Molecular dynamics , chiral recognition

Noncovalent interactions play a key role in biodisciplines. A celebrated example is the secondary structure of proteins. The 20 natural amino acids are each characterized by different structures with more or less acidic or basic, hydrophilic or hydrophobic functionalities and thus capable of different intermolecular interactions. Due to the formation of hydrogen bonds between nearby C=0 and N-H groups, protein polypeptide backbones can be twisted into a-helixes, even in the gas phase in the absence of any solvent." A protein function is determined more directly by its three-dimensional structure and dynamics than by its sequence of amino acids. Three-dimensional structures are strongly influenced by weak non-covalent interactions between side functionalities, but the central importance of these weak interactions is by no means limited to structural effects. Life relies on biological specificity, which arises from the fact that individual biomolecules communicate through non-covalent interactions." " Molecular and chiral recognition rely on... 

Dodziuk H, Lukin O (2000) Modelling of molecular and chiral recognition by cyclodextiins. Is it reliable Part 2. Molecular dynamics calculations in vacuum pertaining to the selective complexation of decahns by P-cyclodextiin. Pol J Chem 74 997-1001... 

Various endeavors have been undertaken to get insight into the 3D selector-selectand complex structures and to elucidate chiral recognition mechanisms of cinchonan carbamate selectors for a few model selectands (in particular, DNB-Leu). Such studies comprised NMR [92-94], ET-IR [94-96], X-ray diffraction [33,59,92,94], and molecular modeling investigations (the latter focusing on molecular dynamics [92,93,97], and 3D-QSAR CoMFA studies [98]). 

Lipkowitz [63] used molecular dynamics simulations to answer the following questions a) What are the intermolecular forces responsible for analyte binding to the CSP b) Where on or in the host does the analyte bind c) What are the differential interactions giving rise to chiral discrimination d) What differences do R and S-enantiomers experience in the CD cavity e) Are existing chiral recognition mechanisms valid His computational work was based on experimental separations... 

Franchi, P., Lucarini, M., Mezzina, E., Pedulli, G.F. (2004) Combining magnetic resonance spectroscopies, mass spectrometry, and molecular dynamics investigation of chiral recognition by 2,6-di-O-methyl-beta-cyclodextrin. /. Am. Chem. Soc.,126, 4343 354. 

For these purposes, various functional TLMs have already been realized. For exanple, sensitive chiral recognition by circular-dichroism TLM (CD-TLM) was reported for synthesis and analysis of drugs on microchips [6], Other reports have described an electrochemical TLM [7], flow sensing TLM, UV TLM [8], and TLM spectrometer [9]. As important functions for science and technology in micro- and nano-fluidics, three functions are highly desired individual molecule detection as the ultimate sensitivity, fast (real-time) imaging, and femtosecond time-resolved measurement for investigating molecular dynamics in a nano-space. 

The chiral recognition mechanism of small molecule-based CSPs has been extensively investigated from theoretical viewpoints, especially by Lipkowitz et al. [35-37], The interaction energies between the CSPs and enantiomers were calculated by molecular-mechanics (MM), molecular-dynamics (MD), and quantum-mechanical calculations, and the rational interaction models between the CSPs and racemates have been proposed. Until now, several attempts have also been carried out for the qualitative understanding of the chromatographic behavior of the polysaccharide-based CSPs. 

Dodziuk H, Ejchart A, Lukin O, Vysotsky MO. H and C NMR and molecular dynamics study of chiral recognition of camphor enantiomers by a-cyclodextrin. J. Org. Chem. 1999 64 1502 1507. 

Structural Elucidation of IsoX Phase. Spectral analysis by C NMR and X-ray diffraction measurements suggests that upon the SmC IsoX transition, an interlayer correlation may be broken, whereas dimerization or tetramerization via a stereospecific intermolecular interaction through fluorines at chiral centers within each layer is assumed to be operating. The dimerization or tetramerization reduces the anisotropy of molecular motion to increase rotation around the short axis. This change in molecular dynamics may release entropy of the system to induce the endothermic transition. The IsoX phase is not a result of the competition between helical structure and mesophase ordering but a result of the chirality-dependent stereospecific interaction or chiral molecular recognition (7. 

All of the experiments in pure and mixed SSME systems, as well as in the Af-stearoyltyrosine systems, have one common feature, which seems characteristic of chiral molecular recognition in enantiomeric systems and their mixtures enantiomeric discrimination as reflected by monolayer dynamic and equilibrium properties has only been detected when either the racemic or enantiomeric systems have reverted to a tightly packed, presumably quasi-crystalline surface state. Thus far it has not been possible to detect clear enantiomeric discrimination in any fluid or gaseous monolayer state. 

Keywords. Lanthanide chelates, Chirality, Conformations, Molecular recognition, Dynamics... 

Mizuno.Y., Aida,T.,Yamaguchi, K., Chirality-Memory Molecule Crystallographic and Spectroscopic Studies on Dynamic Molecular Recognition Events by Fully Substituted Chiral Porphyrins,... 

The dipole pairing model is based on the pair formation of molecules in adjacent layers through the dipole-dipole interaction. Because of the experimental observation (2), pairing must be made between like enantiomers, as shown in Figure 9.14 [32]. Otherwise, anticlinic orientation cannot be formed in the racemic compoimds. Therefore, in this model, chiral molecular recognition is required. The pairing may be dynamic and may occur in optically resolved local enantiomeric domains. 

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