Hydrogen bonding donation of N-methylformamide with dimethylsulfoxide and water

20% N-methylformamide (NMF) mixtures with water and with dimethylsulfoxide (DMSO) have been studied. A comparison between the hydrogen bonding (H-bond) donation of N-methylformamide with both solvents in the mixtures is presented. Results of radial distribution functions, pair distribution energies, molecular dipole moment correlation, and geometry of the H-bonded species in each case are shown. The results indicate that the NMF-solvent H-bond is significantly stronger with DMSO than with water. The solvation shell is best organized in the DMSO mixture than in the aqueous one. © 2013 Elsevier B.V. All rights reserved.

On the hydrogen bonding between N-methylformamide and acetone and tetrahydrofuran

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Quantum chemical topological analysis of hydrogen bonding in HX…HX and CH3X…HX dimers (X = Br, Cl, F)

We present a systematic investigation of the nature and strength of the hydrogen bonding in HX···HX and CH3X…HX (X = Br, Cl and F) dimers using ab initio MP2/aug-cc-pVTZ calculations in the framework of the quantum theory of atoms in molecules (QTAIM) and electron localisation functions (ELFs) methods. The electron density of the complexes has been characterised, and the hydrogen bonding energy, as well as the QTAIM and ELF parameters, is consistent, providing deep insight into the origin of the hydrogen bonding in these complexes. It was found that in both linear and angular HX…HX and CH3X…HX dimers, F atoms form stronger HB than Br and Cl, but they need short (∼2 Å) X…HX contacts.

Controlling the formation of ionic-liquid-based aqueous biphasic systems by changing the hydrogen-bonding ability of polyethylene glycol end groups

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Quantum confinement in hydrogen bond

In this work, the quantum confinement effect is proposed as the cause of the displacement of the vibrational spectrum of molecular groups that involve hydrogen bonds. In this approach, the hydrogen bond imposes a space barrier to hydrogen and constrains its oscillatory motion. We studied the vibrational transitions through the Morse potential, for the NH and OH molecular groups inside macromolecules in situation of confinement (when hydrogen bonding is formed) and nonconfinement (when there is no hydrogen bonding). The energies were obtained through the variational method with the trial wave functions obtained from supersymmetric quantum mechanics formalism. The results indicate that it is possible to distinguish the emission peaks related to the existence of the hydrogen bonds. These analytical results were satisfactorily compared with experimental results obtained from infrared spectroscopy. (c) 2015 Wiley Periodicals, Inc.

Non-inclusion complexes between riboflavin and cyclodextrins

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda)

The binding selectivity of the M(phen)(edda) (M = Cu, Co, Ni, Zn; phen = 1,10-phenanthroline, edda = ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(11) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N4O2 octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling. (C) 2008 Elsevier B.V. All rights reserved.

3-(1-Hydroxy-2-phenylprop-2-en-1-yl)phenol

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis and characterization of mono and polymeric cyclopalladated compounds: Crystal and molecular structure of [{Pd(dmba)(ONO2)}(2)(mu-pz)] center dot H2O (pz = pyrazine)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Bronsted Acid Catalyzed Morita-Baylis-Hillman Reaction: A New Mechanistic View for Thioureas Revealed by ESI-MS(/MS) Monitoring and DFT Calculations

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Three-dimensional structure of ribonuclease T-1 complexed with an isosteric phosphonate substrate analogue of GpU: Alternate substrate binding modes and catalysis

The X-ray crystal structure of a complex between ribonuclease T-1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2.0 Angstrom resolution. This Ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. on the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T-1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(S-p)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [:Steyaert, J., and Engleborghs (1995) fur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T-1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.

Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis, Infrared Spectroscopy and Crystal Structure Determination of a New Decavanadate

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Macromolecular properties of cepacian in water and in dimethylsulfoxide

Cepacian is the exopolysaccharide produced by the majority of the so far investigated clinical strains of the Burkholderia cepacia complex. This is a group of nine closely related bacterial species that might cause serious lung infections in cystic fibrosis patients, in some cases leading to death. In this paper the aggregation ability and the conformational properties of cepacian chain were investigated to understand its role in biofilm formation. Viscosity and atomic force microscopy studies in water and in mixed (dimethylsulfoxide/water) solvent indicated the formation of double stranded molecular structures in aqueous solutions. Inter-residue short distances along cepacian chain were investigated by NOE NMR, which showed that two side chains of cepacian were not conformation ally free due to strong interactions with the polymer backbone. These interactions were attributed to hydrogen bonding and contributed to structure rigidity. (c) 2007 Elsevier Ltd. All rights reserved.