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Search for "simulations" in Full Text gives 157 result(s) in Beilstein Journal of Organic Chemistry.
Catalysis: transition-state molecular recognition?
Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117
- transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable
- AM1/OPLS/TIP3P simulations [19] with ensemble averaging to include the effect of thermal fluctuations in the enzyme and solvent environments to obtain a value for the α-D3 KIE = 0.82 ± 0.05, which is in excellent accord with the experimental value [11] of VCH3 /VCD3 = 0.83 ± 0.05 for methylation of
- for the COMT-catalysed reaction were computed as 2.06 ± 0.02 Å and 2.11 ± 0.01 Å, the sum of which is scarcely different from the sum of the corresponding average bond lengths, 2.18 ± 0.04 Å and 2.00 ± 0.04 Å, for the uncatalysed reaction. Thus the simulations did not provide any structural evidence
Oxalyl retro-peptide gelators. Synthesis, gelation properties and stereochemical effects
Beilstein J. Org. Chem. 2010, 6, 945–959, doi:10.3762/bjoc.6.106
- promising biomedicinal properties, very little is known about the self-assembly potential of this class of compounds in solution. Computer simulations of some malonamide retro-peptides have shown that the extended conformations are less stable than the helical ones [48][49]. Nevertheless, the crystal
EPR and pulsed ENDOR study of intermediates from reactions of aromatic azides with group 13 metal trichlorides
Beilstein J. Org. Chem. 2010, 6, 713–725, doi:10.3762/bjoc.6.84
- appear different at first sight, the hfs derived from the simulations (Table 1) are actually quite similar. The contrasts in the spectral appearances are mainly the result of different line widths with consequently different resolutions. It is evident that the main species in each case is the radical
- , gave essentially the same strong spectrum, see Figure 5a and Supporting Information. The hfs derived from the simulations (Table 1) suggest that this is also a dimer type radical cation 17b+•. However, with the passage of time a central peak began to appear in this spectrum. When 5 was treated with
- intensity were obtained at around 300 K. Most of the EPR spectra were recorded with 2.0 mW power, 1.0–0.2 Gpp modulation intensity and a gain of ~106. In all cases where spectra were obtained, hfs were assigned with the aid of computer simulations using the Bruker SimFonia and NIEHS Winsim2002 software
Symmetry breaking and structure of a mixture of nematic liquid crystals and anisotropic nanoparticles
Beilstein J. Org. Chem. 2010, 6, No. 74, doi:10.3762/bjoc.6.74
- align parallel. By contrast, we set JLC–NP < 0, tending to orient LC molecules and NP perpendicularly. In the simulations we take JLC–LC = JNP–NP = 1, and JLC–NP is either set to −1, −2 or −4. The exponent a is equal to 1 for magnetic–magnetic coupling while for nematic–nematic or nematic–magnetic
- results of numerical simulations, we find that G is indeed equal in cases with the same r, except for small unimportant statistical variations which are subsequently annulled by averaging G for data pairs (r, G) with the same r. To extract structural details from a calculated G(r) dependence, we fit it
- finite value of s. However, with increasing x the value of s decreases monotonously. Our numerical simulations suggest, that above a threshold value x = xc long range ordering is replaced by short range ordering. Therefore, for a sufficiently large concentration the degree of disorder introduced by
(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties
Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20
- , temperature coefficient (Δδ/ΔT) measurements of amide protons and constrained MD simulations revealed that all the cyclic oligomers had symmetrical structures, although none of the unprotected cyclic oligomers displayed any ability to transport ions across model membranes according to ion flux studies. Cyclic
Competition between local disordering and global ordering fields in nematic liquid crystals
Beilstein J. Org. Chem. 2010, 6, No. 2, doi:10.3762/bjoc.6.2
- temperature). In simulations we either originate from randomly distributed orientations of directors, or from homogeneously aligned samples along a symmetry breaking direction. In the latter case the directors are initially homogeneously aligned along ex. We henceforth refer to these cases as the i) random
- . The ii) homogeneous case can be realized by applying first a strong homogeneous external field B along a symmetry breaking direction. After a well enough alignment is achieved the field is switched off. In order to diminish the influence of statistical variations we carry out several simulations
- simulations for 2D systems which demand less computational time. A typical G(r) dependence in 2D and 3D is shown in Figure 1a and Figure 1b, respectively. We plot G(r) for both homogeneous and random initial configuration in the presence of external field and without it. For B = 0 it holds ξ(hom) > ξ(ran
Chiral amplification in a cyanobiphenyl nematic liquid crystal doped with helicene-like derivatives
Beilstein J. Org. Chem. 2009, 5, No. 50, doi:10.3762/bjoc.5.50
- intermolecular interactions and opposes director distortions [24]. Different theories [25][26][27] have contributed to elucidate the molecular mechanism behind cholesteric induction, as well as Molecular Dynamics simulations [28][29][30]; for the connection between structure of the chiral dopant and cholesteric
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