Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• results were consistent with the compression hypothesis for catalysis of methyl transfer. Origin of COMT catalytic power To assess whether compression actually operates in COMT-catalysed methyl transfer, hybrid QM/MM calculations have been performed at the AM1/MM level [17][18][19]. The secondary α-D3 KIE

• 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

• (PMF), computed from MD simulations at the AM1/CHARMM/TIP3P level with umbrella sampling along a reaction coordinate defined as the difference in bond lengths from Cα to the nucleophile and nucleofuge, predicted a 44 kJ mol−1 increase ΔG‡enz in free energy in going from the enzymic reactant complex

Donor-acceptor substituted phenylethynyltriphenylenes – excited state intramolecular charge transfer, solvatochromic absorption and fluorescence emission

• Ritesh Nandy and
• Sethuraman Sankararaman

Beilstein J. Org. Chem. 2010, 6, 992–1001, doi:10.3762/bjoc.6.112

• -spherical in nature. Hence, the above assumption of substituting molecular radius for cavity radius is only approximate. The molecular radii for 1c (8.8 Å), 1e (10.2 Å) and 1g (9.1 Å) were obtained from semi-empirical AM1 calculations [46]. The change in the dipole moments (Δμ) were, 25.7 D for 1c, 43.0 D

Anthracene coupled adenine for the selective sensing of copper ions

• Kumaresh Ghosh and
• Tanushree Sen

Beilstein J. Org. Chem. 2010, 6, No. 44, doi:10.3762/bjoc.6.44

• sensor, shown in Figure 1. In both 1 and 2, adenine is defined as the binding site, which is connected to the anthracene probe via –CH2– spacer at the different regions of adenine. In order to find out the possible site for binding of metal ions, we optimized the geometries of both 1 and 2 at AM1 level

• adenine moiety and Cu2+ ions should serve as the basis for new strategies to design new chemosensors based on adenine even although copper ion recognition by other systems has been described. Further progress along this direction is underway in our laboratory. Design principle for 1 and 2. AM1 optimized

Synthesis of indolo[3,2-b]carbazole-based new colorimetric receptor for anions: A unique color change for fluoride ions

• Ajit Kumar Mahapatra,
• Giridhari Hazra and
• Prithidipa Sahoo

Beilstein J. Org. Chem. 2010, 6, No. 12, doi:10.3762/bjoc.6.12

• CH3CN in the presence of I2 for 45 min afforded the desired receptor 1 in 82% yield. To look into the orientation of hydrogen bond donors around the carbazole motif, we optimized the structure by the AM1 method [45] (Figure 2). It is evident from Figure 2 that the two catechol units do not lie in the

• their stable conformation of receptor 1 at the AM1 level was carried out using the minimal valence basis as STO 3G in ArgusLab 4.0.1 software suite. We have refrained from citing calculated total energy value, the calculation being for molecule only in the gas phase. Receptor 1 3,3′-Bis(indolyl)-3,4

• , 118.59, 118.0, 115.4, 115.1, 11.0, 110.1; FTIR (KBr, cm−1): 3472, 3430, 1521, 1457, 1262, 1224; C30H20N2O4 (473.1496); Anal. Calcd C, 76.26; H, 4.27; N, 5.93; O, 13.54; found C, 76.35; H, 4.19; N, 5.73; O, 13.60; HRMS (MH+ + 2): 475.21. The structure of the indolocarbazole-based chemosensor 1. The AM1

Control of stilbene conformation and fluorescence in self-assembled capsules

• Mark R. Ams,
• Dariush Ajami,
• Stephen L. Craig,
• Jye-Shane Yang and
• Julius Rebek Jr

Beilstein J. Org. Chem. 2009, 5, No. 79, doi:10.3762/bjoc.5.79

• ) The shape of the space inside (A), a schematic view along the central axis with two aromatic guests (B) and an energy-minimized (AM1) complex of stilbene in 1.1 (C). Room temperature fluorescence spectra at λexc = 318 nm for 10 µM mesitylene solutions of 4,4′-dimethylstilbene (2); 4-ethyl-4

Ring strain and total syntheses of modified macrocycles of the isoplagiochin type

• Andreas Speicher,
• Timo Backes,
• Kerstin Hesidens and
• Jürgen Kolz

Beilstein J. Org. Chem. 2009, 5, No. 71, doi:10.3762/bjoc.5.71

• are possible for 1 (and analogously for 2) (Figure 2). The ethylene bridge D is more flexible in these two molecules. Temperature dependent NMR investigations did not provide any evidence for the existence of different diastereomers configurationally stable within the NMR timescale. AM1-based

• reaction. AM1 energies [18], angular strain and torsion stress of different modified macrocycles of the isoplagiochin type. Supporting Information Supporting Information File 110: Full experimental details and characterization data.

Molecular length distribution and the formation of smectic phases

• Nadia Kapernaum,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2009, 5, No. 65, doi:10.3762/bjoc.5.65

• PhP14, 6PhPz and 2PhP differing in molecular lengths by a factor of approximately two. The molecular lengths were determined from the most extended conformers, after optimizing their energy using molecular modelling with MOPAC/AM1. Phase diagram of the system 2PhP/PhP14. Over a broad temperature and

Synthesis of rigidified flavin–guanidinium ion conjugates and investigation of their photocatalytic properties

• Harald Schmaderer,
• Mouchumi Bhuyan and
• Burkhard König

Beilstein J. Org. Chem. 2009, 5, No. 26, doi:10.3762/bjoc.5.26

• spectra of compounds 1 and 2 revealed several NOE contacts, but the flexibility of the molecule did not allow the determination of preferred conformations. The most stable conformer of compound 1 in the gas phase was determined by computational methods (semi-empirical AM1, Spartan program package, Figure

• ). Structure of compound 1 in the solid state. Calculated lowest energy conformation of 1 in the gas phase (AM1, Spartan program package). Flavin–guanidinium ion conjugates 1 and 2 and tetraacetyl riboflavin (3). Synthesis of flavins 1 and 2. Conditions: (i) DMAP, H2O, Δ, 20 h, 71–78%, (ii) HOBt, EDC, NEt(iPr

Quinoline based receptor in fluorometric discrimination of carboxylic acids

• Kumaresh Ghosh,
• Suman Adhikari,
• Asoke P. Chattopadhyay and
• Purnendu Roy Chowdhury

Beilstein J. Org. Chem. 2008, 4, No. 52, doi:10.3762/bjoc.4.52

• AM1 level [21]. It is evident from the optimized geometry of the complex of 1 in Figure 15a that citric acid is strongly complexed in the cleft involving a large number of hydrogen bonding interactions. Both the amides as well as the isophthaloyl peri proton form hydrogen bonds with one of the

• = 1.67 × 10−5 M) upon addition citric acid dissolved in CHCl3 containing 0.8% DMSO (λex = 290 nm). 1H NMR (in CDCl3) spectra of receptor 1 (c = 3.57 × 10−3 M; bottom) and the 1:1 complex with citric acid (top); *indicates signals of quinoline rings. AM1 optimized geometries of the complexes of 1 with (a

• , h = 2.95 Å, i = 2.28 Å. AM1 optimized geometry of the complex of 2 with citric acid, hydrogen bond distances: a = 2.12 Å, b = 2.39 Å, c = 2.19 Å, d = 2.36 Å, e = 2.66 Å, f = 2.92 Å, g = 2.69 Å, h = 2.32 Å, i = 2.93 Å, j = 2.25 Å, k = 2.25 Å, l = 2.38 Å. Syntheses of receptors 1 and 2. Association

Control of asymmetric biaryl conformations with terpenol moieties: Syntheses, structures and energetics of new enantiopure C₂-symmetric diols

• Y. Alpagut,
• B. Goldfuss and
• J.-M. Neudörfl

Beilstein J. Org. Chem. 2008, 4, No. 25, doi:10.3762/bjoc.4.25

• conformations: a M-(R)-sense is found for BIMOL, P-(S)- for BIVOL, P-(S)- for BICOL and likewise P-(S)- for partially hydrogenated BIMEOL (Figure 1–Figure 4, Scheme 2). The C2-C1-C1′-C2′ dihedral angles are −103°, +94°, +96° and +99° respectively (Table 1 and Table 2). Computational ONIOM (B3LYP/6-31++G**:AM1

• ++G*) levels of theory were applied to the hydroxyl groups, while the rest of the structures were computed by the semiempirical AM1 method. Hydrogen atoms were used as link atoms between the two layers. The structures were analyzed by frequency computations and showed no imaginary frequencies. X-Ray

• the external OH group, is omitted for clarity (cf. Scheme 3). X-Ray crystal structure of (P)-BIMEOL. An ethanol molecule, binding to the external OH group, is omitted for clarity (cf. Scheme 3) B3LYP/6-31++G**:AM1 optimized structure of (M)-BIMOL, Erel. = 0.0 kcal/mol. B3LYP/6-31++G**:AM1 optimized

Effect of transannular interaction on the redox- potentials in a series of bicyclic quinones

• Grigoriy Sereda,
• Jesse Van Heukelom,
• Miles Koppang,
• Sudha Ramreddy and
• Nicole Collins

Beilstein J. Org. Chem. 2006, 2, No. 26, doi:10.1186/1860-5397-2-26

• ) model 273 potentiostat equipped with PAR model 270 computer controlled software. All computational methods were used as implemented to the GAUSSIAN 98W package [12], running on a PC Pentium 4 computer. The molecular structures 1–5 were pre-optimized in vacuum at the AM1 semi-empirical level and then