Parsing of the free energy of aromatic–aromatic stacking interactions in solution

Kostjukov, Victor V.; Khomytova, N. M.; Santiago, Adrian A. Hernandez; Tavera, Anna-Maria Cervantes; Alvarado, Julieta Salas; Evstigneev, Maxim P.

doi:10.1016/j.jct.2011.04.014

Cited by 32 publications

(78 citation statements)

References 51 publications

(76 reference statements)

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“…(1), this relation demonstrated a good agreement with the experiment for a large number of various DNA-binding ligands [17,18]. The energy contribution ΔΔ HB has meaning of a correction to the energy of VdW and electrostatic interactions in Eq.…”

Section: Hydrogen Bondssupporting

confidence: 62%

“…The energy analysis technique was described in our previous works [17,18] in detail. In brief, its essence consists in the following.…”

Section: General Approach To the Energy Analysismentioning

confidence: 99%

“…The terms in Eq. (1) were calculated using a combination of empirical and nonempirical techniques [17,18].…”

Section: General Approach To the Energy Analysismentioning

confidence: 99%

“…The coordinates of all atoms were stored in 1 ps. Earlier, it was demonstrated [18] that, in the case of complexes of small molecules in a solution, the used time parameters of the evolution of the system turned out rather sufficient for the time-averaged values of energy components in Eq. (1) to be determined quite reliably.…”

Section: Molecular Dynamics (Md)mentioning

confidence: 99%

“…In the literature, there are the experimental values concerning the total Gibbs energy Δ exp only for the dimerization of four-ring MGB ligands AIK-18/51 (an analog of TZA) [9] and Hoechst33258 [8]; they are equal to −6.0 and −5.0 kcal/mol, respectively. A typical calculation error for the total Gibbs energy of DNA-binding ligands has an order of magnitude of the energy itself [18,33], because each contribution to Δ total in Eq. (1) is a difference between large values.…”

Section: General Energy Analysis Of Dimerizationmentioning

confidence: 99%

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Dimerization Energetics of DNA Minor Groove Binders

Kostjukov¹,

Miloserdova²,

Shram³

et al. 2014

Ukr. J. Phys.

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The energy analysis of a dimerization in aqueous solutions of seven biologically active lexitropsins, which are different by structure, was carried out with the use of the molecular simulation method. The main stabilization of dimers was shown to take place owing to hydrophobic and intermolecular van der Waals interactions. The latter are mainly associated with energyfavorable contacts between the aromatic rings of molecules and their peptide groups. Despite the significant dipole moments of the molecules concerned, the electrostatic interactions are relatively weak and destabilize the complexes because of the unfavorable relative arrangement of molecular dipoles. Entropic factors and the dehydration were shown to also hinder the dimerization. K e y w o r d s: lexitropsins, dimer, peptide group, aromatic ring, energy contributions.

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Section: Hydrogen Bondssupporting

confidence: 62%

“…The energy analysis technique was described in our previous works [17,18] in detail. In brief, its essence consists in the following.…”

Section: General Approach To the Energy Analysismentioning

confidence: 99%

“…The terms in Eq. (1) were calculated using a combination of empirical and nonempirical techniques [17,18].…”

Section: General Approach To the Energy Analysismentioning

confidence: 99%

Section: Molecular Dynamics (Md)mentioning

confidence: 99%

Section: General Energy Analysis Of Dimerizationmentioning

confidence: 99%

See 3 more Smart Citations

Dimerization Energetics of DNA Minor Groove Binders

Kostjukov¹,

Miloserdova²,

Shram³

et al. 2014

Ukr. J. Phys.

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Complexation of C₆₀ Fullerene with Aromatic Drugs

et al. 2013

Self Cite

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The contributions of various physical factors to the energetics of complexation of aromatic drug molecules with C(60) fullerene are investigated in terms of the calculated magnitudes of equilibrium complexation constants and the components of the net Gibbs free energy. Models of complexation are developed taking into account the polydisperse nature of fullerene solutions in terms of the continuous or discrete (fractal) aggregation of C(60) molecules. Analysis of the energetics has shown that stabilization of the ligand-fullerene complexes in aqueous solution is mainly determined by intermolecular van der Waals interactions and, to lesser extent, by hydrophobic interactions. The results provide a physicochemical basis for a potentially new biotechnological application of fullerenes as modulators of biological activity of aromatic drugs.

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Free radical polymerization of caffeine‐containing methacrylate monomers

Nelson

Hemp

Chau

et al. 2015

J. Polym. Sci. Part A: Polym. Chem.

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The incorporation of acrylic functionality into caffeine enables the preparation of a vast array of novel thermoplastics and thermosets. A two-step derivatization provided a novel caffeine-containing methacrylate monomer capable of free radical polymerization. Copolymers of 2-ethylhexyl methacrylate and caffeine methacrylate (CMA) allowed for a systematic study of the effect of covalently bound caffeine on polymer properties.1 H NMR and UV-vis spectroscopy confirmed caffeine incorporation at 5 and 13 mol %, and SEC revealed the formation of high molecular weight (co)polymers (>40,000 g/mol). CMA incorporation resulted in a multistep degradation profile with initial mass loss closely correlating to caffeine content. Differential scanning calorimetry, rheological, and thermomechanical analysis demonstrated that relatively low levels of CMA increased the glass transition temperature, resulting in higher moduli and elucidating the benefits of incorporating caffeine into polymers.

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Parsing of the free energy of aromatic–aromatic stacking interactions in solution

Cited by 32 publications

References 51 publications

Dimerization Energetics of DNA Minor Groove Binders

Dimerization Energetics of DNA Minor Groove Binders

Complexation of C₆₀ Fullerene with Aromatic Drugs

Free radical polymerization of caffeine‐containing methacrylate monomers

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Parsing of the free energy of aromatic–aromatic stacking interactions in solution

Cited by 32 publications

References 51 publications

Dimerization Energetics of DNA Minor Groove Binders

Dimerization Energetics of DNA Minor Groove Binders

Complexation of C60 Fullerene with Aromatic Drugs

Free radical polymerization of caffeine‐containing methacrylate monomers

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Product

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Complexation of C₆₀ Fullerene with Aromatic Drugs