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ABSTRACT: A series of methylated and non-methylated β-cyclodextrin (β-CD) structures in three macrocyclic configurations (a-c) were studied with molecular dynamics (MD) simulations to elucidate the dynamic behavior of the different CD structures using a continuum water model with the AMBER* force field. A set of parameters were defined to describe the geometric dimensions of the CD, such as its cavity shape, the upper and lower rim sizes, and the tilting of each of the glucose rings. Correlation analyses between the different parameters were carried out, and they have provided insights into the different dynamic behaviors for the different CD structures. Detailed analyses on the crystal structures of the different methylated and non-methylated β-CD complexes were also carried out using the defined parameters. Correlation of parameters from crystal structures and MD simulations has allowed us to identify the effect that crystal packing/guest inclusion has on the CD geometries. The overall analysis approach can be a useful tool for other related macrocyclic structures, such as modified α-, β-CDs or even calixarenes.
The Journal of Physical Chemistry B 03/2012; 116(11):3477-89. · 3.70 Impact Factor
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ABSTRACT: Several series of novel banana-shaped H-bonded symmetric trimers (with two H-bonds) and asymmetric heterodimers (with one H-bond) were self-assembled by appropriate molar ratios of proton donors (H-donors) and acceptors (H-acceptors). The influences of H-bonded linking positions and aromatic ring numbers (4-8 aromatic rings in the rigid cores) as well as the chain lengths (n, m = 12 or 16, respectively, in the flexible parts) on the mesomorphism and the switching behavior of the bent-core supramolecules were evaluated and theoretically analyzed. Except for the supramolecular structures with longer rigid cores or shorter flexible chains possessing the rectangular columnar (Col(r) or B1) phase, the SmC(A)P(A) phase was revealed in most supramolecular asymmetric heterodimers and switched to the SmC(S)P(F) phase by applying electric fields. The polar smectic C phase was dominated for those with H-bonded sites apart from the core center. Interestingly, the SmA and nematic phases were observed in H-bonded asymmetric dimers with H-bonded sites close to the core center, which theoretically proved that the polar smectic C phase was disfavored due to an unfavorable bend angle (smaller than the lower limit of 110 degrees ) in the lowest-energy H-bonded conformer. Compared with the fully covalently bonded analogue, lower transition temperatures and lower threshold voltages were developed in the H-bonded asymmetric dimers with the polar smectic C phase. On the basis of the theoretical calculations of molecular modeling, the existence of polar switching behavior in the polar smectic C phase of asymmetric heterodimers was proven to be associated with their configurations with higher dipole moments and suitable bend angles. Furthermore, the lack of polar switching behavior in supramolecular symmetric trimers, which exhibited the regular SmC phase with weak electrical stabilities, was related to their configurations with smaller dipole moments and confirmed by theoretical calculations.
The Journal of Physical Chemistry B 10/2009; 113(44):14648-60. · 3.70 Impact Factor
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ABSTRACT: We report a molecular cage-based [2]rotaxane that functions as an artificial molecular muscle through the control of the addition and removal of fluoride anions. The percentage change in molecular length of the [2]rotaxane is about 36% between the stretched and contracted states, which is larger than the percentage change (approximately 27%) in human muscle.
Organic Letters 01/2009; 11(2):385-8. · 5.86 Impact Factor
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ABSTRACT: [Structure: see text] We report a molecular switch that not only can be switched between its complexed and decomplexed states through the sequential addition of an acid and a base (NH4+ and Proton Sponge, respectively) but also can be operated equally through the sequential addition of basic and acidic reagents (Et2NH and TFA, respectively).
Organic Letters 08/2006; 8(15):3223-6. · 5.86 Impact Factor
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Pin-Nan Cheng,
Po-Yi Huang, Wan-Sheung Li,
Shau-Hua Ueng,
Wei-Chung Hung,
Yi-Hung Liu,
Chien-Chen Lai,
Yu Wang,
Shie-Ming Peng,
Ito Chao,
Sheng-Hsien Chiu
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ABSTRACT: We report a new host molecule in which one diethylene glycol chain (i.e., a loop possessing only three oxygen atoms) incorporated along with two phenolic aromatic rings is linked by a xylene spacer into a macroring. The design of the molecular structure of this macrocycle "amplifies" any potential [cation...pi], [N+-H...pi], and [N+C-H...pi] interactions between the dibenzylammonium (DBA+) ion and the phenolic rings of the macrocycle; as such, these species display a very strong binding affinity in CD3NO2 (Ka = 15,000 M(-1)). The macroring also coordinates to bipyridinium ions in a [2]pseudorotaxane fashion, which makes it the smallest macrocycle (i.e., a 25-membered ring) known to complex both DBA+ and bipyridinium ions in solution. To confirm unambiguously that these pseudorotaxanes exist in solution, we synthesized their corresponding interlocked molecules, namely rotaxanes and catenanes.
The Journal of Organic Chemistry 04/2006; 71(6):2373-83. · 4.45 Impact Factor
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ABSTRACT: Remote control of hydrogen bond strengths has been studied based on conjugated donor-bridge-acceptor (pyrrole-bridge-imine) systems. The neutral and protonated states of the imine can change the hydrogen bonding ability of the pyrrole because, in the protonated state, significant partial intramolecular charge transfer (ICT) is induced that causes partial delocalization of the positive charge onto the pyrrole moiety. An efficient bridge, regardless of its length, should help electrons to flow out of pyrrole. A previously developed design strategy for the bridge (low bridge HOMO/LUMO) leads to the study of cyano- and fluoro-substituted conjugated systems. Substitution positions are found to be of key importance for maximizing the protonation-induced response from the donor-bridge-acceptor systems. Our results not only help to identify useful bridge substitution patterns, but also highlight interesting issues regarding the bridge conformation and the fluorine lone-pair effect.
Chemistry 12/2005; 11(22):6533-42. · 5.93 Impact Factor
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ABSTRACT: The use of a cyclodextrin.Diels-Alder transition structure complex (CD.TS) as a model in molecular dynamics simulations has enabled us to gain insight into the controlling factors in the cyclodextrin-mediated Diels-Alder reaction of methyl-p-benzoquinone with isoprene. MD simulations were carried out with multiple binding configurations of the CD.TS (TS=meta-TS, para-TS) complexes at the top and bottom rims of beta-CD. We discovered that i) only shallow binding with the CD is necessary for the regioselectivity, and multiple binding geometries are possible; ii) the narrow bottom rim, with the primary hydroxyl groups, of the CD binds both regio-TSs better than at the wider top rim (secondary hydroxyl groups), which was unexpected from the perspective of shape complementarity that governs the stability of most CD.guest complexes. Overall, the bottom rim of the CD exhibits higher regioisomer discrimination for the meta-TS; iii) structural clustering analyses of the CD.TS configurations (sampled during MD simulations) have enabled us to evaluate the binding energies of the different binding configurations. The result indicates that there is a direct correlation between meta-product selectivity and a higher number of binding configurations favoring the formation of the CD.meta-TS complex. The main forces of stabilization in the CD.TS complexes are the van der Waals interactions when the TS is bound at the top rim. At the bottom rim, closer contacts between polar functional groups of the TS and CD have increased the importance of electrostatic interactions. We found that van der Waals, solvation, and torsional forces are less favorable for complexation at the bottom rim; however, this is compensated by large favorable electrostatic interactions. With insights obtained from the study of CD.TS complexes and MD simulations of the modified heptakis-[6-O-(2-hydroxy)propyl]-beta-CD, we were able to explain why a low selectivity was observed when the Diels-Alder reaction was carried out in this modified CD. Two types of search method [Monte Carlo and multiple minimum (MCMM) and molecular dynamics (MD)] to explore and evaluate the different possible binding geometries of the TS within beta-CD, were discussed.
Chemistry 03/2003; 9(4):951-62. · 5.93 Impact Factor
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Tetrahedron. 60(42):9493-9501.
