Analysis on Solvated Molecules with a New Energy Partitioning Scheme for Intra- and Intermolecular Interactions

Molecular dynamics (MD) simulations in water solution were performed on six large ring cyclodextrins (LR-CDs) with a degree of polymerization (DP) 24,25, 27,28,29, and 30, using as starting structures geometries derived from CD26, which was studied previously by MD. The present research was aimed at further extending our knowledge on the structural dynamics and the energetics of this new class of compounds, focusing on several representatives flanking CD26, the largest LR-CD for which X-ray data are available. The most recent parameterization for carbohydrates, Glycam-04, and explicit water molecules (TIP3P) were used in the 10.0-ns simulations. Preceding 10.0-ns simulations of CD26, with the AMBER parm99 force field, revealed that the overall shape of the macromolecule did not change significantly during the last 5.0-ns simulations. We now further test for the probability of prevalence of this conformation by using a different force field and by examining the effect of the size of the macro-ring on the preferred conformations of LR-CDs with DP within a range of 24 -30. Indeed, we found CD26-like geometries present for CD25, CD27, and CD28, which could be interpreted as an indication for an enhanced stability of the CD26 conformation in water solution. Again, we witnessed high flexibility of the macrocycles, and different local structural motifs were detected: twisted helical double parallel strand (CD25, CD30), single helix of three turns (CD29), a spiral (CD25, CD27, CD30), open-shaped loops and helical turns (CD28; "CD26-like geometry"), a rectangular cavity (CD24), a triple-lobe fragment (CD29) or a portion shaped like a jaw (CD24, CD27), and an overall shape of the macromolecule that resembled a butterfly (CD27) or "X" (CD28). Thus, we conclude that the same conformation of CD26 could be also the preferred conformation in water solution of other LR-CDs with DP in the close vicinity of 26. Wiley Periodicals, Inc. Int J Quantum Chem 107: 1657-1672, 2007 Key words: cyclodextrins; molecular dynamics; conformational analysis; AMBER Introduction A new class of compounds, the large-ring cyclodextrins (LR-CDs) [1] attracted attention in recent years. Advances were marked by the study of their physicochemical properties [2], in spite of existing difficulties in their synthesis [3][4][5], isolation, and purification [6 -8]. LR-CDs were first prepared by French et al. [9]. The crystal structure determinations of the CDs composed by 9 [10], 10 [11], 14 [7, 11a], and 26 [12] glucose units provided information on the conformations of these molecules in the crystal lattice. New structural motifs were detected, and it became evident that their geometries differ considerably from the native CDs (i.e., those composed of 6, 7, and 8 glucose units). More recently, the thermal and structural characterization of ␦-CD, -CD, and -CD have been carried out [13], and references to CDs with more than 60 [14] and several hundred [15] glucose units have been made. The 13 C nuclear magnetic resonance (NMR) spectra in D 2 O at...

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“…Unified quantum mechanical treatment with appropriate energy partitioning analysis (e.g., Ref. 47) can shed light on this problem.…”

Section: Discussionmentioning

confidence: 99%

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

Gotsev

Ivanov

2006

Int J of Quantum Chemistry

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“…(5) by a space-partitioning function, numerical integration with respect to r 1 and r 2 is required because analytical integration is difficult. However, the full numerical evaluation may lead to numerical errors due to singularities, which occur in 1/r 12 . 22 Here, the PS technique, which combines numerical and analytical integrations, is used to evaluate two-body interactions.…”

Section: Energy Density Analysis For Ccsd and Mp2mentioning

confidence: 99%

Energy density analysis for second‐order Møller‐Plesset perturbation theory and coupled‐cluster theory with singles and doubles: Application to C₂H₄CH₄ complexes

Imamura

Nakai

2008

J Comput Chem

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Grid-based energy density analysis (EDA), in which numerical integration is performed for two-electron integrals by the pseudospectral method (Imamura et al., J. Chem. Phys. 2007, 126, 034103), is extended to correlated methods: second-order Møller-Plesset (MP2) perturbation and coupled-cluster singles and doubles (CCSD). Using EDA for MP2 and CCSD, we estimate atomic correlation energy differences and correlation energy density difference maps for C(2)H(4)--CH(4) complexes. The analyses confirm that polarization and diffuse functions essentially contribute to the descriptions of weak interaction around the nuclei and in the area between C(2)H(4) and CH(4), respectively.

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“…The difference between IY99 and M03 originates from the partitioning of the HF exchange term. Sato and Sakaki 9 advocated a combination between IY99 and M03 to represent the long‐range behavior.…”

Section: Introduction and Overviewmentioning

confidence: 99%

One‐body energy decomposition schemes revisited: Assessment of Mulliken‐, Grid‐, and conventional energy density analyses

Kikuchi

Imamura

Nakai

2009

Int J of Quantum Chemistry

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ABSTRACT:We propose a new energy density analysis (EDA) that evaluates atomic contributions of all energy terms, i.e., the kinetic, nuclear-attraction, Coulomb, and Hartree-Fock (HF) exchange and density functional theory (DFT) exchange-correlation energies using the Mulliken-type partitioning. Although widely used DFT exchangecorrelation functionals are nonlinear expressions in terms of density, they are decomposed into atomic contributions by focusing the linear part of the density. Numerical assessment on Mulliken-EDA, Grid-EDA, and conventional EDA has been carried out for the G2-1 set. Correlations between HF and DFT exchanges demonstrate that a consistent partitioning of all energy terms is essential for EDA. These numerical results confirm that the present Mulliken-EDA offers a more reasonable picture for the atomization process.

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Analysis on Solvated Molecules with a New Energy Partitioning Scheme for Intra- and Intermolecular Interactions

Cited by 17 publications

References 28 publications

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

Energy density analysis for second‐order Møller‐Plesset perturbation theory and coupled‐cluster theory with singles and doubles: Application to C₂H₄CH₄ complexes

One‐body energy decomposition schemes revisited: Assessment of Mulliken‐, Grid‐, and conventional energy density analyses

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Analysis on Solvated Molecules with a New Energy Partitioning Scheme for Intra- and Intermolecular Interactions

Cited by 17 publications

References 28 publications

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

Large‐ring cyclodextrins. Further support for the preferred conformations of CD26 in water solution: Molecular dynamics studies on CD26‐derived conformations of CDn (n = 24, 25, 27, 28, 29, 30)

Energy density analysis for second‐order Møller‐Plesset perturbation theory and coupled‐cluster theory with singles and doubles: Application to C2H4CH4 complexes

One‐body energy decomposition schemes revisited: Assessment of Mulliken‐, Grid‐, and conventional energy density analyses

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Energy density analysis for second‐order Møller‐Plesset perturbation theory and coupled‐cluster theory with singles and doubles: Application to C₂H₄CH₄ complexes