On the differential hydration of various forms of glycine in diluted aqueous solutions: a Monte Carlo study

2012 ◽  
Vol 31 (2) ◽  
pp. 295
Author(s):  
Biljana Bujaroska ◽  
Kiro Stojanoski ◽  
Ljupco Pejov
Keyword(s):  
Monte Carlo ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Hydrogen Bonding Interaction ◽  
Liquid Environment ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Bonding Interaction ◽  
Solvent Molecules

Rigid-body Monte Carlo simulations were carried out to study the differential hydration of zwitterionic and neutral forms of glycine in water. To account for the solute polarization by the rather polar liquid environment, initial geometries were chosen as minima on the MP2/aug-cc-pVTZ potential energy surfaces of neutral and zwitterionic glycine continuously solvated by water, implementing the polarizable continuum model (PCM) within the integral equation formalism (IEFPCM). The dynamically changing hydrogen bonding network between the solute and solvent molecules was analyzed imposing distance, energy and angular distribution-based criteria. It was found that, on average, the zwitterionic form of glycine acts as an acceptor of 4.53 hydrogen bonds, while it plays the role of a proton donor in (on average) 2.73 hydrogen bonds with the solvent water molecules. In particular, we have found out that 2.73 solvent water molecules are involved in hydrogen bonding interaction with the ammonium group, acting as proton-acceptors. This is in excellent agreement with the recent experimental neutron diffraction studies, which have indicated that 3.0 water molecules reside in the vicinity of the NH3+ group of aqueous zwitterionic glycine. Neutral form of aqueous glycine, on the other hand, on average donates protons in 1.63 hydrogen bonds with the solvent water molecules, while at the same time it accepts 2.53 hydrogen bonds from the solvent molecules. The greater charge polarization in the zwitterionic form thus makes it much more exposed to hydrogen bonding interaction in polar medium such as water, which is certainly the main reason of the larger stability of this form of glycine in condensed media.

Synthesis, Characterization and Molecular Structure of 2-Pyridyl-formamide N(4)-Dimethylthiosemicarbazone and Some Five-Coordinated Zinc(II) and Cadmium(II) Complexes

2001 ◽  
Vol 56 (12) ◽  
pp. 1297-1305 ◽  
Author(s):  
Elena Bermejo ◽  
Alfonso Castiñeiras ◽  
Larissa M. Fostiak ◽  
Isabel García ◽  
Antonio L. Llamas-Saiz ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonding ◽  
Sulfur Atom ◽  
Hydrogen Bonding Interaction ◽  
Pyridyl Nitrogen ◽  
Zwitterionic Form ◽  
Anionic Ligand ◽  
Imine Nitrogen ◽  
Thiosemicarbazone Ligand ◽  
Bonding Interaction

AbstractSodium in dry methanol reduces 2-cyanopyridine in the presence of N(4)-dimethylthiosemicarbazide to produce 2-pyridyl-formamide N(4)-dimethylthiosemicarbazone, HAm4DM. Com­plexes with zinc(II) and cadmium(II) of formulae [M(Am4DM)(OAc)]2 and [M(HAm4DM)X2] (M = Zn or Cd, X = Cl, Br or I) have been prepared and characterized by spectro­scopic techniques. In addition, the crystal structures of HAm4DM, [Zn(HAm4DM)Br2], and [Cd(HAm4DM)l2] DMSO have been solved. HAm4DM is in the zwitterionic form with a hydrogen bonding interaction between the iminium hydrogen and the thiolato sulfur atom. Co­ ordination of the neutral thiosemicarbazone ligand is via the pyridyl nitrogen, imine nitrogen and thione sulfur atoms, while the anionic ligand in [M(Am4DM)(OAc)]2 coordinates with the same two nitrogen atoms and a thiolato sulfur atom. The [M(HAm4DM)X2] complexes are 5-coordinate with the tridentate thiosemicarbazone and two halogen ligands approaching a square pyramidal stereochemistry.

scholarly journals Bis(lysine-κ2 N,O)hexa-μ2-oxido-hexaoxidobis(1,10-phenanthroline-κ2 N,N′)dicopper(II)tetravanadium(V) tetrahydrate

IUCrData ◽  
2017 ◽  
Vol 2 (7) ◽  
Author(s):  
Ana Karen Giron-Moreno ◽  
Nancy Lara-Sánchez ◽  
Gabriela Moreno-Martínez ◽  
Cándida Pastor-Ramírez ◽  
Eduardo Sánchez-Lara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Water Molecules ◽  
Formula Unit ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The heterometallic coordination compound [Cu(Lys)(phen)]2V4O12·4H2O (Lys is the amino acid lysine, C6H14N2O2, and phen is 1,10-phenanthroline, C12H8N2) lies across an inversion centre. Two [Cu(Lys)(phen)]2+ units coordinate to the cyclo-vanadate fragment and the formula unit is completed by four solvent water molecules. The lysine ligand is in the zwitterionic form and chelates the CuII atom via the α-NH2 and α-COO− donor groups, while the ∊-NH3 + group is involved in intramolecular hydrogen bonds with the central [V4O12]4− core and with solvent water molecules. In the crystal, N—H...O and O—H...O hydrogen bonds connect the components of the structure to form a three-dimensional network. The crystal structure is further stabilized by π–π interactions involving the phen ligands. The lysine group is disordered over two sets of sites with refined occupancies of 0.534 (11) and 0.466 (11).

Hydrogen bonding in polyamino-polyalcohols: a monohydrated cocrystal of 1,3-diamino-5-azaniumyl-1,3,5-trideoxy-cis-inositol iodide and 1,3,5-triamino-1,3,5-trideoxy-cis-inositol

2014 ◽  
Vol 70 (4) ◽  
pp. 396-399 ◽  
Author(s):  
Christian Neis ◽  
Kaspar Hegetschweiler
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Chair Conformation ◽  
Structural Motif ◽  
Water Molecules ◽  
Intermolecular Hydrogen Bonds ◽  
Solvent Water ◽  
Entire Structure ◽  
Dimensional Network

In the title monohydrated cocrystal, namely 1,3-diamino-5-azaniumyl-1,3,5-trideoxy-cis-inositol iodide–1,3,5-triamino-1,3,5-trideoxy-cis-inositol–water (1/1/1), C6H16N3O3+·I−·C6H15N3O3·H2O, the neutral 1,3,5-triamino-1,3,5-trideoxy-cis-inositol (taci) molecule and the monoprotonated 1,3-diamino-5-azaniumyl-1,3,5-trideoxy-cis-inositol cation (Htaci+) both adopt a chair conformation, with the three O atoms in axial and the three N atoms in equatorial positions. The cation, but not the neutral taci unit, exhibits intramolecular O—H...O hydrogen bonding. The entire structure is stabilized by a complex three-dimensional network of intermolecular hydrogen bonds. The neutral taci entities and the Htaci+cations are each aligned into chains along [001]. In these chains, two O—H...N interactions generate a ten-membered ring as the predominant structural motif. The rings consist of vicinal 2-amino-1-hydroxyethylene units of neighbouring molecules, which are pairedviacentres of inversion. The chains are interconnected into undulating layers parallel to theacplane, and the layers are further held together by O—H...N hydrogen bonds and additional interactions with the iodide counter-anions and solvent water molecules.

scholarly journals Understanding the effects of vicinal carbon substituents and configuration on organofluorine hydrogen-bonding interaction

RSC Advances ◽  
2018 ◽  
Vol 8 (68) ◽  
pp. 38980-38986 ◽  
Author(s):  
Qingqing Jia ◽  
Qingzhong Li ◽  
Mo Luo ◽  
Hai-Bei Li
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Hydrogen Bonding Interaction ◽  
Bonding Interaction

The vicinal substituents, with gauche/stagger isomer in CH2XCH2F and cis/trans isomer in CHXCHF, affect the interaction of C(spn)–F⋯H–O organofluorine hydrogen bonds differently.

Three anilides of 2,2′-thiodibenzoic acid

2012 ◽  
Vol 68 (10) ◽  
pp. o387-o391 ◽  
Author(s):  
Madeleine Helliwell ◽  
Salma Moosun ◽  
Minu G. Bhowon ◽  
Sabina Jhaumeer-Laulloo ◽  
John A. Joule
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Hydrogen Bonding Interaction ◽  
Bonding Interaction

The structures ofN,N′-bis(2-methylphenyl)-2,2′-thiodibenzamide, C28H24N2O2S, (Ia),N,N′-bis(2-ethylphenyl)-2,2′-thiodibenzamide, C30H28N2O2S, (Ib), andN,N′-bis(2-bromophenyl)-2,2′-thiodibenzamide, C26H18Br2N2O2S, (Ic), are compared with each other. For the 19 atoms of the consistent thiodibenzamide core, the r.m.s. deviations of the molecules in pairs are 0.29, 0.90 and 0.80 Å for (Ia)/(Ib), (Ia)/(Ic) and (Ib)/(Ic), respectively. The conformations of the central parts of molecules (Ia) and (Ib) are similar due to an intramolecular N—H...O hydrogen-bonding interaction. The molecules of (Ia) are further linked into infinite chains along thecaxis by intermolecular N—H...O interactions, whereas the molecules of (Ib) are linked into chains alongbby an intermolecular N—H...π contact. The conformation of (Ic) is quite different from those of (Ia) and (Ib), since there is no intramolecular N—H...O hydrogen bond, but instead there is a possible intramolecular N—H...Br hydrogen bond. The molecules are linked into chains alongcby intermolecular N—H...O hydrogen bonds.

scholarly journals Three-dimensional hydrogen-bonded structures in the hydrated proton-transfer salts of isonipecotamide with the dicarboxylic oxalic and adipic acid homologues

2013 ◽  
Vol 69 (10) ◽  
pp. 1192-1195
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Adipic Acid ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Solvent Water ◽  
Hydrated Proton ◽  
Hydrogen Bonded

The structures of the 1:1 hydrated proton-transfer compounds of isonipecotamide (piperidine-4-carboxamide) with oxalic acid, 4-carbamoylpiperidinium hydrogen oxalate dihydrate, C6H13N2O+·C2HO4−·2H2O, (I), and with adipic acid, bis(4-carbamoylpiperidinium) adipate dihydrate, 2C6H13N2O+·C6H8O42−·2H2O, (II), are three-dimensional hydrogen-bonded constructs involving several different types of enlarged water-bridged cyclic associations. In the structure of (I), the oxalate monoanions give head-to-tail carboxylic acid O—H...Ocarboxylhydrogen-bonding interactions, formingC(5) chain substructures which extend alonga. The isonipecotamide cations also give parallel chain substructures through amide N—H...O hydrogen bonds, the chains being linked acrossband downcby alternating water bridges involving both carboxyl and amide O-atom acceptors and amide and piperidinium N—H...Ocarboxylhydrogen bonds, generating cyclicR43(10) andR32(11) motifs. In the structure of (II), the asymmetric unit comprises a piperidinium cation, half an adipate dianion, which lies across a crystallographic inversion centre, and a solvent water molecule. In the crystal structure, the two inversion-related cations are interlinked through the two water molecules, which act as acceptors in dual amide N—H...Owaterhydrogen bonds, to give a cyclicR42(8) association which is conjoined with anR44(12) motif. Further N—H...Owater, water O—H...Oamideand piperidinium N—H...Ocarboxylhydrogen bonds give the overall three-dimensional structure. The structures reported here further demonstrate the utility of the isonipecotamide cation as a synthon for the generation of stable hydrogen-bonded structures. The presence of solvent water molecules in these structures is largely responsible for the non-occurrence of the common hydrogen-bonded amide–amide dimer, promoting instead various expanded cyclic hydrogen-bonding motifs.

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