Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.
Identifieur interne : 000879 ( Ncbi/Merge ); précédent : 000878; suivant : 000880Molecular dynamics simulation studies of caffeine aggregation in aqueous solution.
Auteurs : Letizia Tavagnacco [Italie] ; Udo Schnupf ; Philip E. Mason ; Marie-Louise Saboungi ; Attilio Cesàro ; John W. BradySource :
- The journal of physical chemistry. B [ 1520-5207 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Caffeine, Water.
- Molecular Dynamics Simulation, Temperature, Thermodynamics.
Abstract
Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.
DOI: 10.1021/jp2021352
PubMed: 21812485
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pubmed:21812485Le document en format XML
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<front><div type="abstract" xml:lang="en">Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molecules, which was not sensitive to the water model used. As expected, extensive aggregation of the caffeine molecules was observed, with the molecules stacking their flat faces against one another like coins, with their methylene groups staggered to avoid steric clashes. A dynamic equilibrum was observed between large n-mers, including stacks with all eight solute molecules, and smaller clusters, with the calculated osmotic coefficient being in acceptable agreement with the experimental value. The insensitivity of the results to water model and the congruence with experimental thermodynamic data suggest that the observed stacking interactions are a realistic representation of the actual association mechanism in aqueous caffeine solutions.</div>
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<ReferenceList><Reference><Citation>Nucleic Acids Res. 1988 Mar 25;16(6):2671-90</Citation>
<ArticleIdList><ArticleId IdType="pubmed">2452403</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Comput Chem. 2009 Jul 30;30(10):1545-614</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19444816</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Phys Chem B. 2010 Apr 29;114(16):5412-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20369858</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biochemistry. 1967 Jan;6(1):272-6</Citation>
<ArticleIdList><ArticleId IdType="pubmed">6030323</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Physiol Behav. 2006 Aug 30;89(1):85-91</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16580033</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proteins. 2011 Jul;79(7):2224-32</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21574187</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Pharm Sci. 2002 Apr;91(4):1000-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11948539</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Phys Chem B. 2008 Jul 24;112(29):8634-44</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18582012</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Chem Phys. 2010 Oct 21;133(15):155103</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20969429</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Appl Physiol Nutr Metab. 2008 Dec;33(6):1269-83</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19088789</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Am Chem Soc. 2001 Oct 31;123(43):10721-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11674005</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Chemistry. 2007;13(10):2908-11</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17200930</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr B. 2005 Jun;61(Pt 3):329-34</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15914898</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Phys Chem B. 2005 Aug 25;109(33):16092-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16853045</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Ann N Y Acad Sci. 1969 Nov 7;164(1):279-93</Citation>
<ArticleIdList><ArticleId IdType="pubmed">5259645</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Am Pharm Assoc Am Pharm Assoc. 1957 Jan;46(1):4-10</Citation>
<ArticleIdList><ArticleId IdType="pubmed">13502116</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2000 Aug 31;406(6799):956-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10984041</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Chemistry. 2004 Dec 17;11(1):271-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15551321</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Am Chem Soc. 2004 Sep 22;126(37):11462-70</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15366892</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Mol Graph. 1996 Feb;14(1):33-8, 27-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">8744570</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Mol Nutr Food Res. 2005 Mar;49(3):274-84</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15704241</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2001 May 22;98(11):5965-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11353861</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Crit Rev Food Sci Nutr. 1999 Sep;39(5):441-56</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10516914</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Phys Chem. 1967 Feb;71(3):564-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">6044492</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Science. 1980 Jul 25;209(4455):451-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17831355</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2005 Sep 29;437(7059):640-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">16193038</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Chem Theory Comput. 2005 Jul;1(4):643-52</Citation>
<ArticleIdList><ArticleId IdType="pubmed">26641686</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Phys Chem B. 2007 May 24;111(20):5669-79</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17469865</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biophys J. 2008 Oct;95(7):3208-21</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18621830</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
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