Conformational analysis. Part 40: a theoretical and NMR investigation of the conformations of <i>cis</i>‐ and <i>trans</i>‐cyclopentane‐1,3‐diol

Abraham, Raymond J.; Koniotou, Rodothea

doi:10.1002/mrc.1300

Cited by 17 publications

(23 citation statements)

References 24 publications

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“…A general trend of overestimating the J-couplings relative to the experimental values is observed in Table VII, similar to the results in Ref 23 . The ring J-couplings, 3 J H 1, H 2 and 3 J H 2, H 3 , show the largest deviation from experimental observation, the Karplus parameters of which are derived for cyclopentane-1,3-diol 87 . Other than the error introduced by the simplified molecular model of the Karplus equation parameterization, Mobli et al suggested that further sources of error include exclusion and/or simplification of solvent effects, basis set limitations and intrinsic properties of DFT 23,88 during the parameterization of Karplus relationships.…”

Section: Resultsmentioning

confidence: 78%

“… a Simulation coupling constants calculated according to Karplus equations in ref 23 b Parameters for Karplus equation obtained from ref 87 c Karplus equations derived for the N-acetyl fragment based on ref 86 …”

Section: Figmentioning

confidence: 99%

“…The ring J-couplings, 3 J H1,H2 and 3 J H2,H3 , show the largest deviation from experimental observation, the Karplus parameters of which are derived for cyclopentane-1,3-diol. [87] Other than the error introduced by the simplified molecular model of the Karplus equation parameterization, Mobli et al suggested that further sources of error include exclusion and/or simplification of solvent effects, basis set limitations, and intrinsic properties of DFT [23,88] during the parameterization of Karplus relationships. Also, insufficient sampling of the corresponding torsions and incorrect torsion populations arising from force field errors can also contribute to the discrepancy between MD and experimental J-couplings.…”

Section: Journal Of Computational Chemistrymentioning

confidence: 99%

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Solvation properties ofN‐acetyl‐β‐glucosamine: Molecular dynamics study incorporating electrostatic polarization

2011

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N-acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural properties of NAG and NAG-containing macromolecules, like peptidoglycans and polymeric chitin, at the atomic level using molecular dynamics simulations. In this work, we develop a polarizable carbohydrate force field for NAG and contrast simulation results of various properties using this novel force field and an analogous non-polarizable (fixed charge) model. Aqueous solutions of NAG and its oligomers are investigated; we explore conformational properties (rotatable bond geometry), electrostatic properties (dipole moment distribution), dynamical properties (self-diffusion coefficient), hydrogen bonding (water bridge structure and dynamics), and free energy of hydration. The fixed-charge carbohydrate force field exhibits deviations from the gas-phase relative rotation energy of exocyclic hydroxymethyl side-chain and of chair/boat ring distortion. The polarizable force field predicts conformational properties in agreement with corresponding first-principles results. NAG-water hydrogen bonding pattern is studied through radial distribution functions and correlation functions. Intermolecular hydrogen bonding between solute and solvent is found to stabilize NAG solution structures while intramolecular hydrogen bonds define glycosidic linkage geometry of NAG oligomers. The electrostatic component of hydration free energy is highly dependent on force field atomic partial charges, influencing a more favorable free energy of hydration in the fixed-charge model compared to the polarizable model.

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Section: Resultsmentioning

confidence: 78%

Section: Figmentioning

confidence: 99%

Section: Journal Of Computational Chemistrymentioning

confidence: 99%

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Solvation properties ofN‐acetyl‐β‐glucosamine: Molecular dynamics study incorporating electrostatic polarization

2011

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“…This equation is a function of the electronegativity of the substituents, the H-C-C-H torsion angle and the orientation of each substituent relative to the coupled protons. In a recent investigation, 47 it was noted that the 1 H, 1 H coupling constants calculated with this equation for the C 4 .C 5 fragment in cis-and trans-cyclopentane-1,2-diol were much larger than the observed values. An alternative equation was derived for the C.CH 2 .CH 2 .C fragment in five-and six-membered rings using a simple form of the Karplus equation 48 with accurate experimental couplings of molecules in known conformations to give Eqn (7), and this equation is implemented in the CHARGE routine.…”

Section: H H Coupling Constantsmentioning

confidence: 73%

1H chemical shifts in NMR: Part 22—Prediction of the1H chemical shifts of alcohols, diols and inositols in solution, a conformational and solvation investigation

et al. 2005

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The (1)H NMR spectra of a number of alcohols, diols and inositols are reported and assigned in CDCl(3), D(2)O and DMSO-d(6) (henceforth DMSO) solutions. These data were used to investigate the effects of the OH group on the (1)H chemical shifts in these molecules and also the effect of changing the solvent. Inspection of the (1)H chemical shifts of those alcohols which were soluble in both CDCl(3) and D(2)O shows that there is no difference in the chemical shifts in the two solvents, provided that the molecules exist in the same conformation in the two solvents. In contrast, DMSO gives rise to significant and specific solvation shifts. The (1)H chemical shifts of these compounds in the three solvents were analysed using the CHARGE model. This model incorporates the electric field, magnetic anisotropy and steric effects of the functional group for long-range protons together with functions for the calculation of the two- and three-bond effects. The long-range effect of the OH group was quantitatively explained without the inclusion of either the C--O bond anisotropy or the C--OH electric field. Differential beta and gamma effects for the 1,2-diol group needed to be included to obtain accurate chemical shift predictions. For DMSO solution the differential solvent shifts were calculated in CHARGE on the basis of a similar model, incorporating two-bond, three-bond and long-range effects. The analyses of the (1)H spectra of the inositols and their derivatives in D(2)O and DMSO solution also gave the ring (1)H,(1)H coupling constants and for DMSO solution the CH--OH couplings and OH chemical shifts. The (1)H,(1)H coupling constants were calculated in the CHARGE program by an extension of the cos(2)phi equation to include the orientation effects of electronegative atoms and the CH--OH couplings by a simple cos(2)phi equation. Comparison of the observed and calculated couplings confirmed the proposed conformations of myo-inositol, chiro-inositol, quebrachitol and allo-inositol. The OH chemical shifts were also calculated in the CHARGE program. Comparison of the observed and calculated OH chemical shifts and CH.OH couplings suggested the existence of intramolecular hydrogen bonding in a myo-inositol derivative.

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“…It optimizes the 3D structures of the compounds with a molecular mechanics force field and calculates vicinal 3 J(H,H) couplings by a modified Karplus equation (including parameters for cyclopentanes). [16] We applied the algorithm BEST for coupling constant calculations (See Sup. Info.).…”

Section: Qc Calculation Of 3 J(hh) Coupling Constants and Evaluationmentioning

confidence: 99%

Theoretical prediction and assignment of vicinal ¹H–¹H coupling constants of diastereomeric 3‐alkoxy‐6,7‐epoxy‐2‐oxabicyclo[3.3.0]octanes

Aav

Pehk

Tamp

et al. 2011

Magnetic Reson in Chemistry

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Spin-spin coupling constants between nuclei in NMR spectroscopy reflect their spatial arrangement. A number of calculation methods, applying different levels of theory, have been developed to support the stereochemical assignment of novel compounds. Nevertheless, revisions of the assignment of structures in the literature are not rare. In the present work, the reliability of the calculation methods amenable for a theoretical prediction of spin-spin coupling constants of vicinal protons to support correct stereochemical assignment of substitution at five-membered rings of 3-alkoxy-6,7-epoxy-2-oxabicyclo[3.3.0]octanes was studied. Experimental (3)J(H,H) coupling constants were compared with the coupling constants calculated for all possible diastereomers. The fully quantum chemical approach provided theoretical (3)J(H,H) coupling constants with an absolute deviation of no more than 1.1 Hz for 91% of the experimentally studied coupled spins, whereas the methods without quantum chemical geometry optimization resulted in completely unreliable predictions. Consequently, for a reliable stereochemical assignment of small and medium size molecules, the protocol for calculating the coupling constants based on the results of the quantum chemical geometry optimization is recommended.

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Conformational analysis. Part 40: a theoretical and NMR investigation of the conformations of cis‐ and trans‐cyclopentane‐1,3‐diol

Cited by 17 publications

References 24 publications

Solvation properties ofN‐acetyl‐β‐glucosamine: Molecular dynamics study incorporating electrostatic polarization

Solvation properties ofN‐acetyl‐β‐glucosamine: Molecular dynamics study incorporating electrostatic polarization

1H chemical shifts in NMR: Part 22—Prediction of the1H chemical shifts of alcohols, diols and inositols in solution, a conformational and solvation investigation

Theoretical prediction and assignment of vicinal ¹H–¹H coupling constants of diastereomeric 3‐alkoxy‐6,7‐epoxy‐2‐oxabicyclo[3.3.0]octanes

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Conformational analysis. Part 40: a theoretical and NMR investigation of the conformations of cis‐ and trans‐cyclopentane‐1,3‐diol

Cited by 17 publications

References 24 publications

Solvation properties ofN‐acetyl‐β‐glucosamine: Molecular dynamics study incorporating electrostatic polarization

Solvation properties ofN‐acetyl‐β‐glucosamine: Molecular dynamics study incorporating electrostatic polarization

1H chemical shifts in NMR: Part 22—Prediction of the1H chemical shifts of alcohols, diols and inositols in solution, a conformational and solvation investigation

Theoretical prediction and assignment of vicinal 1H–1H coupling constants of diastereomeric 3‐alkoxy‐6,7‐epoxy‐2‐oxabicyclo[3.3.0]octanes

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Theoretical prediction and assignment of vicinal ¹H–¹H coupling constants of diastereomeric 3‐alkoxy‐6,7‐epoxy‐2‐oxabicyclo[3.3.0]octanes