Intramolecular Hydrogen Bonding and Cooperative Interactions in Carbohydrates via the Molecular Tailoring Approach (original) (raw)

2008, The Journal of Physical Chemistry A

In spite of many theoretical and experimental attempts for understanding intramolecular hydrogen bonding (H-bonding) in carbohydrates, a direct quantification of individual intramolecular H-bond energies and the cooperativity among the H-bonded networks has not been reported in the literature. The present work attempts, for the first time, a direct estimation of individual intramolecular O-H...O interaction energies in sugar molecules using the recently developed molecular tailoring approach (MTA). The estimated H-bond energies are in the range of 1.2-4.1 kcal mol(-1). It is seen that the OH...O equatorial-equatorial interaction energies lie between 1.8 and 2.5 kcal mol(-1), with axial-equatorial ones being stronger (2.0-3.5 kcal mol(-1)). The strongest bonds are nonvicinal axial-axial H-bonds (3.0-4.1 kcal mol(-1)). This trend in H-bond energies is in agreement with the earlier reports based on the water-water H-bond angle, solvent-accessible surface area (SASA), and (1)H NMR analysis. The contribution to the H-bond energy from the cooperativity is also estimated using MTA. This contribution is seen to be typically between 0.1 and 0.6 kcal mol(-1) when H-bonds are a part of a relatively weak equatorial-equatorial H-bond network and is much higher (0.5-1.1 kcal mol(-1)) when H-bonds participate in an axial-axial H-bond network.

Sign up for access to the world's latest research.

checkGet notified about relevant papers

checkSave papers to use in your research

checkJoin the discussion with peers

checkTrack your impact

Estimation of Intramolecular Hydrogen Bond Energy via Molecular Tailoring Approach

The Journal of Physical Chemistry A, 2006

A novel method, based on the molecular tailoring approach for estimating intramolecular hydrogen bond energies, is proposed. Here, as a case study, the O-H...O bond energy is directly estimated by addition/subtraction of the single point individual fragment energies. This method is tested on polyhydroxy molecules at MP2 and B3LYP levels of theory. It is seen to be able to distinguish between weak ( approximately 1 kcal mol(-1)) and moderately strong ( approximately 5 kcal mol(-1)) hydrogen bonds in polyhydroxy molecules.

Carbohydrate Intramolecular Hydrogen Bonding Cooperativity and Its Effect on Water Structure

The Journal of Physical Chemistry B, 2005

Molecular dynamics (MD) simulations combined with water-water H-bond angle analysis and calculation of solvent accessible surface area and approximate free energy of solvation were used to determine the influence of hydroxyl orientation on solute hydration and surrounding water structure for a group of chemically identical solutessthe aldohexopyranose sugars. Intramolecular hydrogen bond cooperativity was closely associated with changes in water structure surrounding the aldohexopyranose stereoisomers. The OH-4 group played a pivotal role in hydration as it was able to participate in a number of hydrogen bond networks utilizing the OH-6 group. Networks that terminated within the molecule (OH-4 f OH-6 f O-5) had relatively more nonpolar-like hydration than those that ended in a free hydroxyl group (OH-6 f OH-4 f OH-3). The OH-2 group modulated the strength of OH-4 networks through syndiaxial OH-2/4 intramolecular hydrogen bonding, which stabilized and induced directionality in the network. Other syndiaxial interactions, such as the one between OH-1 and OH-3, only indirectly affected water structure. Water structure surrounding hydrogen bond networks is discussed in terms of water-water hydrogen bond populations. The impact of syndiaxial versus vicinal hydrogen bonds is also reviewed. The results suggest that biological events such as proteincarbohydrate recognition and cryoprotection by carbohydrates may be driven by intramolecular hydrogen bond cooperativity.

Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

Molecules

Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.

Intramolecular Hydrogen Bond Energy in Polyhydroxy Systems: A Critical Comparison of Molecular Tailoring and Isodesmic Approaches

The Journal of Physical Chemistry A, 2007

The intramolecular hydrogen bond (H-bond) energies in several polyhydroxy systems are estimated using an isodesmic/homodesmic reaction approach as well as a molecular tailoring approach (MTA) [Deshmukh, M. M.; Gadre, S. R.; Bartolotti, L. J. J. Phys. Chem. A 2006, 110, 12519]. It is shown that the isodesmic/homodesmic reaction approach as advocated in the literature does not give true H-bond energy but includes the effect of strain energy due to the formation of a ring structure. Such a ring strain is duly accounted for in the MTA method. The isodesmic H-bond energies are found to be smaller than their MTA energy counterparts typically by the strain energy. The MTA is applied to decitol, a system with more than five different H-bonds for which an application of an appropriate isodesmic reaction is extremely difficult. It has been shown that the MTA method is able to predict not only the H-bond energies but also the trends in conformational energies for three different conformers of decitol studied in the present work.

Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

Journal of The American Society for Mass Spectrometry, 2014

This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the −7 charge state) of complexes of bovine βlactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA) 7ions, compared with that of the (Lg + PA) 7ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 -11 kcal mol -1 ) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (K a ) measured for 7-OHPA [(2.3 ± 0.2) × 10 5 M -1 ] is similar to the value for the PA [(3.8 ± 0.1) × 10 5 M -1 ]; K a for 3-OHPA [(1.1 ± 0.3) × 10 6 M -1 ] is approximately three-times larger, whereas K a for 16-OHPA [(2.3 ± 0.2) × 10 4 M -1

Multiple Weak C-H Intramolecular Hydrogen Bonding as an Aid to Minimizing Bond Rotation Flexibility

Crystal Growth & Design, 2016

Supplementary Data Table S1: X-Ray crystallographic and DFT functional comparison of important bond distances (Å), bond angles (o) and separations (Å). Supplementary Data Table S2: NBO donor-acceptor properties for energy minimised structure and the single point calculation of the X-ray structure. Supplementary Data Table S3: Close contact distances (Å) and NCI iso-surface colour comparisons for the calculated X-ray (X-rayC) and PBE-D3 energy minimised (Emin) structures. Supplementary Data Table S4: Close contact distances (Å) and bond critical point (bcp) data comparisons for the calculated X-ray (X-rayC) and PBE-D3 energy minimised (Emin) structures. Supplementary Data Table S5: Atomic charge [q(A), q(B) partner] comparisons for the calculated X-ray (X-rayC) and PBE-D3 energy minimised (Emin)structures. Supplementary Data Table S6: Cartesian coordinates and total energies for the energy minimised and single point calculation versions of [Mo(NC 6 H 4 CMe 3-2)(O)Cl 2 (bipy)]. Supplementary Date Table S7: Comparison of structural and QTAIM parameters of Energy minimised (Emin), X-ray (xray), and the complexes (a-d), structures. Supplementary Figures S1-S10: Comparison of energy minimised (EM) and single point (SP) iso-surfaces. Supplementary Figure S11: Molecular graphs for the calculated X-ray (X-rayC) and PBE-D3 energy minimised (Emin) structures. Supplementary Figure S12: Unit cell obtained from the X-ray crystal structure. Supplementary Figure S13: Molecular graphs showing intermolecular bond critical points with dicholoromethane solvent molecules for complexes ad. Supplementary Figure S14: Geometries of the complexes (a-d) containing CH 2 Cl 2. Supplementary Data Table S1: X-Ray crystallographic and DFT functional comparison of important bond distances (Å), bond angles (o) and separations (Å). Parameter X-Ray 3σ PBE-D3 diff BP86 diff B3LYP diff Mo=O(1) 1.686(2)

An examination ofintermolecular andintramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

Journal of Computational Chemistry, 1991

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intmmolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions

An approach to estimate the energy of the intramolecular hydrogen bond

Chemical Physics Letters, 2002

The problem of the energy of the intramolecular hydrogen bond is widely discussed in the literature, but it has not found an unequivocal univocal solution yet. The partition of the energy of the intramolecular hydrogen bond ðDE T Þ in chloro-derivatives of 2-(N-dimethylaminomethyl)-phenols calculated by ab initio and DFT methods was proposed and 'pure' DE T values were estimated. These values correlate well with those of rðH Á Á Á NÞ and electron density qðrÞ obtained by the AIM method. Ó

Hydrogen-bonding in glycine and malonaldehyde: Performance of the Lap1 correlation functional

The conformational equilibrium of gaseous glycine presents a severe challenge to quantum chemistry and, in particular, to density functional theory DFT, due to the presence of internal hydrogen bonds. We present new DFT results for the structure and the energetics of glycine and malonaldehyde, using the recently developed nonlocal exchange-correlation functionals BLap1 and PLap1. A comparative analysis is made with the results of the generalized-gradient-approximation GGA schemes Becke–Perdew BP86 and Becke–Lee–Yang–Parr BLYP, the hybrid Hartree– Fock HF-DFT methods B3PW91 and B3LYP, with post-HF methods, and with the available experimental data. Our BLap1/TZVP and PLap1/TZVP values for the energy margin between the two lowest conformers of glycine 0.84 and 1.05 kcal/mol, respectively are within the experimental error bars (1.00.5 kcal/mol). MP2 underestimates this energy difference by about 0.5 kcal/mol, BLYP and the hybrid methods are off by about 0.9 kcal/mol. The optimized geometry of malonaldehyde is improved with the Lap1 functionals, compared to the GGA results reported previously. Improvement over the GGA is also achieved for the energy barrier for the internal proton transfer in malonaldehyde. Recent high quality post-HF G2 calculations of Barone and Adamo 1 yield 4.4 kcal/mol. The best GGA PP86 value of 2.1 kcal/mol is seriously underestimated. The best B3LYP estimate is 3.0 kcal/mol. 1 Our BLap1/TZVP 3.28 kcal/mol and PLap1/TZVP 4.56 kcal/mol values are in the correct energy range, the latter being, in fact, very close to the G2 estimate.

Loading...

Loading Preview

Sorry, preview is currently unavailable. You can download the paper by clicking the button above.

Theoretical studies of hydrogen-bonded dimers. Complexes involving HF, H2O, NH3, CH1, H2S, PH3, HCN, HNC, HCP, CH2NH, H2CS, H2CO, CH4, CF3,H, C2H2, C2H4, C6H6, F- and H3O

Journal of The American Chemical Society, 1975