MP2, density functional theory, and molecular mechanical calculations of C-H⋯π and hydrogen bond interactions in a cellulose-binding module-cellulose model system

Mohamed Naseer Ali Mohamed, Heath D. Watts, Jing Guo, Jeffrey M. Catchmark, James D. Kubicki

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Exploring non-covalent interactions, such as C-H⋯π stacking and classical hydrogen bonding (H-bonding), between carbohydrates and carbohydrate-binding modules (CBMs) is an important task in glycobiology. The present study focuses on intermolecular interactions, such as C-H⋯π (sugar-aromatic stacking) and H-bonds, between methyl β-d-glucopyranoside and l-tyrosine - a proxy model system for a cellulose-CBM complex. This work has made use of various types of quantum mechanics (QM) and molecular mechanics (MM) methods to determine which is the most accurate and computationally efficient. The calculated interaction potential energies ranged between -24 and -38 kJ/mol. The larger interaction energy is due to H-bonding between the phenyl hydroxyl of tyrosine and the O4 of the sugar. Density functional theory (DFT) methods, such as BHandHLYP and B3LYP, exaggerate the H-bond. Although one of the MM methods (viz. MM+) considered in this study does maintain the C-H⋯π stacking configuration, it underestimates the interaction energy due to the loss of the H-bond. When the O-H bond vector is in the vicinity of O4 (O-H⋯O4 ≈ 2 , e.g., in the case of MP2/6-31G(d)), the torsional energy drops to a minimum. For this configuration, natural bond orbital (NBO) analysis also supports the presence of this H-bond which arises due to orbital interaction between one lone pair of the sugar O4 and the σ(O-H) orbital of the phenyl group of tyrosine. The stabilization energy due to orbital delocalization of the H-bonded system is ∼13 kJ/mol. This H-bond interaction plays an important role in controlling the CH/π interaction geometry. Therefore, the C-H⋯π dispersive interaction is the secondary force, which supports the stabilization of the complex. The meta-hybrid DFT method, M05-2X, with the 6-311++G(d,p) basis set agrees well with the MP2 results and is less computationally expensive. However, the M05-2X method is strongly basis set dependent in describing this CH/π interaction. Computed IR spectra with the MP2/6-31G(d) method show blue shifts for C1-H, C3-H, and C5-H stretching frequencies due to the C-H⋯π interaction. However, the M05-2X/6-311++G(d,p) method shows a small red shift for the C1-H stretching region and blue shifts for the C2-H and C3-H stretches. For the aromatic tyrosine Cδ1-C1 and Cδ2-C 2 bonds in the complex, the calculated IR spectra show red shifts of 12 cm-1 (MP2/6-31G(d)) and 5 cm-1 (M05-2X/6-311++G(d,p)). This study also reports the upfield shifts of computed 1H NMR chemical shifts due to the C-H⋯π interaction.

Original languageEnglish (US)
Pages (from-to)1741-1751
Number of pages11
JournalCarbohydrate Research
Volume345
Issue number12
DOIs
StatePublished - Aug 16 2010

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Cellulose
Molecular mechanics
Density functional theory
Tyrosine
Hydrogen
Hydrogen bonds
Sugars
Mechanics
Carbohydrates
Stretching
Stabilization
Hydrogen Bonding
Quantum theory
Chemical shift
Potential energy
Hydroxyl Radical
Glycomics
Nuclear magnetic resonance
Proxy
Geometry

All Science Journal Classification (ASJC) codes

  • Analytical Chemistry
  • Biochemistry
  • Organic Chemistry

Cite this

@article{84196461122c48389b28cbb4695a0244,
title = "MP2, density functional theory, and molecular mechanical calculations of C-H⋯π and hydrogen bond interactions in a cellulose-binding module-cellulose model system",
abstract = "Exploring non-covalent interactions, such as C-H⋯π stacking and classical hydrogen bonding (H-bonding), between carbohydrates and carbohydrate-binding modules (CBMs) is an important task in glycobiology. The present study focuses on intermolecular interactions, such as C-H⋯π (sugar-aromatic stacking) and H-bonds, between methyl β-d-glucopyranoside and l-tyrosine - a proxy model system for a cellulose-CBM complex. This work has made use of various types of quantum mechanics (QM) and molecular mechanics (MM) methods to determine which is the most accurate and computationally efficient. The calculated interaction potential energies ranged between -24 and -38 kJ/mol. The larger interaction energy is due to H-bonding between the phenyl hydroxyl of tyrosine and the O4 of the sugar. Density functional theory (DFT) methods, such as BHandHLYP and B3LYP, exaggerate the H-bond. Although one of the MM methods (viz. MM+) considered in this study does maintain the C-H⋯π stacking configuration, it underestimates the interaction energy due to the loss of the H-bond. When the O-H bond vector is in the vicinity of O4 (O-H⋯O4 ≈ 2 , e.g., in the case of MP2/6-31G(d)), the torsional energy drops to a minimum. For this configuration, natural bond orbital (NBO) analysis also supports the presence of this H-bond which arises due to orbital interaction between one lone pair of the sugar O4 and the σ(O-H) orbital of the phenyl group of tyrosine. The stabilization energy due to orbital delocalization of the H-bonded system is ∼13 kJ/mol. This H-bond interaction plays an important role in controlling the CH/π interaction geometry. Therefore, the C-H⋯π dispersive interaction is the secondary force, which supports the stabilization of the complex. The meta-hybrid DFT method, M05-2X, with the 6-311++G(d,p) basis set agrees well with the MP2 results and is less computationally expensive. However, the M05-2X method is strongly basis set dependent in describing this CH/π interaction. Computed IR spectra with the MP2/6-31G(d) method show blue shifts for C1-H, C3-H, and C5-H stretching frequencies due to the C-H⋯π interaction. However, the M05-2X/6-311++G(d,p) method shows a small red shift for the C1-H stretching region and blue shifts for the C2-H and C3-H stretches. For the aromatic tyrosine Cδ1-C1 and Cδ2-C 2 bonds in the complex, the calculated IR spectra show red shifts of 12 cm-1 (MP2/6-31G(d)) and 5 cm-1 (M05-2X/6-311++G(d,p)). This study also reports the upfield shifts of computed 1H NMR chemical shifts due to the C-H⋯π interaction.",
author = "Mohamed, {Mohamed Naseer Ali} and Watts, {Heath D.} and Jing Guo and Catchmark, {Jeffrey M.} and Kubicki, {James D.}",
year = "2010",
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MP2, density functional theory, and molecular mechanical calculations of C-H⋯π and hydrogen bond interactions in a cellulose-binding module-cellulose model system. / Mohamed, Mohamed Naseer Ali; Watts, Heath D.; Guo, Jing; Catchmark, Jeffrey M.; Kubicki, James D.

In: Carbohydrate Research, Vol. 345, No. 12, 16.08.2010, p. 1741-1751.

Research output: Contribution to journalArticle

TY - JOUR

T1 - MP2, density functional theory, and molecular mechanical calculations of C-H⋯π and hydrogen bond interactions in a cellulose-binding module-cellulose model system

AU - Mohamed, Mohamed Naseer Ali

AU - Watts, Heath D.

AU - Guo, Jing

AU - Catchmark, Jeffrey M.

AU - Kubicki, James D.

PY - 2010/8/16

Y1 - 2010/8/16

N2 - Exploring non-covalent interactions, such as C-H⋯π stacking and classical hydrogen bonding (H-bonding), between carbohydrates and carbohydrate-binding modules (CBMs) is an important task in glycobiology. The present study focuses on intermolecular interactions, such as C-H⋯π (sugar-aromatic stacking) and H-bonds, between methyl β-d-glucopyranoside and l-tyrosine - a proxy model system for a cellulose-CBM complex. This work has made use of various types of quantum mechanics (QM) and molecular mechanics (MM) methods to determine which is the most accurate and computationally efficient. The calculated interaction potential energies ranged between -24 and -38 kJ/mol. The larger interaction energy is due to H-bonding between the phenyl hydroxyl of tyrosine and the O4 of the sugar. Density functional theory (DFT) methods, such as BHandHLYP and B3LYP, exaggerate the H-bond. Although one of the MM methods (viz. MM+) considered in this study does maintain the C-H⋯π stacking configuration, it underestimates the interaction energy due to the loss of the H-bond. When the O-H bond vector is in the vicinity of O4 (O-H⋯O4 ≈ 2 , e.g., in the case of MP2/6-31G(d)), the torsional energy drops to a minimum. For this configuration, natural bond orbital (NBO) analysis also supports the presence of this H-bond which arises due to orbital interaction between one lone pair of the sugar O4 and the σ(O-H) orbital of the phenyl group of tyrosine. The stabilization energy due to orbital delocalization of the H-bonded system is ∼13 kJ/mol. This H-bond interaction plays an important role in controlling the CH/π interaction geometry. Therefore, the C-H⋯π dispersive interaction is the secondary force, which supports the stabilization of the complex. The meta-hybrid DFT method, M05-2X, with the 6-311++G(d,p) basis set agrees well with the MP2 results and is less computationally expensive. However, the M05-2X method is strongly basis set dependent in describing this CH/π interaction. Computed IR spectra with the MP2/6-31G(d) method show blue shifts for C1-H, C3-H, and C5-H stretching frequencies due to the C-H⋯π interaction. However, the M05-2X/6-311++G(d,p) method shows a small red shift for the C1-H stretching region and blue shifts for the C2-H and C3-H stretches. For the aromatic tyrosine Cδ1-C1 and Cδ2-C 2 bonds in the complex, the calculated IR spectra show red shifts of 12 cm-1 (MP2/6-31G(d)) and 5 cm-1 (M05-2X/6-311++G(d,p)). This study also reports the upfield shifts of computed 1H NMR chemical shifts due to the C-H⋯π interaction.

AB - Exploring non-covalent interactions, such as C-H⋯π stacking and classical hydrogen bonding (H-bonding), between carbohydrates and carbohydrate-binding modules (CBMs) is an important task in glycobiology. The present study focuses on intermolecular interactions, such as C-H⋯π (sugar-aromatic stacking) and H-bonds, between methyl β-d-glucopyranoside and l-tyrosine - a proxy model system for a cellulose-CBM complex. This work has made use of various types of quantum mechanics (QM) and molecular mechanics (MM) methods to determine which is the most accurate and computationally efficient. The calculated interaction potential energies ranged between -24 and -38 kJ/mol. The larger interaction energy is due to H-bonding between the phenyl hydroxyl of tyrosine and the O4 of the sugar. Density functional theory (DFT) methods, such as BHandHLYP and B3LYP, exaggerate the H-bond. Although one of the MM methods (viz. MM+) considered in this study does maintain the C-H⋯π stacking configuration, it underestimates the interaction energy due to the loss of the H-bond. When the O-H bond vector is in the vicinity of O4 (O-H⋯O4 ≈ 2 , e.g., in the case of MP2/6-31G(d)), the torsional energy drops to a minimum. For this configuration, natural bond orbital (NBO) analysis also supports the presence of this H-bond which arises due to orbital interaction between one lone pair of the sugar O4 and the σ(O-H) orbital of the phenyl group of tyrosine. The stabilization energy due to orbital delocalization of the H-bonded system is ∼13 kJ/mol. This H-bond interaction plays an important role in controlling the CH/π interaction geometry. Therefore, the C-H⋯π dispersive interaction is the secondary force, which supports the stabilization of the complex. The meta-hybrid DFT method, M05-2X, with the 6-311++G(d,p) basis set agrees well with the MP2 results and is less computationally expensive. However, the M05-2X method is strongly basis set dependent in describing this CH/π interaction. Computed IR spectra with the MP2/6-31G(d) method show blue shifts for C1-H, C3-H, and C5-H stretching frequencies due to the C-H⋯π interaction. However, the M05-2X/6-311++G(d,p) method shows a small red shift for the C1-H stretching region and blue shifts for the C2-H and C3-H stretches. For the aromatic tyrosine Cδ1-C1 and Cδ2-C 2 bonds in the complex, the calculated IR spectra show red shifts of 12 cm-1 (MP2/6-31G(d)) and 5 cm-1 (M05-2X/6-311++G(d,p)). This study also reports the upfield shifts of computed 1H NMR chemical shifts due to the C-H⋯π interaction.

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