O2 Hydrogen Bonds Research Articles

Hydrogen bonding and aromaticity in the guanine–cytosine base pair interacting with metal cations (M = Cu+, Ca2+ and Cu2+)§

The influence of metal cations (M = Cu+, Ca2+ and Cu2+) coordinated to the N7 of guanine on hydrogen bonding and aromaticity of the guanine–cytosine base pair has been analysed with the help of delocalization indices using the B3LYP functional. Our analysis shows that the strengthening of the N1···N3 and N2···O2 hydrogen bonds and the weakening of the O6···N4 hydrogen bond is mainly caused by the modification of donor–acceptor (covalent) interactions rather than to a significant change of electrostatic interactions. On the other hand, the increase of the aromaticity of the guanine and cytosine six-membered rings because of the interaction with Cu+ and Ca2+ is attributed to the strengthening of hydrogen bonding in the guanine–cytosine pair. The observed reduction of aromaticity in the five- and six-membered rings of guanine due to ionization or interaction with Cu2+ is caused by the oxidation process that removes a π electron disrupting the π electron distribution.

Conformational investigation of ?,?-dehydropeptides.N-acetyl-(E)-dehydrophenylalanineN?-methylamide: conformational properties from infrared and theoretical studies, part XIV

N-Acetyl-(E)-dehydrophenylalanine N'-methylamide [Ac-(E)-DeltaPhe-NHMe], one of a few representative (E)-alpha,beta-dehydroamino acids, was studied by FTIR in dichloromethane and acetonitrile. To support spectroscopic interpretations and to gain some deeper insight into the Ac-(E)-DeltaPhe-NHMe molecule, the Ramachandran potential energy surface was calculated by the B3LYP/6-31G*//HF/3-21G method and the conformers localized were fully optimized at the B3LYP/6-31 + G** level. The spectra and calculations were compared with those of the related molecules Ac-DeltaAla-NHMe and Ac-(Z)-DeltaPhe-NHMe. The title compound assumes two conformational states in equilibrium in dichloromethane solution with a predominance of the extended conformer E. The Ac-(E)-DeltaPhe-NHMe spectrum is like that of Ac-DeltaAla-NHMe, particularly in the region of bands AI and AII, and unlike that of Ac-(Z)-DeltaPhe-NHMe. The positions of bands AI and II together with the nu(s)(N1--H1) band proves that the conformers E of both DeltaAla and (E)-DeltaPhe compounds are stabilized by the quite strong C5 hydrogen bonds N1--H1...O2. The same conclusion is drawn from the Ramachandran diagrams. The conformers E of both compounds are placed in the global minima and the gaps in energy order between them and the second conformer are large. The conformers E of DeltaAla and (E)-DeltaPhe, apart from the N1--H1...O2 hydrogen bond, show the Cbeta--H...O1 interaction, and Ac-(E)-DeltaPhe-NHMe displays the NH/pi interaction with the N2--H2 projecting in the first carbon atom of the phenyl ring. The C5 hydrogen bond is stronger in (E)-DeltaPhe than that in the DeltaAla compound. This is in agreement with interactions found in the calculated structures and can be explained by the influence of the phenyl ring in position (E). In acetonitrile, the molecule of Ac-(E)-DeltaPhe-NHMe loses its C5 hydrogen bond and becomes unfolded, whereas that of Ac-DeltaAla-NHMe does not vary practically. Adopting conformation E in a non-polar solvent seems to be a general feature of the (E)-DeltaXaa residues.

Crystal Structures ofβ-Cyclodextrin Complexes with Formic Acid and Acetic Acid

β-Cyclodextrin (β–CD)-formic acid (1) andβ-CD–acetic acid (2) inclusion complexes crystallizeas β-CD...0.3HCOOH...7.7H2O andβ-CD...0.4CH3COOH...7.7H2O in themonoclinic space group P21 with comparable unit cell constants.Anisotropic refinement of atomic parameters against X-ray diffractiondata with Fo2 > 2σ (Fo2) (986/8563 and 991/8358)converged at R-factors of 0.051 and 0.054 for 1 and 2,respectively. In both complexes, the β-CD molecularconformation, hydration pattern and crystal packing are similar,but the inclusion geometries of the guest molecules are different.The β-CD macrocycles adopt a ``round'' conformationstabilized by intramolecular, interglucose O3(n)...O2(n + 1)hydrogen bonds and their O6–H groups are systematically hydratedby water molecules. In the asymmetric unit, each complex contains oneβ-CD, 0.3 formic acid (or 0.4 acetic acid), and 7.7 water moleculesthat are distributed over 9 positions. Water sites located in theβ-CD cavity hydrogen bond to the guest molecule. In thecrystal lattice, β-CD molecules are packed in a typical ``herringbone'' fashion. In 1, the formic acid (occupancy 0.3) is entirely included in the β-CD cavity such that its C atom is shifted from the O4-plane center to the β-CD O6-side by 2.90 A and C=O, C–-O bonds point to this side. In 2, the acetic acid (occupancy 0.4) is completely embedded in the β-CD cavity, in which the carboxylic C atom is displaced from the O4-plane centerto the β-CD O6-side by 0.87 A; the C=O bond directsto the β-CD O6-side and makes an angle of 15°to the β-CD molecular axis. Furthermore, bothdimethyl-β-CD-acetic acid and β-CD-acetic acidcomplexes form a cage structure, showing that the small guestsenclosed entirely in the cavity either in β-CD or indimethyl-β-CD do not affect the packing of the host macrocycles.

Structural Insights into the Effect of Hydration and Ions on A-Tract DNA: A Molecular Dynamics Study

DNA structure is known to be sensitive to hydration and ionic environment. To explore the dynamics, hydration, and ion binding features of A-tract sequences, a 7-ns Molecular dynamics (MD) study has been performed on the dodecamer d(CGCAAATTTGCG)2. The results suggest that the intrusion of Na+ ion into the minor groove is a rare event and the structure of this dodecamer is not very sensitive to the location of the sodium ions. The prolonged MD simulation successfully leads to the formation of sequence dependent hydration patterns in the minor groove, often called spine of hydration near the A-rich region and ribbon of hydration near the GC regions. Such sequence dependent differences in the hydration patterns have been seen earlier in the high resolution crystal structure of the Drew-Dickerson sequence, but not reported for the medium resolution structures (2.0∼ 3.0Å). Several water molecules are also seen in the major groove of the MD simulated structure, though they are not highly ordered over the extended MD. The characteristic narrowing of the minor groove in the A-tract region is seen to precede the formation of the spine of hydration. Finally, the occurrence of cross-strand C2H2…O2 hydrogen bonds in the minor groove of A-tract sequences is confirmed. These are found to occur even before the narrowing of the minor groove, indicating that such interactions are an intrinsic feature of A-tract sequences.

Contribution of Opening and Bending Dynamics to Specific Recognition of DNA Damage

Guanine-uracil (G·U) wobble base-pairs are a detrimental lesion in DNA. Previous investigations have shown that such wobble base-pairs are more prone to base-opening than the normal G·C base-pairs. To investigate the sequence-dependence of base-pair opening we have performed 5 ns molecular dynamics simulations on G·U wobble base-pairs in two different sequence contexts, TGT/AUA and CGC/GUG. Furthermore, we have investigated the effect of replacing the guanine base in each sequence with a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Our results indicate that each sequence opens spontaneously towards the major groove in the course of the simulations. The TGT/AUA sequence has a greater proportion of structures in the open state than the CGC/GUG sequence. Incorporation of 6MI yields wobble base-pairs that open more readily than their guanine counterparts. In order of increasing open population, the sequences are ordered as CGC<TGT<CMC<TMT, where M represents 6MI. Both members of the base-pair open towards the major groove in a symmetrically coupled motion. Opening results in breakage of the H3(U)–O6(G/6MI) hydrogen bond, and distortion of the H1(G/6MI)–O2(U) hydrogen bond. Structural consequences of the opening include the formation of the H21(G/6MI)–O2(U) hydrogen bond and a change in local solvation in the grooves and particularly near N3–H3 of uracil. Additionally, DNA flexibility is reduced in the open state for bending towards the major groove generating two nearly discrete states: closed unbent and open bent. The observed differences in the local structural and dynamical properties of the G·U base-pair may play an important role in the activity of DNA repair enzymes that initiate base excision by distorting the DNA and flipping the target base from inside the DNA helix.

Methyl 2-O-beta-D-glucopyranosyl-alpha-L-rhamnopyranoside.

The overall conformation of the title compound, C(13)H(24)O(10), is described by the glycosidic torsion angles phi(H) (H1(g)[bond]C1(g)[bond]O2(r)[bond]C2(r)) and psi(H) (C1(g)[bond]O2(r)[bond]C2(r)[bond]H2(r)), which have values of 13.6 and 16.1 degrees, respectively. The former is significantly different from the value predicted by consideration of the exo-anomeric effect (phi(H) approximately 60 degrees ) and from that in solution (phi(H) approximately 50 degrees ), as determined previously by NMR spectroscopy. An intramolecular O3(r)[bond]H...O2(g) hydrogen bond may help to stabilize the conformation in the solid state. The orientation of the hydroxymethyl group of the glucose residue is gauche-gauche, with a torsion angle omega (O5(g)[bond]C5(g)[bond]C6(g)[bond]O6(g)) of -70.4 (4) degrees. Both pyranose rings are in their expected chair conformations, i.e. (4)C(1) for D-glucose and (1)C(4) for L-rhamnose.

Revised molecular structure and vibrational spectra of tetraaqua(orotato)nickel(II) monohydrate: band assignment based on density functional calculations

The crystal and molecular structure and vibrational spectra of [Ni(orotato)(H2O)4]·H2O have been reinvestigated. Single crystal X-ray diffraction studies have revealed new structural features. It is shown that two uracilate rings from the orotate ligands are linked through the pair of N3–H3⋯O2 (−x+1, −y, −z+1) hydrogen bonds which lead to the formation of centrosymmetric dimer of the title complex in the crystal unit cell. The nickel atom is bound to the deprotonated N1 pyrimidine atom and to the carboxylate oxygen atom of the orotate ligand, and to four water molecules. The lattice water molecule is involved in hydrogen bond to the coordinated water molecule, and not to the N3H group, as previously reported. The Raman and infrared spectra (4000–50cm−1) of the title complex are presented, for the first time. The theoretical frequencies, infrared intensities and Raman scattering activities have been calculated by the second-order Möller–Plesset and density functional (B3LYP) methods with the LanL2DZ and D95V∗∗/LanL2DZ basis sets, respectively. The B3LYP-predicted infrared and Raman spectra show a very good agreement with experiment. Detailed band assignment has been made on the basis of the calculated potential energy distribution (PED). The results provide new information on the strength of nickel–ligand bonding in this complex. The Ni–N1(pyrimidine) stretching vibration is assigned to the strong Raman band at 256cm−1, and the Ni–O(carboxylate) stretching vibration is assigned at 357cm−1. It is demonstrated that B3LYP method is extremely helpful in the reliable assignment of vibrational spectra of the Ni(II) complex with orotic acid.

Crystal engineering in the gem-alkynol family: the key role of water in the structure of 2,3,5,6-tetrabromo-trans-1,4-diethynyl-cyclohexa-2,5-diene-1,4-diol dihydrate determined by X-ray and neutron diffraction at 150 K.

The structure of the title compound has been determined using low-temperature (150 K) single-crystal X-ray and neutron diffraction data. Crystals adopt the uncommon space group P4(2)/ncm and display a complex set of intermolecular interactions in which the water molecules play the crucial role: the water O-atom [O2(w)] accepts two hydrogen bonds and both water H atoms act as bifurcated donors. A set of O--H...O hydrogen bonds is formed around the 4(2) axis comprising (a) a cyclic tetrameric synthon involving four donor-H from two water molecules and two O(hydroxy) acceptors from two parent molecules, and (b) short discrete O(hydroxy)--H...O2(w) hydrogen bonds which link these tetramers along the c axis. Four Br...Br interactions [3.708 (1) A] form cyclic Br(4) tetramers around the 4 axis and are linked to the O--H...O system via O2(w)--H...Br bonds with H...Br = 2.995 (2) A. Finally, the O--H...O system is further linked to the parent molecules via C identical with C...H...O2(w) bonds of 2.354 (3) A. The supramolecular structure of the title hydrate is compared with that of the non-hydrated parent molecule, which also forms cyclic O--H...O bonded tetrameric synthons, and with its (non-hydrated) tetrachloro analogue, which forms cyclic tetrameric Cl(4) synthons [Madhavi, Desiraju et al. (2000b). Acta Cryst. B56, 1063--1070].

C-H..O hydrogen bonds in minor groove of A-tracts in DNA double helices

Analysis of available B-DNA type oligomeric crystal structures as well as protein-bound DNA fragments (solved using data with resolution <2.6 Å) indicates that in both data sets, a majority of the (3′-Ade) H2..O2(3′-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance. Since the electropositive C2-H2 group of adenine is in close proximity of the electronegative keto oxygen atoms of both pyrimidine bases in the antiparallel strand of the double-helical DNA structures, it suggests the possibility of intra-base-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within the A.T base-pairs could be a natural consequence of Watson-Crick pairing. However, the close cross-strand interactions between the bases at the 3′-ends of the AA.TT and GA.TC steps arise due to the local sequence-dependent geometry of these steps. While the base-pair propeller twist in these steps is comparable to the fibre model, some of the other local parameters such as base-pair opening angle and inter-base-pair slide show coordinated changes, leading to these shorter C2-H2..O2 distances. Hence, in addition to the well-known minor groove hydration, it appears that favourable C2-H2..O2 cross-strand interactions may play a role in imparting a characteristic geometry to AA.TT and GA.TC steps, as well as A n . T n and GA n . T n C tracts, which leads to a narrow minor groove in these regions.

Three-centre C-H---O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures.

AA.TT and GA.TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 A) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA.TT and GA.TC steps the electropositive C2-H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C-H---O hydrogen bonds in the DNA minor groove. The C2--H2---O2 hydrogen bonds in the A.T base pairs could be a natural consequence of Watson-Crick pairing. However, the cross-strand interactions between the bases at the 3'-end of the AA.TT and GA.TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2---O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 A) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A.T base pairs and the hydration of the minor groove, these C2-H---O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA).poly(dT).

Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.

Uracil phosphoribosyltransferase (UPRTase) catalyzes the transfer of a ribosyl phosphate group from alpha-D-5-phosphoribosyl-1-pyrophosphate to the N1 nitrogen of uracil. The UPRTase from the opportunistic pathogen Toxoplasma gondii is a rational target for antiparasitic drug design. To aid in structure-based drug design studies against toxoplasmosis, the crystal structures of the T.gondii apo UPRTase (1.93 A resolution), the UPRTase bound to its substrate, uracil (2.2 A resolution), its product, UMP (2.5 A resolution), and the prodrug, 5-fluorouracil (2.3 A resolution), have been determined. These structures reveal that UPRTase recognizes uracil through polypeptide backbone hydrogen bonds to the uracil exocyclic O2 and endocyclic N3 atoms and a backbone-water-exocyclic O4 oxygen hydrogen bond. This stereochemical arrangement and the architecture of the uracil-binding pocket reveal why cytosine and pyrimidines with exocyclic substituents at ring position 5 larger than fluorine, including thymine, cannot bind to the enzyme. Strikingly, the T. gondii UPRTase contains a 22 residue insertion within the conserved PRTase fold that forms an extended antiparallel beta-arm. Leu92, at the tip of this arm, functions to cap the active site of its dimer mate, thereby inhibiting the escape of the substrate-binding water molecule.

Structure of methyl 2'-acetoxy-6'-tert-butyl-2-hydroxy-1,1'-binaphthalene-3-carboxylate, C28H26O5

An intramolecular O1-HO1...O2 hydrogen bond is observed in the crystal structure of the title compound. The dihedral angle between the two naphthalene ring systems is 86.34 (3) o . The carbonyl group of the 2'-acetoxy fragment is oriented on the opposite side of the Cl'-C10' aromatic ring plane to the C2-O2 hydroxy fragment; the C2'-O1'-C11'-O2' torsion angle is -7.6 (3) o

The Crystal and Molecular Structure of Butorphanol Hydrogen Tartrate

The structure of butorphanol hydrogen tartrate {(9R,13S,14S)-(-)-17-(cyclobutylmethyl)morphinan-3,14-diol (2S,3S)-(-)-hydrogen tartrate} (C21H29NO2 .C4H6O6) was solved by direct methods and refined anisotropically to the R value of 0.029 for 2 069 observed reflections. The title morphine analogue crystallizes in the triclinic space group P1 with lattice parameters a = 7.620(1), b = 9.140(1), c = 9.591(1) Å, α = 105.48(1), β = 112.91(1), γ = 84.29(1)°, Z = 1. The butorphanol B ring possesses the 3E envelope conformation with small 3H2 distortion, C and D rings have a regular chair conformation. The intramolecular N17-H17...O2 hydrogen bond is observed in crystal structure of the title compound. The butorphanol and hydrogen tartrate molecules are joined together by means of O2-H(O2)...O7, O1-H(O1)...O7' and O3-H(O3)...O8" hydrogen bonds to form networks.

Structure and conformation of 5-bromo-2',3'-dideoxyuridine

C9H11BrN2O4, Mr = 291.11, monoclinic, P2(1), a = 11.307 (1), b = 5.954 (1), c = 15.829 (2) A, beta = 93.25 (1) degree, V = 1063.90 A3, Z = 4, Dx = 1.82 g cm-3, lambda(Cu K alpha) = 1.54184 A, mu = 53.58 cm-1, F(000) = 584, T = 295 K, R = 0.034 for 1927 observed reflections [I greater than 3 sigma(I)]. The crystal structure contains two independent molecules forming a dimer linked by a pair of N3--H...O2 hydrogen bonds; the crystal structure is stabilized by four additional hydrogen bonds. Two of these are internal C6--H6...O5' hydrogen bonds, one in molecule A and another in molecule B. These two molecules exhibit two different conformations; their sugar ring puckers are 2'-endo-3'-exo for molecule A and 3'-endo-2'-exo for molecule B. The Cl'--N1 distance, the chi CN torsion angle and the glycosidic conformation are 1.464 (8) A, -130.0 degrees and -anticlinal for molecule A and 1.506 (8) A, -168.9 degrees and -antiperiplanar for molecule B, respectively.

1 7O NQR study of the antiferroelectric phase transition in TlH2PO4

The temperature dependence of the 17O NQR spectra in TlH2PO4 has been measured using a proton-17 O nuclear quadrupole double resonance technique. The results show that the protons in the short one-dimensionally linked O1–H1--O1 and O2–H2--O2 hydrogen bonds are moving between two equilibrium sites above Tc and freeze into one of the off-center sites below Tc. The protons in the asymmetric O3–H3--O4 hydrogen bonds are static and ordered above and below Tc.

Energy of planar autoassociation of xanthine and spatial structure of poly(riboxanthylic acid)

AbstractFirst‐ and second‐order perturbation theory in a polarization approximation was employed to calculate interaction energies of planar xanthine–xanthine pairs in stable configurations. Electrostatic energy was obtained in the atomic‐dipole approximation. The results provided a basis for formulation of a four‐stranded model of poly(xanthylic acid) that allows two hydrogen bonds per base. The model accounts satisfactorily for the unusual thermal stability and the observed pH transition of the polymer. The latter is due to the gradual dissociation of the N3 protons accompanying by disrupture of the weak N3H ··· O6 hydrogen bonds. However, the structure is only moderately weakened since the configuration of the coplanar bases remains stabilized by four N1H ··· O2 hydrogen bonds.