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Highly Efficient, and Fast Solid State Deprotection of 1,3-Dithianes and 1,3-Dithiolanes using Mercury(II) Nitrate Trihydrate  [PDF]
Mohammad H. Habibi,Shahram Tangestaninejad,Morteza Montazerozohori,Iraj Mohamadpoor-Baltork
Molecules , 2003, DOI: 10.3390/80900663
Abstract: A variety of 1,3-dithianes and 1,3-dithiolanes are deprotected in the solid state to the corresponding parent carbonyl compounds in excellent yields using mercury(II) nitrate trihydrate in a mild, efficient and fast method.
Eco-friendly Conditions for the Production of 1,3-Dithianes Using Microwave Irradiation  [cached]
Lidia Ballesteros,Olivia Noguez,Gabriel Arroyo,Benjamín Velasco
Revista de la Sociedad Química de México , 2005,
Abstract: La reacción entre varios aldehídos y cetonas con 1,3- propanditiol se llevo a cabo en la ausencia de disolvente, utilizando irradiación de microondas como fuente de calor. Bajo estas condiciones, se obtuvieron los correspondientes 1,3-ditianos, en tiempos cortos de reacción (5 min). Complementariamente, se evaluó la capacidad de una arcilla bentonitíca como promotora de esta reacción
Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions  [PDF]
Tridip Sheet, Subhrangshu Supakar, Raja Banerjee
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0057366
Abstract: Among several ‘anion binding motifs’, the recently described ‘CαNN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘CαNN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘CαNN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘CαNN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘CαNN’ sequence for anion recognition through “local” interaction.
Conformational analysis of ethyl mercaptan as a model of glutathione and its oxidation by peroxide: an exploratory first principle molecular computational study  [cached]
Natalie J Galant,Sinisa Vukovic,David H Setiadi,Imre G Czismadia
University of Toronto Journal of Undergraduate Life Sciences , 2009,
Abstract: First principle quantum molecular computations were carried out using Restricted Hartree-Fock method utilizing the 3-21G level of theory (RHF/3-21G) on ethyl mercaptan (Et-SH) and diethyl disulfide (Et-SS-Et) to study their full conformational space. The axis chirality associated with the rotation about the S-S linkage has been related to the potential energy hypersurface of diethyl disulfide. The energetics of the redox reaction Et-SH + H2O2 + HS-Et ? 2H2O + Et-S-S-Et was chosen to be a mimic of the biologically important redox reactions of glutathione (G-SH +H2O2 + HS-G ? 2H2O + G-S-S-G). Using first principle molecular computations, the redox reaction of Et-SH ? Et-S-S-Et has been found to be exothermic. Depending on the conformers involved, the exothermicity computed at the RHF/3-21G level of theory ranges from -62.0 kCal mol-1 to -64.2 kCal mol-1.
Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin  [cached]
Jongkon Nipa,Mokmak Wanwimon,Chuakheaw Daungmanee,Shaw Philip J
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-s3-s24
Abstract: Background It is known that the highly pathogenic avian influenza A virus H5N1 binds strongly and with high specificity to the avian-type receptor by its hemagglutinin surface protein. This specificity is normally a barrier to viral transmission from birds to humans. However, strains may emerge with mutated hemagglutinin, potentially changing the receptor binding preference from avian to human-type. This hypothesis has been proven correct, since viral isolates from Vietnam and Thailand have been found which have increased selectivity toward the human cell receptor. The change in binding preference is due to mutation, which can be computationally modelled. The aim of this study is to further explore whether computational simulation could be used as a prediction tool for host type selectivity in emerging variants. Results Molecular dynamics simulation was employed to study the interactions between receptor models and hemagglutinin proteins from H5N1 strains A/Duck/Singapore/3/97, mutated A/Duck/Singapore/3/97 (Q222L, G224S, Q222L/G224S), A/Thailand/1(KAN-1)/2004, and mutated A/Thailand/1(KAN-1)/2004 (L129V/A134V). The avian receptor was represented by Siaα(2,3)Gal substructure and human receptor by Siaα(2,6)Gal. The glycoside binding conformation was monitored throughout the simulations since high selectivity toward a particular host occurs when the sialoside bound with the near-optimized conformation. Conclusion The simulation results showed all hemagglutinin proteins used the same set of amino acid residues to bind with the glycoside; however, some mutations alter linkage preferences. Preference toward human-type receptors is associated with a positive torsion angle, while avian-type receptor preference is associated with a negative torsion angle. According to the conformation analysis of the bound receptors, we could predict the relative selectivity in accordance with in vitro experimental data when disaccharides receptor analogs were used.
Ethyl 1,3-dimethyl-1H-indole-2-carboxylate  [cached]
A. Marx,G. Chakkaravarthi,G. Gobirajeshwaran,A. K. Mohanakrishnan
Acta Crystallographica Section E , 2008, DOI: 10.1107/s1600536808034156
Abstract: In the title compound, C13H15NO2, the plane of the indole ring forms a dihedral angle of 5.26 (6)° with the ester group and the ethyl side-chain C atoms. The crystal packing is stabilized by weak intermolecular C—H...O and C—H...π interactions.
Ethyl 4-(1,3-dioxo-2,3-dihydro-1H-benzo[de]isoquinolin-2-yl)benzoate  [cached]
Yi Chen Chan,Abdussalam Salhin,Melati Khairuddean,Madhukar Hemamalini
Acta Crystallographica Section E , 2011, DOI: 10.1107/s160053681005049x
Abstract: The title compound, C21H15NO4, was synthesized by reducing the Schiff base obtained from acenaphthenequinone and ethyl-4-aminobenzoate. The dihedral angle between the essentially planar 1,3-dioxo-2,3-dihydro-1H-benzo[de]isoquinoline ring system [maximum deviation = 0.061 (2) ] and the benzene ring is 75.08 (10)°. In the crystal, molecules are connected via weak intermolecular C—H...O hydrogen bonds, forming a two-dimensional network. The ethyl group is disordered over two sets of sites with a refined occupancy ratio of 0.502 (12):0.498 (12).
Bis[1,3-bis(1-ethyl-1H-benzimidazol-2-yl)-2-oxapropane]cadmium(II) dipicrate dimethylformamide disolvate  [cached]
Huilu Wu,Bin Liu,Fan Kou,Fei Jia
Acta Crystallographica Section E , 2011, DOI: 10.1107/s1600536811018228
Abstract: In the title compound, [Cd(C20H22N4O)2](C6H2N3O7)2·2C3H7NO, the CdII ion is coordinated by four N atoms and two O atoms from two tridentate 1,3-bis(1-ethyl-1H-benzimidazol-2-yl)-2-oxapropane ligands in a distorted octahedral environment.
Effect of Counteranions on the Conformational Equilibrium of 1-Butyl-3-methylimidazolium-Based Ionic Liquids  [PDF]
Naohiro Hatano,Takahiro Takekiyo,Hiroshi Abe,Yukihiro Yoshimura
International Journal of Spectroscopy , 2011, DOI: 10.1155/2011/648245
Abstract: We have investigated the nonspherical anion effect on the trans-trans (TT) and gauche-trans (GT) equilibrium in pure 1-butyl-3-methylimidazolium ([bmim]+)-based room temperature ionic liquids (RTILs) by the Raman spectroscopy. The intensity ratio of the [bmim]+ cation in [bmim]+-based RTILs having nonspherical anions changes with nature of the anions. However, the enthalpy change of the [bmim]+ cation is approximately ?1.0?kJ/mol for all [bmim]+-based RTILs used in this study and is independent of the anionic species. The present results indicate that the conformational stability of the [bmim]+ cation in [bmim]+-based RTILs including nonspherical anions is driven by the entropic contribution associated with the orientation and configuration of the [bmim]+ cation with respect to the counteranion. 1. Introduction Room temperature ionic liquids (RTILs) consisting of organic cations and anions remain in the liquid state at room temperature [1]. The conformational behavior of RTILs has been studied to identify correlations with chemical and physical properties of RTILs, such as conductivity, viscosity, and melting point [1–5]. The conformational equilibria of imidazolium cations, such as 1-ethyl-3-methylimidazolium and 1-butyl-3-methylimidazolium ([emim]+) of the imidazolium-based RTILs, the so-called prototype ionic liquids, have been investigated by the Raman spectroscopy combined with density functional theory calculations [2, 5–12]. The [bmim]+ cation has a trans-trans and gauche-trans ( - ) equilibrium for NCCC and CCCC angles of the butyl group, as shown in Figure 1. Thermodynamic studies of the conformational equilibrium of RTILs are useful to clarify the relationship between the conformation and the complicated phase transition behavior of these RTILs [3–5]. Figure 1: Optimized structures of the (a) trans-trans ( ) and (b) gauche-trans ( ) conformers of 1-butyl-3-methylimidazolium ([bmim] +) cation by B3LYP/6-311+(d) level. The effect of spherical anions, such as halide anions (Cl?, Br?, and I?), on the - equilibrium of the [bmim]+ cation in pure [bmim]+-based RTILs has been studied [3, 10–12]. Katayanagi et al. [3] reported that the conformational preference of the [bmim]+ cation varies with different halide anions. In relation to this, using the Raman spectroscopy and molecular dynamics (MD) simulations, Umebayashi et al. [12] showed that the thermodynamic stability of the conformational equilibrium of the [bmim]+ cation is affected by the halide anion. Important conclusion is that anions localized near the C2-H atoms of the [bmim]+ cation
Intramolecular H-bonding interaction in angular 3-pi-EWG substituted imidazo[1,2-a]pyridines contributes to conformational preference
Manuel Velázquez-Ponce, Héctor Salgado-Zamora, Hugo A Jiménez-Vázquez, Maria Elena Campos-Aldrete, Rogelio Jiménez, Humberto Cervantes, Taibi Ben Hadda
Chemistry Central Journal , 2013, DOI: 10.1186/1752-153x-7-20
Abstract: Theoretical calculations were performed aimed to obtain evidence of the existence of an intramolecular non-bonding interaction between H-5 and the oxygen atom of the EWG. Results derived from conformational and vibrational analysis at the DFT B3LYP/6-311++G(d,p) level of theory, the determination of Bond Critical Points derived from AIM theory, and the measurement of some geometrical parameters, support the hypothesis that the higher stability of the prevailing conformation in these molecules (that in which the oxygen of the EWG is oriented towards H-5) has its origin in an intramolecular interaction,Computational calculations predicted correctly the conformational preferences in angular 3-pi-EWG-substituted imidazo[1,2-a]pyridines. The existence of an electrostatic hydrogen bond between H-5 and the oxygen atom of the pi-EWG was supported by several parameters, including X-ray crystallography. The existence of such structural array evidently impacts the H-5 chemical shift.
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