The flip-flop hydrogen bonding phenomenon

Koehler, Juergen; Saenger, Wolfram; Gunsteren, Wilfred F. van

doi:10.1007/bf00261901

Cited by 96 publications

(54 citation statements)

References 16 publications

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“…This dynamical behavior, so called flip-flop phenomenon, has been already observed experimentally in the crystalline state of β-CD 77,78 and reported in previous MD simulations. 32 Our findings are in agreement with references 32 and 77-78 and suggest that the flip-flop phenomenon may be an intrinsic property of these cyclic molecules. It is worth to point that the dynamics of these interactions are probably influenced by the nature of the solvent.…”

supporting

confidence: 82%

“…Molecular dynamics (MD) simulations are more timeconsuming but provide a better connection between atomistic constitution and macroscopic properties when compared to pure geometry optimizations methods. 29 In addition to structural [30][31][32]35,36,39,41 and solvation 33,34,[37][38][39][40][41][42][43] aspects, dynamic information can be monitored. The latter is essential to the understanding of the properties and mechanisms involved in host-guest complexation.…”

mentioning

confidence: 99%

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Revisiting the internal conformational dynamics and solvation properties of cyclodextrins

Pereira¹,

Moura²,

Freitas³

et al. 2007

J. Braz. Chem. Soc.

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Simulações de dinâmica molecular são utilizadas para investigar a dinâmica conformacional interna e propriedades de solvatação das três ciclodextrinas naturais, α-, β-e γ-ciclodextrina em água e temperatura ambiente. Estes oligossacarídeos derivados da glicose apresentam uma estrutura molecular peculiar que lhes confere a habilidade de formar complexos de inclusão e modificar as propriedades físico-químicas das moléculas complexadas. As características estruturais das ciclodextrinas em solução são determinantes para a complexação. As análises das trajetórias obtidas mostram que ligações de hidrogênio secundárias entre resíduos de glicose adjacentes estão presentes em solução e apresentam um caráter altamente dinâmico, onde ligações de hidrogênio alternativas podem ser formadas com moléculas de água. Apesar do baixo caráter hidrofílico, as cavidades apresentam-se solvatadas e o número de moléculas de água dentro da cavidade é aproximadamente duplicada por unidade de glicose adicionada ao macrociclo. Os tempos de residência para as moléculas de água dentro das cavidades são inversamente proporcionais ao seu respectivo tamanho.Molecular dynamics simulations were used to investigate the internal conformational dynamics and solvation properties of the three natural cyclodextrins, α-, β-and γ-cyclodextrin in aqueous solution at room temperature. These glucose-derived oligosacharides present a molecular structure that confers them the ability to complex guest molecules and change their physicochemical properties. The structural behavior of cyclodextrins in solution is crucial for their complexation abilities. Analyses of the obtained trajectories show that inter-glucose hydrogen bonds between the secondary hydroxyl groups are present in solution, but show a very dynamical character where alternative hydrogen bonds to water molecules can be formed. Despite the lower hydrophilicity of the cyclodextrins inner-cavities, they were found to be solvated and the number of water molecules inside the cavity roughly doubles per glucose unit added to the ring. The residence times for water molecules inside the cavities are inversely proportional to the cavity size. Keywords: cyclodextrins, molecular dynamics, solvation, flexibility IntroductionCyclodextrins (CDs) have been extensively studied since their discovery in the late nineteenth century.1 Their peculiar properties and behavior have interested scientists in many different fields.2 These cyclic oligosaccharides, obtained from starch by glucanotransferase degradation, are formed by a certain number of α-D-glucopyranose units linked by α(1→4) glycosidic bonds. This arrangement produces a truncated cone shape with a central cavity relatively hydrophobic and an external surface relatively hydrophilic.1-3 Naturally occurring CDs, known as α-, β-and γ-CD, present six, seven and eight glucose units, respectively.1-3 The structural features of these saccharides allow them to form inclusion complexes with a great variety of compounds.3 Due to their ability to form host-guest complexe...

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supporting

confidence: 82%

mentioning

confidence: 99%

Revisiting the internal conformational dynamics and solvation properties of cyclodextrins

Pereira¹,

Moura²,

Freitas³

et al. 2007

J. Braz. Chem. Soc.

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“…These three-centered hydrogen bonds occur frequently in solid-state structures [1][2][3][4][5] and also in biologically relevant molecules. [6][7][8][9] An array of interlinked three-center hydrogen bonds is expected to exhibit cooperative enhancement just as it is observed in regular two-center hydrogen-bond arrays. [10][11][12][13] Considerable attention has been given to the study of cooperative effects in molecular clusters containing conventional two-center H bonds.…”

Section: Introductionmentioning

confidence: 96%

Cooperative effects in two-dimensional ring-like networks of three-center hydrogen bonding interactions

Parra

Bulusu

Zeng

2005

The Journal of Chemical Physics

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Cooperative effects in two-dimensional cyclic networks containing intermolecular three-centered hydrogen bonding interactions of the type H 1 …A…H 2 are investigated by means of ab intio molecular orbital and density functional theory calculations. Ring-like clusters consisting of three and up to nine monomers of the cis-cis isomer of carbonic acid H 2 CO 3 are used as basic models, where each unit acts simultaneously as a double hydrogen-bond donor and double hydrogen-bond acceptor. Cooperative effects based on binding energies are evident for ͑H 2 CO 3 ͒ n , where n goes from 2 to 9. Thus, the ZPVE-corrected dissociation energy per bifurcated hydrogen bond increases from 11.52 kcal/ mol in the dimer to 20.42 kcal/ mol in the nonamer, i.e., a 77% cooperative enhancement. Cooperative effects are also manifested in such indicators as geometries, and vibrational frequencies and intensities. The natural bond orbital analysis method is used to rationalize the results in terms of the substantial charge delocalization taking place in the cyclic clusters. Cooperativity seems close to reaching an asymptotic limit in the largest ring considered, n = 9.

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“…Molecular dynamics (MD) simulation studies of carbohydrates in the literature 10;11 deal with maltose or cellobiose composed of two glucose units [12][13][14][15][16] or with cyclic chains including a-, b, and c-cyclodextrins [17][18][19][20][21][22][23] as well as the single glucose units of a-and b-anomers. 15;24;25 However, there are only a few studies dealing with longer amylose or cellulose chains.…”

Section: Introductionmentioning

confidence: 99%

Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

Yu¹,

Amann

Hansson³

et al. 2004

Carbohydrate Research

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The flip-flop hydrogen bonding phenomenon

Cited by 96 publications

References 16 publications

Revisiting the internal conformational dynamics and solvation properties of cyclodextrins

Revisiting the internal conformational dynamics and solvation properties of cyclodextrins

Cooperative effects in two-dimensional ring-like networks of three-center hydrogen bonding interactions

Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study

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