Entropies and heat capacities of cyclic and polycyclic compounds

O’Neal, H. E.; Benson, Sidney W.

doi:10.1021/je60045a042

Cited by 48 publications

(9 citation statements)

References 7 publications

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“…Therefore, to determine whether the rigidity of six-membered pyranose rings might enhance their ability to pack with aromatic rings in protein–carbohydrate interactions, we compared the folding energetics of Pin WW variant 10 , in which R 1 = cyclohexyl, to variants 11 , 12 , and 13 , in which R 1 = cyclobutyl, cyclopentyl, and cycloheptyl, respectively, since four- five- and seven-membered rings are more conformationally heterogeneous than six-membered rings. 51,52 …”

Section: Resultsmentioning

confidence: 99%

“…Unfortunately, it is difficult to test this notion with carbohydrates because many factors would be confounded with the conformational entropy difference between the pyranose and furanose forms of a carbohydrate, in particular the types and positions of the substituents on the ring. Therefore, to determine whether the rigidity of six-membered pyranose rings might enhance their ability to pack with aromatic rings in protein–carbohydrate interactions, we compared the folding energetics of Pin WW variant 10 , in which R 1 = cyclohexyl, to variants 11 , 12 , and 13 , in which R 1 = cyclobutyl, cyclopentyl, and cycloheptyl, respectively, since four- five- and seven-membered rings are more conformationally heterogeneous than six-membered rings. , …”

Section: Resultsmentioning

confidence: 99%

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The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate

et al. 2016

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Interactions between proteins and carbohydrates are ubiquitous in biology. Therefore, understanding the factors that determine their affinity and selectivity are correspondingly important. Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. We employed the enhanced aromatic sequon, a structural motif found in the reverse turns of some N-glycoproteins, to facilitate face-to-face monosaccharide–aromatic interactions. A protein host was used because the dependence of the folding energetics on the identity of the monosaccharide can be accurately measured to assess the strength of the carbohydrate–aromatic interaction. Our data demonstrate that the carbohydrate–aromatic interaction strengths are moderately affected by changes in the stereochemistry and identity of the substituents on the pyranose rings of the sugars. Galactose seems to make the weakest and allose the strongest sugar–aromatic interactions, with glucose, N-acetylglucosamine (GlcNAc) and mannose in between. The NMR solution structures of several of the monosaccharide-containing N-glycoproteins were solved to further understand the origins of the similarities and differences between the monosaccharide–aromatic interaction energies. Peracetylation of the monosaccharides substantially increases the strength of the sugar–aromatic interaction in the context of our N-glycoprotein host. Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH–π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate

et al. 2016

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“…Similarly, attaining an appropriate balance of conformational flexibility and pre-organization is also essential in the synthesis of complex supramolecular topologies . The cost of restricting the rotation of a C sp 3 –C sp 3 bond at 298 K has been estimated between 1 and 7 kJ mol –1 based on the properties of alkanes, ring-closing reactions, and molecular recognition events occurring in both biomolecules , and supramolecular complexes . While broadly similar behavior is seen in many different contexts, there are numerous interesting examples where generalized principles of flexibility do not account for the observed behavior.…”

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confidence: 99%

The Limit of Intramolecular H-Bonding

Hubbard¹,

Brown²,

Bell³

et al. 2016

J. Am. Chem. Soc.

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Hydrogen bonds are ubiquitous interactions in molecular recognition. The energetics of such processes are governed by the competing influences of pre-organization and flexibility that are often hard to predict. Here we have measured the strength of intramolecular interactions between H-bond donor and acceptor sites separated by a variable linker. A striking distance-dependent threshold was observed in the intramolecular interaction energies. H-bonds were worth less than -1 kJ mol when the interacting groups were separated by ≥6 rotating bonds, but ranged between -5 and -9 kJ mol for ≤5 rotors. Thus, only very strong external H-bond acceptors were able to compete with the stronger internal H-bonds. In addition, a constant energetic penalty per rotor of ∼5-6 kJ mol was observed in less strained situations where the molecule contained ≥4 rotatable bonds.

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“…< 7-8, involves an average drop of 4.0 eu per added single bond, which implies a nearly complete freezing of the torsional motion of a single bond, whose contribution to the entropy has been estimated as 4.4-4.8 eu. [64] On the other hand, systems with an higher number of rotatable bonds exhibit a much smaller dependence on chain length, because the incremental torsional contribution brought about by an additional single bond is largely retained in the cyclic transition state. [57] This method, by the authors own statement, can be only applied when there is no significant barrier around a single bond rotation.…”

Section: Catalystmentioning

confidence: 99%

Conformational Mobility and Efficiency in Supramolecular Catalysis. A Computational Approach to Evaluate the Performances of Enzyme Mimics

Salvio

D’Abramo

2020

Eur J Org Chem

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In the present study, we apply a computational approach, based on DFT calculations and molecular dynamics simulations, to investigate the catalytic behavior of four supramolecular catalysts active in the cleavage of phosphodiesters. The QM data indicate the operation of a synchronous associative mechanism with limited differences in the structures and energies of the transition states. The comparison with the experimental data, expressed in terms of effective molarity (EM), suggests that the difference in catalytic performance are not ascribable to a difference in the enthalpy of activation. On the

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Entropies and heat capacities of cyclic and polycyclic compounds

Cited by 48 publications

References 7 publications

The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate

The Dependence of Carbohydrate–Aromatic Interaction Strengths on the Structure of the Carbohydrate

The Limit of Intramolecular H-Bonding

Conformational Mobility and Efficiency in Supramolecular Catalysis. A Computational Approach to Evaluate the Performances of Enzyme Mimics

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