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Donor and acceptor atomsDonors and acceptorsAtomsBasicityRotatable BondsLigandsSubstrateMolecularAmideInteractsFluorineComputationalSubstratesHydrophobicCarbonylOrganicExperimentalAtomSynthesisInteractionsMoleculesPairsCompoundsOxygenPolarResiduesGroupsWaterConstantsInteractionStructureStudyPropertiesFormEffectTypesGroupChemical
Donor and acceptor atoms3
  • PyMOL will not properly recognize donor and acceptor atoms if molecular valences are not specified in the input file. (pymol.org)
  • Each of the four different nucleobases are characterized by distinct edge-specific distribution patterns of their respective hydrogen bond donor and acceptor atoms, complementarity with which, in turn, define the hydrogen bonding patterns involved in base pairing. (wikiversity.org)
  • At the same time, the helically twisted backbones in the double helical duplex DNA form two grooves, major and minor, through which the hydrogen bond donor and acceptor atoms corresponding respectively to the Hoogsteen and sugar edges are accessible for additional potential molecular recognition events. (wikiversity.org)
Donors and acceptors2
  • Because of their inability to serve both as hydrogen-bond donors and acceptors, ketones tend not to "self-associate" and are more volatile than alcohols and carboxylic acids of comparable molecular weights. (wikipedia.org)
  • In the design of supramolecular complexes, a well known and effective strategy is the matching of suitable hydrogen bond donors and acceptors (Wuest, 2005). (iucr.org)
Atoms5
  • the N and O atoms act as both donor and acceptor for these inter-actions. (who.int)
  • This is in part because the introduced serines are all within alpha-helices and at congested sites can avoid steric clashes with surrounding atoms by making a hydrogen bond to a backbone carbonyl oxygen in the preceding turn of the helix. (rcsb.org)
  • 3. Possible H-bond acceptors and donators close to the HD1 and NE2 atoms. (lu.se)
  • If the residue is exposed to water it is probably HIP (especially if there is a strong H-bond to one of the atoms), otherewise it is probably neutral, unless it interacts with Asp, Glu, or another negatively charged residue. (lu.se)
  • You should also consider the possibility that the crystallographers have mixed up the ND1 and CD2, and the NE2 and CE1 atoms (can only be decided from the H-bond pattern, not from the electron density). (lu.se)
Basicity2
  • interlocks our study with Laurence's scale of H-bond basicity of organic molecules. (whiterose.ac.uk)
  • Comparison of the GMIPp values is made with two experimental hydrogen-bond scales: i) the hydrogen-bond basicity scale for N-heteroaromatics in carbon tetrachloride, and ii) the hydrogen-bond acidities for NH/OH donors and hydrogen-bond basicities of N/O acceptors determined in 1,1,1-trichloroethane. (irbbarcelona.org)
Rotatable Bonds1
  • Hydroxyl groups also have more rotatable bonds than most commonly used directing groups, making the complexes more flexible,' explains Daniel Strassfeld , a postdoc in the Yu group at The Scripps Research Institute, US. (chemistryworld.com)
Ligands6
  • These measurements allow placement of these fluoride ligands on the scales of organic H-bond acceptor strength. (whiterose.ac.uk)
  • This is most commonly a problem with PDB files that do not contain bond valence information for ligands. (pymol.org)
  • The final project area aims to engineer hydrogen-bond acceptors on ligands of hydrogen-atom transfer catalysts to achieve enantioselective C-H functionalization. (msu.edu)
  • Designer ligands have promoted what the team behind the work believes is the first alcohol-directed activation of unreactive sp 3 C-H bonds. (chemistryworld.com)
  • Directed C-H activation attempts to overcome this by employing existing functionality within the substrate to anchor the metal catalyst close to a particular bond and carefully designed ligands allow chemists to use carbonyl and nitrogen-containing groups to direct the initial metal association interaction. (chemistryworld.com)
  • Using an arylation reaction as a model, they began by systematically screening bidentate ligands containing both a hydrogen-bond acceptor and an internal base. (chemistryworld.com)
Substrate5
  • However, Strassfeld and fellow researcher Chia-Yu Chen hypothesised that by designing a ligand that promotes hydrogen-bonding, they could strengthen and organise the crucial interaction between the alcohol substrate and palladium catalyst. (chemistryworld.com)
  • At the same time, this two-point contact between the substrate and the catalyst restricts bond rotation and holds the complex in a orientation ideal for reaction. (chemistryworld.com)
  • The ligand's internal base simultaneously forms a hydrogen bond with the hydrogen of the target C-H bond, reducing the energy barrier for the activation step and providing a third point of contact between the catalyst and substrate. (chemistryworld.com)
  • Removal of hydrogen-bond acceptor or donor groups in either the ligand or substrate resulted in no reaction whilst DFT modelling confirmed the strongly stabilising influence of the hydrogen-bonding interactions. (chemistryworld.com)
  • Xylose appears to be the optimal acceptor substrate for galactosylation by beta 4GalT7. (lu.se)
Molecular3
  • Calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities). (chemaxon.com)
  • The mol-ecules are linked through O-H⋯O and N-H⋯O hydrogen-bonding inter-actions, forming a three-dimensional supra-molecular network. (iucr.org)
  • Based on enzymatic studies, that is galactosylation and its inhibition, conformational analysis and molecular modeling using the crystal structure, we propose that the binding pocket of beta 4GalT7 is very narrow, with a precise set of important hydrogen bonds. (lu.se)
Amide2
Interacts2
  • Because the carbonyl group interacts with water by hydrogen bonding, ketones are typically more soluble in water than the related methylene compounds. (wikipedia.org)
  • As the palladium weakly coordinates to the hydroxyl oxygen, the hydrogen-bond acceptor interacts with the hydroxyl proton, strengthening the binding of the directing group to the catalyst. (chemistryworld.com)
Fluorine2
  • Dalvit C, Invernizzi C, Vulpetti A. Fluorine as a hydrogen-bond acceptor: experimental evidence and computational calculations. (unine.ch)
  • We show that the presence of fluorine in the GlcNAc acceptor facilitates the formation of longer ß-mannan-like glycans. (bvsalud.org)
Computational2
  • The statistical analysis of the results reveals that the GMIP functional, which combines electrostatic and steric energy components, predicts with reasonable accuracy and computational efficiency the hydrogen-bond strength for a wide variety of compounds. (irbbarcelona.org)
  • Strassfeld and Chen quickly identified promising ligand candidates for a range of benzylic and cyclobutyl substrates and next sought to validate the hydrogen-bonding mechanism using a combination of crystallographic, reactivity and computational studies. (chemistryworld.com)
Substrates2
  • The most obvious next steps are to directly expand on these results in terms of the scope of alcohol substrates and the functionalisation step, including other classes of C-C bond forming reactions and C-heteroatom bond formation. (chemistryworld.com)
  • The biosynthesis can also be initiated by exogenously added beta-D-xylopyranosides with hydrophobic aglycons, which thus can act as acceptor substrates for beta 4GalT7. (lu.se)
Hydrophobic1
  • Both of the models consisted of six features (hydrogen bond acceptors, hydrogen bond donor and hydrophobic feature) besides the exclusion volumes. (helsinki.fi)
Carbonyl3
  • Ketones contain a carbonyl group −C(=O)− (which contains a carbon-oxygen double bond C=O). The simplest ketone is acetone (where R and R' is methyl), with the formula (CH3)2CO. (wikipedia.org)
  • Ketones differ from aldehydes in that the carbonyl group (C=O) is bonded to two carbons within a carbon skeleton. (wikipedia.org)
  • In aldehydes, the carbonyl is bonded to one carbon and one hydrogen and are located at the ends of carbon chains. (wikipedia.org)
Organic3
  • The suitability of the GMIPp energy functional as a fast, efficient method for estimating the hydrogen-bond donor and acceptor propensities of a wide variety of organic compounds is examined. (irbbarcelona.org)
  • Alcohols - organic analog of water Hydrogen bond donor O-Hd+. (powershow.com)
  • C-H functionalisation is one of the most versatile reactions in organic synthesis but the ubiquity and inertness of these bonds make selective transformations incredibly challenging. (chemistryworld.com)
Experimental1
  • Experimental evidences reveal that the nucleotide bases are also capable of forming a wide variety of pairing between bases in various geometries, having hydrogen bonding patterns different from those observed in Canonical Base Pairs (Figure 1). (wikiversity.org)
Atom3
  • The bond angles around the cobalt atom are close to that expected for an ideal octahedron. (iucr.org)
  • so atom 1 and 5, 2 and 1, 3 and 1 are examples of donor/acceptor pairs? (charmm.org)
  • If a nitrogen atom is an acceptor, the other nitrogen must be protonated. (lu.se)
Synthesis2
  • The results revealed that α -lipoic acid mainly interacted with N-vinyl caprolactam (NVCL) by weak hydrogen bonds, and the best conditions for MIP synthesis were an optimum molar ratio of 1 : 4 ( α -lipoic acid/NVCL). (hindawi.com)
  • They also continue to evolve methods for breaking and re-forming bonds during chemical reactions to improve on the synthesis, properties, and performance of existing chemicals and materials. (acs.org)
Interactions3
  • NADES media primarily depends on the intermolecular interactions (hydrogen bonding) among their components to form a eutectic mixture with a much lower final melting point than its individual components. (frontiersin.org)
  • Incorporating hydrogen-bonding interactions into the design strengthened and organised the reactive complex, an approach which could be applied to other catalytic systems. (chemistryworld.com)
  • Their thorough and rational ligand design exploits H-bonding to supplement the weak interactions in the pre-reactive complex and transition state and is validated by well-designed computations. (chemistryworld.com)
Molecules1
Pairs3
  • Non-canonical base pairs are planar hydrogen bonded pairs of nucleobases, having hydrogen bonding patterns which differ from the patterns observed in Watson-Crick base pairs, as in the classic double helical DNA. (wikiversity.org)
  • They involve specific hydrogen bonding patterns corresponding to their respective Watson-Crick edges, and are considered as Canonical Base Pairs. (wikiversity.org)
  • These base pairs, which are generally referred to as Non-Canonical Base Pairs, are held together by multiple hydrogen bonds, and are mostly planar and stable. (wikiversity.org)
Compounds1
  • Chemical bonding enables scientists to take the 100-plus elements of the periodic table and combine them in myriad ways to form chemical compounds and materials. (acs.org)
Oxygen1
  • The main B 1s peak at 190.6 eV evolved into multiple peaks at a higher binding energy position due to oxygen impurities tending to occupy nitrogen sites and form the B-O bond. (osti.gov)
Polar1
  • The results are consistent with the view that many hydrogen bonds within proteins contribute only marginally to stability but that noncharged polar groups that lack a hydrogen-bonding partner are very destabilizing (delta delta G approximately greater than 3 kcal/mol). (rcsb.org)
Residues2
  • The flipped binding mode in 11β-HDS2 enables hydrogen bonds to Ser310 and to Asn171, both residues that are only present in 11β-HSD2. (helsinki.fi)
  • HIP residues are characterised by strong and short hydrogen bonds, often to negatively charged residues. (lu.se)
Groups4
  • which exhibits an extended chain structure assembled by hydrogen bonds between the amine and metal-fluoride groups, confirms this hypothesis. (whiterose.ac.uk)
  • The binding of donor-acceptor Stenhouse adducts (DASAs) bearing hydrogen-bond recognition groups by Hamilton-type receptors significantly influenced their photoswitching properties by altering thermal barriers to isomerization. (chalmers.se)
  • Both, the [OMs] and the [OTf] anions can act as HB acceptors, which can accept multiple HBs via their respective SO 3 -groups. (rsc.org)
  • Both of these mean that hydroxyl directing groups simply aren't very good at directing palladium to the C-H bond we want to activate. (chemistryworld.com)
Water2
  • In the most extreme case, Val 149-->Thr, which is also the most destabilizing variant (delta delta G = 2.8 kcal/mol), a water molecule is incorporated in the mutant structure in order to provide a hydrogen-bonding partner. (rcsb.org)
  • in the second and a hydrogen-bond defect, known as the "gap", case, it is related to the mean water residence time between b-strands D and E.2 The portal and the in the individual intra-cavity hydration sites. (lu.se)
Constants1
  • Time constants of the oxidation process have been determined, revealing that the formation process of the B-O bond is very fast and within minutes in h -BN. (osti.gov)
Interaction1
  • The interaction pair for this hydrogen bond donor feature was not observed in the homology model. (helsinki.fi)
Structure1
  • The results illustrate how a protein structure will adapt in different ways to avoid the presence of an unsatisfied hydrogen bond donor or acceptor. (rcsb.org)
Study1
  • Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. (irbbarcelona.org)
Properties1
  • Metal aqua-ions may act as excellent, readily available hydrogen bond donors with limited acceptor properties. (iucr.org)
Form1
  • These nucleobases can be schematically represented as triangles with one of their vertices linked to the sugar, and the three sides accounting for three edges through which they can form hydrogen bonds with other moieties, including with other nucleobases. (wikiversity.org)
Effect1
  • A striking illustration of this phenomenon can be seen in what has been dubbed the "magic methyl effect", whereby replacing a hydrogen with a methyl group in a complex molecule can dramatically improve the potency of drugs. (msu.edu)
Types1
Group1
  • The polarity of the group 10 metal fluorides indicates their potential as building blocks for hydrogen-bonded assemblies. (whiterose.ac.uk)
Chemical1
  • For some, the work of scientists who spend most of their time thinking about chemical bonding-both the well-seasoned principles and newly discovered aspects-can seem mystifying. (acs.org)