum energy positions. Electronic energy, zero point vibrational energy, enthalpy, entropy, stress energy on glucose and the water cluster, hydrogen-bond energy, and relative free energy were obtained for each configuration using thermodynamic procedures and an analytical Hessian program. The lowest energy complex was that of a clustering of water molecules around the 1- and 6-hydroxyl positions of the beta-gt Anomer. Configurations in which the water molecules created a favorable network completely around and under glucose were found to have low energy for both alpha and beta Anomers. Calculation of the alpha/beta Anomeric ratio using the zero point corrected energy gave, approximately 32/68%, highly favoring the beta Anomer in agreement with the experimental approximately 36/64% value. This ratio is better than the approximately 50/50% ratio found in our previous monohydrate study. An approximate hydroxymethyl population was obtained by noting average relative energies among the three conformational states, gt, gg, and tg. In the beta Anomer complexes the gt conformation was favored over the gg state, while in the alpha Anomer complexes the gg state was favored over the gt conformation, with the tg conformations all being of higher energy making little or no contribution to the rotamer population. Some geometry variances, found between glucose in vacuo and glucose after interaction with water molecules, are described and account for some observed C-5-C-6 bond length anomalies reported by us previously for the vacuum glucose structures.
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b3lyp 6 311 g study of monohydrates of α and β d glucopyranose hydrogen bonding stress energies and effect of hydration on internal coordinates
Carbohydrate Research, 2004Co-Authors: Frank A Momany, Michael Appell, Gina L Strati, J L WillettAbstract:Abstract Twenty-six monohydrates of α- and β- d -glucopyranose were studied using gradient methods at the B3LYP/6-311++G** level of theory. Geometry optimization was carried out with the water molecules at different configurations around the glucose molecule. A new nomenclature for hydrated carbohydrates was developed to describe the water configurations. Zero-point vibrational energy, enthalpy, entropy, and relative free energy were obtained using the harmonic approximation. Hydrogen-bond energies for the monohydrates range from ∼−5 to −12 kcal/mol, and the average relative free energy is ∼5 kcal/mol. The 1-hydroxy position is the most energetically favored site for hydration, and the region between the two and three positions is the next-most favored site. A water molecule approaching α- d -glucose between the 1- and 2-hydroxy positions pulls the 2-hydroxyl hydrogen atom away from the 1-hydroxy oxygen atom, thus increasing the hydrogen-bond length and also increasing the α- d -glucose energy. The increase in energy that occurs with a similar interaction on the β-Anomer is much less effective since the hydrogen bond is much longer. Using the calculated free energies of all 26 configurations, the Anomer population (α/β) increases in the β-Anomer population relative to the in vacuo case by ∼10% at the expense of the α-Anomer, giving an (α/β) ratio of ∼50/50. This result arises from entropy contributions favoring the β-Anomer more than the α-Anomer. From analysis of donor and acceptor hydrogen-bond lengths, excellent correlation is found between the DFT calculated distances and those taken from carbohydrate structures in the Cambridge Crystallographic Data Bank.
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b3lyp 6 311 g study of α and β d glucopyranose and 1 5 anhydro d glucitol 4c1 and 1c4 chairs 3 ob and b3 o boats and skew boat conformations
Carbohydrate Research, 2004Co-Authors: Michael Appell, Gina L Strati, J L Willett, Frank A MomanyAbstract:Geometry optimization, at the B3LYP/6-311++G** level of theory, was carried out on 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations of alpha- and beta-D-glucopyranose. Similar calculations on 1,5-anhydro-D-glucitol allowed examination of the effect of removal of the 1-hydroxy group on the energy preference of the hydroxymethyl rotamers. Stable minimum energy boat conformers of glucose were found, as were stable skew boats, all having energies ranging from approximately 4-15 kcal/mol above the global energy 4C1 chair conformation. The 1C4 chair electronic energies were approximately 5-10 kcal/mol higher than the 4C1 chair, with the 1C4 alpha-Anomers being lower in energy than the beta-Anomers. Zero-point energy, enthalpy, entropy, and relative Gibbs free energies are reported at the harmonic level of theory. The alpha-Anomer 4C1 chair conformations were found to be approximately 1 kcal/mol lower in electronic energy than the beta-Anomers. The hydroxymethyl gt conformation was of lowest electronic energy for both the alpha- and beta-Anomers. The glucose alpha/beta Anomer ratio calculated from the relative free energies is 63/37%. From a numerical Hessian calculation, the tg conformations were found to be approximately 0.4-0.7 kcal/mol higher in relative free energy than the gg or gt conformers. Transition-state barriers to rotation about the C-5-C-6 bond were calculated for each glucose Anomer with resulting barriers to rotation of approximately 3.7-5.8 kcal/mol. No energy barrier was found for the path between the alpha-gt and alpha-gg B(3,O) boat forms and the equivalent 4C1 chair conformations. The alpha-tg conformation has an energy minimum in the 1S3 twist form. Other boat and skew-boat forms are described. The beta-Anomer boats retained their starting conformations, with the exception of the beta-tg-(3,O)B boat that moved to a skew form upon optimization.
Shinsuke Inuki - One of the best experts on this subject based on the ideXlab platform.
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Chemical Synthesis of d-glycero-d-manno-Heptose 1,7-Bisphosphate and Evaluation of Its Ability to Modulate NF-κB Activation
Organic letters, 2017Co-Authors: Shinsuke Inuki, Toshihiko Aiba, Shota Kawakami, Taishin Akiyama, Jun-ichiro Inoue, Yukari FujimotoAbstract:d-glycero-d-manno-Heptose 1,7-bisphosphate (HBP) is the precursor for heptose residues found in Gram-negative bacterial membrane surface glycoproteins and glycolipids. HBP β-Anomer was recently reported to be a pathogen-associated molecular pattern (PAMP) that regulates TIFA-dependent immunity. Herein, we report the chemical synthesis of HBP α- and β-Anomers, which highlights a C-7 carbon homologation via the Corey–Chaykovsky reaction, and the introduction of a phosphate group at the Anomeric position using the Mitsunobu reaction. Furthermore, NF-κB reporter assaying revealed that HBP β-Anomer activates the NF-κB signaling pathway.
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Chemical Synthesis of d-glycero-d-manno-Heptose 1,7-Bisphosphate and Evaluation of Its Ability to Modulate NF-κB Activation
2017Co-Authors: Shinsuke Inuki, Toshihiko Aiba, Shota Kawakami, Taishin Akiyama, Jun-ichiro Inoue, Yukari FujimotoAbstract:d-glycero-d-manno-Heptose 1,7-bisphosphate (HBP) is the precursor for heptose residues found in Gram-negative bacterial membrane surface glycoproteins and glycolipids. HBP β-Anomer was recently reported to be a pathogen-associated molecular pattern (PAMP) that regulates TIFA-dependent immunity. Herein, we report the chemical synthesis of HBP α- and β-Anomers, which highlights a C-7 carbon homologation via the Corey–Chaykovsky reaction, and the introduction of a phosphate group at the Anomeric position using the Mitsunobu reaction. Furthermore, NF-κB reporter assaying revealed that HBP β-Anomer activates the NF-κB signaling pathway
Stephan Irle - One of the best experts on this subject based on the ideXlab platform.
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statistical mechanics based theoretical investigation of solvation effects on glucose Anomer preferences
Journal of Physical Chemistry B, 2018Co-Authors: Daisuke Yokogawa, Udo Schnupf, Stephan IrleAbstract:The importance of solvation effects on the stability of glucose Anomers has been studied by the combination of quantum mechanics and statistical mechanics, namely, the reference interaction site model self-consistent field spatial electron density distribution. The preferences of α- and β-glucose in H2O are well reproduced with the obtained ratio of 35:65 for α- and β-glucose, respectively. Indirect interactions and bulk effects, described by the Onsager model, are relatively small compared to the direct solute–solvent interactions, especially in [DMIM]Cl and dimethyl sulfoxide. From the decomposition of solvation free energy and solvation structures, it can be seen that the interactions with the solvent molecules greatly contribute to the Anomer preferences.
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statistical mechanics based theoretical investigation of solvation effects on glucose Anomer preferences b
The Journal of Physical Chemistry, 2018Co-Authors: Daisuke Yokogawa, Udo Schnupf, Stephan IrleAbstract:The importance of solvation effects on the stability of glucose Anomers has been studied by the combination of quantum mechanics and statistical mechanics, namely, the reference interaction site model self-consistent field spatial electron density distribution. The preferences of α- and β-glucose in H₂O are well reproduced with the obtained ratio of 35:65 for α- and β-glucose, respectively. Indirect interactions and bulk effects, described by the Onsager model, are relatively small compared to the direct solute–solvent interactions, especially in [DMIM]Cl and dimethyl sulfoxide. From the decomposition of solvation free energy and solvation structures, it can be seen that the interactions with the solvent molecules greatly contribute to the Anomer preferences.
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Statistical Mechanics-Based Theoretical Investigation of Solvation Effects on Glucose Anomer Preferences
2017Co-Authors: Daisuke Yokogawa, Udo Schnupf, Stephan IrleAbstract:The importance of solvation effects on the stability of glucose Anomers has been studied by the combination of quantum mechanics and statistical mechanics, namely, the reference interaction site model self-consistent field spatial electron density distribution. The preferences of α- and β-glucose in H2O are well reproduced with the obtained ratio of 35:65 for α- and β-glucose, respectively. Indirect interactions and bulk effects, described by the Onsager model, are relatively small compared to the direct solute–solvent interactions, especially in [DMIM]Cl and dimethyl sulfoxide. From the decomposition of solvation free energy and solvation structures, it can be seen that the interactions with the solvent molecules greatly contribute to the Anomer preferences
J L Willett - One of the best experts on this subject based on the ideXlab platform.
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b3lyp 6 311 g geometry optimization study of pentahydrates of α and β d glucopyranose
Carbohydrate Research, 2005Co-Authors: Frank A Momany, Michael Appell, J L Willett, Wayne B BosmaAbstract:Five water molecules were placed in 37 different configurations around alpha- and beta-D-glucopyranose in the gt, gg, and tg conformational states, and the glucose-water complexes were geometry optimized using density functionals at the B3LYP/6-311++G** level of theory. The five water molecules were organized in space and energy minimized using an empirical potential, AMB02C, and then further geometry optimized using DFT algorithms to minimum energy positions. Electronic energy, zero point vibrational energy, enthalpy, entropy, stress energy on glucose and the water cluster, hydrogen-bond energy, and relative free energy were obtained for each configuration using thermodynamic procedures and an analytical Hessian program. The lowest energy complex was that of a clustering of water molecules around the 1- and 6-hydroxyl positions of the beta-gt Anomer. Configurations in which the water molecules created a favorable network completely around and under glucose were found to have low energy for both alpha and beta Anomers. Calculation of the alpha/beta Anomeric ratio using the zero point corrected energy gave, approximately 32/68%, highly favoring the beta Anomer in agreement with the experimental approximately 36/64% value. This ratio is better than the approximately 50/50% ratio found in our previous monohydrate study. An approximate hydroxymethyl population was obtained by noting average relative energies among the three conformational states, gt, gg, and tg. In the beta Anomer complexes the gt conformation was favored over the gg state, while in the alpha Anomer complexes the gg state was favored over the gt conformation, with the tg conformations all being of higher energy making little or no contribution to the rotamer population. Some geometry variances, found between glucose in vacuo and glucose after interaction with water molecules, are described and account for some observed C-5-C-6 bond length anomalies reported by us previously for the vacuum glucose structures.
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b3lyp 6 311 g study of monohydrates of α and β d glucopyranose hydrogen bonding stress energies and effect of hydration on internal coordinates
Carbohydrate Research, 2004Co-Authors: Frank A Momany, Michael Appell, Gina L Strati, J L WillettAbstract:Abstract Twenty-six monohydrates of α- and β- d -glucopyranose were studied using gradient methods at the B3LYP/6-311++G** level of theory. Geometry optimization was carried out with the water molecules at different configurations around the glucose molecule. A new nomenclature for hydrated carbohydrates was developed to describe the water configurations. Zero-point vibrational energy, enthalpy, entropy, and relative free energy were obtained using the harmonic approximation. Hydrogen-bond energies for the monohydrates range from ∼−5 to −12 kcal/mol, and the average relative free energy is ∼5 kcal/mol. The 1-hydroxy position is the most energetically favored site for hydration, and the region between the two and three positions is the next-most favored site. A water molecule approaching α- d -glucose between the 1- and 2-hydroxy positions pulls the 2-hydroxyl hydrogen atom away from the 1-hydroxy oxygen atom, thus increasing the hydrogen-bond length and also increasing the α- d -glucose energy. The increase in energy that occurs with a similar interaction on the β-Anomer is much less effective since the hydrogen bond is much longer. Using the calculated free energies of all 26 configurations, the Anomer population (α/β) increases in the β-Anomer population relative to the in vacuo case by ∼10% at the expense of the α-Anomer, giving an (α/β) ratio of ∼50/50. This result arises from entropy contributions favoring the β-Anomer more than the α-Anomer. From analysis of donor and acceptor hydrogen-bond lengths, excellent correlation is found between the DFT calculated distances and those taken from carbohydrate structures in the Cambridge Crystallographic Data Bank.
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b3lyp 6 311 g study of α and β d glucopyranose and 1 5 anhydro d glucitol 4c1 and 1c4 chairs 3 ob and b3 o boats and skew boat conformations
Carbohydrate Research, 2004Co-Authors: Michael Appell, Gina L Strati, J L Willett, Frank A MomanyAbstract:Geometry optimization, at the B3LYP/6-311++G** level of theory, was carried out on 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations of alpha- and beta-D-glucopyranose. Similar calculations on 1,5-anhydro-D-glucitol allowed examination of the effect of removal of the 1-hydroxy group on the energy preference of the hydroxymethyl rotamers. Stable minimum energy boat conformers of glucose were found, as were stable skew boats, all having energies ranging from approximately 4-15 kcal/mol above the global energy 4C1 chair conformation. The 1C4 chair electronic energies were approximately 5-10 kcal/mol higher than the 4C1 chair, with the 1C4 alpha-Anomers being lower in energy than the beta-Anomers. Zero-point energy, enthalpy, entropy, and relative Gibbs free energies are reported at the harmonic level of theory. The alpha-Anomer 4C1 chair conformations were found to be approximately 1 kcal/mol lower in electronic energy than the beta-Anomers. The hydroxymethyl gt conformation was of lowest electronic energy for both the alpha- and beta-Anomers. The glucose alpha/beta Anomer ratio calculated from the relative free energies is 63/37%. From a numerical Hessian calculation, the tg conformations were found to be approximately 0.4-0.7 kcal/mol higher in relative free energy than the gg or gt conformers. Transition-state barriers to rotation about the C-5-C-6 bond were calculated for each glucose Anomer with resulting barriers to rotation of approximately 3.7-5.8 kcal/mol. No energy barrier was found for the path between the alpha-gt and alpha-gg B(3,O) boat forms and the equivalent 4C1 chair conformations. The alpha-tg conformation has an energy minimum in the 1S3 twist form. Other boat and skew-boat forms are described. The beta-Anomer boats retained their starting conformations, with the exception of the beta-tg-(3,O)B boat that moved to a skew form upon optimization.