Browse
Submit Data
Databases
API
Help

Dataset Information

3 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

ABSTRACT: In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

SUBMITTER: Karthikeyan A

PROVIDER: S-EPMC4770981 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Supra-molecular hydrogen-bonding patterns in a 1:1 co-crystal of the N(7)-H tautomeric form of <i>N</i><sup>6</sup>-benzoyl-adenine with 4-hy-droxy-benzoic acid.

Project description:The asymmetric unit of the title co-crystal, C12H9N5O·C7H6O3, contains one mol-ecule of N6-benzoyl-adenine (BA) and one mol-ecule of 4-hy-droxy-benzoic acid (HBA). The N6-benzoyl-adenine (BA) has an N(7)-H tautomeric form with nonprotonated N-1 and N-3 atoms. This tautomeric form is stabilized by a typical intra-molecular N-H?O hydrogen bond between the carbonyl (C=O) group and the N(7)-H hydrogen on the Hoogsteen face of the purine ring, forming a graph-set S(7) ring motif. The primary robust R22(8) ring motif is formed in the Watson-Crick face via N-H?O and O-H?N hydrogen bonds (involving N1, N6-H and the carboxyl group of HBA). Weak inter-actions, such as, C-H?? and ?-? are also observed in this crystal structure.

| S-EPMC5347060 | biostudies-literature

Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

Project description:The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.

| S-EPMC4908553 | biostudies-literature

Hydrogen bonding in 1-carb-oxy-propanaminium nitrate.

Project description:There are two crystallographically independent cations and two anions in the asymmetric unit of the title compound, C(4)H(5)NO(2) (+)·NO(3) (-). In the crystal, the 1-carb-oxy-propanaminium cations and nitrate anions are linked to each other through strong N-H?O and O-H?O hydrogen bonds, forming a three-dimensional complex network. C-H?O inter-actions also occur.

| S-EPMC3344452 | biostudies-literature

Mutual Relations between Substituent Effect, Hydrogen Bonding, and Aromaticity in Adenine-Uracil and Adenine-Adenine Base Pairs.

Project description:The electronic structure of substituted molecules is governed, to a significant extent, by the substituent effect (SE). In this paper, SEs in selected nucleic acid base pairs (Watson-Crick, Hoogsteen, adenine-adenine) are analyzed, with special emphasis on their influence on intramolecular interactions, aromaticity, and base pair hydrogen bonding. Quantum chemistry methods-DFT calculations, the natural bond orbital (NBO) approach, the Harmonic Oscillator Model of Aromaticity (HOMA) index, the charge of the substituent active region (cSAR) model, and the quantum theory of atoms in molecules (QTAIM)-are used to compare SEs acting on adenine moiety and H-bonds from various substitution positions. Comparisons of classical SEs in adenine with those observed in para- and meta-substituted benzenes allow for the better interpretation of the obtained results. Hydrogen bond stability and its other characteristics (e.g., covalency) can be significantly changed as a result of the SE, and its consequences are dependent on the substitution position. These changes allow us to investigate specific relations between H-bond parameters, leading to conclusions concerning the nature of hydrogen bonding in adenine dimers-e.g., H-bonds formed by five-membered ring nitrogen acceptor atoms have an inferior, less pronounced covalent nature as compared to those formed by six-membered ring nitrogen. The energies of individual H-bonds (obtained by the NBO method) are analyzed and compared to those predicted by the Espinosa-Molins-Lecomte (EML) model. Moreover, both SE and H-bonds can significantly affect the aromaticity of adenine rings; long-distance SEs on ?-electron delocalization are also documented.

| S-EPMC7464026 | biostudies-literature

Anion control of tautomeric equilibria: Fe-H vs. N-H influenced by NH···F hydrogen bonding.

Project description:Counterions can play an active role in chemical reactivity, modulating reaction pathways, energetics and selectivity. We investigated the tautomeric equilibrium resulting from protonation of Fe(PEtNMePEt)(CO)3 (PEtNMePEt = (Et2PCH2)2NMe) at Fe or N. Protonation of Fe(PEtNMePEt)(CO)3 by [(Et2O)2H]+[B(C6F5)4]- occurs at the metal to give the iron hydride [Fe(PEtNMePEt)(CO)3H]+[B(C6F5)4]-. In contrast, treatment with HBF4·OEt2 gives protonation at the iron and at the pendant amine. Both the FeH and NH tautomers were characterized by single crystal X-ray diffraction. Addition of excess BF4 - to the equilibrium mixture leads to the NH tautomer being exclusively observed, due to NH···F hydrogen bonding. A quantum chemical analysis of the bonding properties of these systems provided a quantification of hydrogen bonding of the NH to BF4 - and to OTf-. Treatment of Fe(PEtNMePEt)(CO)3 with excess HOTf gives a dicationic complex where both the iron and nitrogen are protonated. Isomerization of the dicationic complex was studied by NOESY NMR spectroscopy.

| S-EPMC6369578 | biostudies-literature

A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues.

Project description:Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen-bonding interactions of a COOH group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function theory. For hydrogen-bonding interactions with polar side-chain groups, our results show a strong correlation between the C=O stretching frequency and the hydrogen bond number of a COOH group: approximately 1759-1776 cm(-1) for zero, approximately 1733-1749 cm(-1) for one, and 1703-1710 cm(-1) for two hydrogen bonds. Experimental evidence for this correlation will be discussed. In addition, we show an approximate linear correlation between the C=O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C=O stretching versus O-H stretching, may be employed to identify the specific type of hydrogen-bonding interaction. This vibrational spectral marker for hydrogen-bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins.

| S-EPMC1305378 | biostudies-literature

Role of Hydrogen Bonding in the Formation of Adenine Chains on Cu(110) Surfaces.

Project description:Understanding the adsorption properties of DNA bases on metal surfaces is fundamental for the rational control of surface functionalization leading to the realisation of biocompatible devices for biosensing applications, such as monitoring of particular parameters within bio-organic environments and drug delivery. In this study, the effects of deposition rate and substrate temperature on the adsorption behavior of adenine on Cu(110) surfaces have been investigated using scanning tunneling microscopy (STM) and density functional theory (DFT) modeling, with a focus on the characterization of the morphology of the adsorbed layers. STM results revealed the formation of one-dimensional linear chains and ladder-like chains parallel to the [110] direction, when dosing at a low deposition rate at room temperature, followed by annealing to 490 K. Two mirror related, well-ordered chiral domains oriented at ±55° with respect to the [110] direction are formed upon deposition on a substrate kept at 490 K. The molecular structures observed via STM are rationalized and qualitatively described on the basis of the DFT modeling. The observation of a variety of ad-layer structures influenced by deposition rate and substrate temperature indicates that dynamic processes and hydrogen bonding play an important role in the self-assembly of adenine on the Cu(110) surface.

| S-EPMC5457020 | biostudies-literature

Protonated form: the potent form of potassium-competitive acid blockers.

Project description:Potassium-competitive acid blockers (P-CABs) are highly safe and active drugs targeting H+,K+-ATPase to cure acid-related gastric diseases. In this study, we for the first time investigate the interaction mechanism between the protonated form of P-CABs and human H+,K+-ATPase using homology modeling, molecular docking, molecular dynamics and binding free energy calculation methods. The results explain why P-CABs have higher activities with higher pKa values or at lower pH. With positive charge, the protonated forms of P-CABs have more competitive advantage to block potassium ion into luminal channel and to bind with H+,K+-ATPase via electrostatic interactions. The binding affinity of the protonated form is more favorable than that of the neutral P-CABs. In particular, Asp139 should be a very important binding site for the protonated form of P-CABs through hydrogen bonds and electrostatic interactions. These findings could promote the rational design of novel P-CABs.

| S-EPMC4028304 | biostudies-literature

How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA.

Project description:Bacteriophages have long been known to use modified bases in their DNA to prevent cleavage by the host's restriction endonucleases. Among them, cyanophage S-2L is unique because its genome has all its adenines (A) systematically replaced by 2-aminoadenines (Z). Here, we identify a member of the PrimPol family as the sole possible polymerase of S-2L and we find it can incorporate both A and Z in front of a T. Its crystal structure at 1.5 Å resolution confirms that there is no structural element in the active site that could lead to the rejection of A in front of T. To resolve this contradiction, we show that a nearby gene is a triphosphohydolase specific of dATP (DatZ), that leaves intact all other dNTPs, including dZTP. This explains the absence of A in S-2L genome. Crystal structures of DatZ with various ligands, including one at sub-angstrom resolution, allow to describe its mechanism as a typical two-metal-ion mechanism and to set the stage for its engineering.

| S-EPMC8065100 | biostudies-literature

Hydrogen bonding in the crystal structure of the molecular salt of pyrazole-pyrazolium picrate.

Project description:The asymmetric unit of the title organic salt [systematic name: 1H-pyrazol-2-ium 2,4,6-tri-nitro-phenolate-1H-pyrazole (1/1)], H(C3H4N2)2 (+)·C6H2N3O7 (-), consists of one picrate anion and one hydrogen-bonded dimer of a pyrazolium monocation. The H atom involved in the dimer N-H?N hydrogen bond is disordered over both symmetry-unique pyrazole mol-ecules with occupancies of 0.52?(5) and 0.48?(5). In the crystal, the component ions are linked into chains along [100] by two different bifurcated N-H?(O,O) hydrogen bonds. In addition, weak C-H?O hydrogen bonds link inversion-related chains, forming columns along [100].

| S-EPMC4908572 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data