*  Frontiers | Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the...
Dashed lines indicate hydrogen-bonded atoms. Hydrogen bonds mediated by more than one water molecule are omitted for clarity. C ... This water is hydrogen-bonded to the side chains of Gln161 and Trp162. The reaction leads to the breakage of two covalent bonds ... Firstly, the covalent C-N bond in that case would need to result from a nucleophilic attack of N atom of PUT on the S-bound ... Although CAD is able to interact via hydrogen bond with Glu187 at the entrance of the pocket, similarly to PUT and DHMP, deep ...
  https://www.frontiersin.org/articles/10.3389/fpls.2016.00350/full
*  Structural Biochemistry/Chemical Bonding/Hydrogen bonds - Wikibooks, open books for an open world
... hydrogen atom, and hydrogen-bond acceptor has a straight, linear structure.. H-bonding[edit]. Hydrogen bonding (H-bond) is a ... A hydrogen-bond donor includes the hydrogen atom and the atom to which it is most tightly linked with. The hydrogen-bond also ... The hydrogen atom in a hydrogen bond is shared by two electronegative atoms such as oxygen or nitrogen.) Hydrogen bonds are ... A hydrogen bond is formed by a dipole-dipole force between an electronegative atom (the hydrogen acceptor) and a hydrogen atom ...
  https://en.wikibooks.org/wiki/Structural_Biochemistry/Chemical_Bonding/Hydrogen_bonds
*  Docking Tutorial
... hydrogens are hydrogens that are bonded to electronegative atoms like oxygen and nitrogen. Non-polar hydrogens are hydrogens ... between atoms: C13_6 and N1_20 REMARK 4 A between atoms: C4_13 and N2_21 REMARK 5 A between atoms: C7_16 and C8_17 REMARK 6 A ... between atoms: C1_2 and C7_16 REMARK 2 A between atoms: C10_3 and C11_4 REMARK 3 A between atoms: C12_5 and C13_6 REMARK I ... atom-specific affinity map map 1t64_lock.C.map # atom-specific affinity map map 1t64_lock.HD.map # atom-specific affinity map ...
  https://www.slideshare.net/bcmenv/docking-tutorial
*  IUCr) N,N′-Di-methyl-piperazinium(2+) bis--[methyl-ene-hydrogendi-phospho-nate(1−)]
... with hydrogen bonds shown as dashed lines. H atoms not involved in hydrogen bonding have been omitted.. ... All N-H and O-H groups act as hydrogen-bond donors in the crystal structure, with unproton-ated O atoms as the acceptors, ... All H atoms bonded to N in the cations and to O in the anions were clearly identified in a difference map. The P-O bond lengths ... Hydrogen-bond geometry (Å, º). top. D-H···A. D-H. H···A. D···A. D-H···A. ...
  http://journals.iucr.org/e/issues/2005/08/00/nc6040/index.html
*  IUCr) 1-[4-(4-Iso-propyl-phen-yl)-6-methyl-2-sulfanyl--idene-1,2,3,4-tetra-hydro-pyrimidin-5-yl]ethanone
Dashed lines indicate hydrogen bonds. H atoms not involved in hydrogen bonding have been omitted. ... O hydrogen bond is observed. In the crystal, molecules are linked via N-H⋯O, N-H⋯S and C-H⋯S hydrogen bonds. ... S2 hydrogen bonds are found in the crystal structure. A weak intramolecular C61-H61A···O51 hydrogen bond is also observed (Fig ... H atoms are shown as small spheres of arbitrary radius. Dashed lines indicate the intramolecular C-H···O hydrogen bond. ...
  http://journals.iucr.org/e/issues/2012/09/00/wn2487/index.html
*  Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase | PNAS
11) (19). The N1 atom is hydrogen-bonded to His 55 in TDO. However, our biochemical studies show that the k cat of TDO is ... At the same time, hydrogen-bonding interactions to these atoms may be absent in IDO, because Tyr 113 of TDO is replaced by Phe ... 4 a). The distal oxygen atom (O2) was placed such that the O1-O2 bond is parallel to the C2-C3 bond of indole ring, giving a Fe ... The N1 atom is directly hydrogen-bonded to the His 55 side chain in TDO (Fig. 3 b), and its methylation will cause steric clash ...
  http://www.pnas.org/content/104/2/473
*  Mechanism of Selective Inhibition of Yohimbine and Its Derivatives in Adrenoceptor α2 Subtypes
... hydrogen bonds between oxygen atom 3 and 4 with polar residues Y5.38 and S5.46; (b) nitrogen atom 1 as a hydrogen bond donor ... Blue arrows represent hydrogen bonds formed with backbone atoms; green arrows represent hydrogen bonds formed with side-chain ... The two oxygen atoms form "W" type 4 hydrogen bonds with Tyr5.38, Ser5.42, and Ser5.46, which all locate on TM5. The hydrogen ... 1 nitrogen atom usually forms hydrogen bond with Tyr6.55; thus, it contributes more for the three ligands' affinity on AR α2. ...
  https://www.hindawi.com/journals/jchem/2013/783058/
*  IUCr) Tri-benzyl-ammonium chloride
H atoms not involved in hydrogen bonding were omitted for clarity). Colour code: C dark grey, H light grey, N blue, Cl green. ... Hydrogen-bond geometry (Å, º). top. D-H···A. D-H. H···A. D···A. D-H···A. ... Hydrogen-bond geometry (Å, º) top. D-H···A. D-H. H···A. D···A. D-H···A. ... In the crystal, the chloride anion is linked to the tribenzylammonium cation via N-H···Cl hydrogen bonding (Table 1). In ...
  http://journals.iucr.org/e/issues/2014/05/00/wm5019/index.html
*  Bifurcation - Wikipedia
Bifurcated bonding, in which a single hydrogen atom participates in two hydrogen bonds ...
  https://en.wikipedia.org/wiki/Bifurcation
*  IUCr) 1-[2-(3-Meth--oxy-phen-yl)eth-yl]pyrroli-dine-2,5-dione
Hydrogen bonds are shown as dashed lines (see Table 1 for details; H atoms not involved in hydrogen bonding have been omitted ... hydrogen-bonded chains running along [101] are generated by connecting neighbouring mol-ecules via C-H⋯O hydrogen bonds. ... O hydrogen bonds (Table 1 and Fig. 2). Parallel chains are linked by further C-H···O hydrogen bonds forming a three-dimensional ... Hydrogen-bond geometry (Å, º). top. D-H···A. D-H. H···A. D···A. D-H···A. ...
  http://journals.iucr.org/e/issues/2013/09/00/su2640/index.html
*  IUCr) 3-[(E)-2-(2-Meth--oxy-phen-yl)vin-yl]-5,5-di-methyl-cyclo-hex-2-enone
The hydrogen bonds are shown as dashed lines (see Table 1 for details; H-atoms not involved in hydrogen bonding have been ... Hydrogen-bond geometry (Å, º). top. D-H···A. D-H. H···A. D···A. D-H···A. ... Hydrogen-bond geometry (Å, º) top. D-H···A. D-H. H···A. D···A. D-H···A. ... Secondary atom site location: difference Fourier map. R[F2 > 2σ(F2)] = 0.085. Hydrogen site location: inferred from ...
  http://journals.iucr.org/e/issues/2014/05/00/su2717/index.html
*  IUCr) 3-Ethyl-3-hy-dr-oxy-8-meth--oxy-quinoline-2,4(1H,3H)-dione monohydrate
O hydrogen bonds, and π-π interactions denoted by dashed lines. Hydrogen atoms not involved in hydrogen bonding have been ... The N-bonded hydrogen atom was located in a difference map and refined with the using distance restraint with N-H = 0.86±0.02 Å ... O hydrogen bonds. These connections altogether with additional O-H···O hydrogen bonding between hydroxyl and carbonyl groups ( ... Hydrogen-bond geometry (Å, º). top. D-H···A. D-H. H···A. D···A. D-H···A. ...
  http://journals.iucr.org/e/issues/2012/11/00/tk5162/index.html
*  IUCr) Methyl 4-(benz-yl-oxy)-3-meth--oxy-benzo-ate
The C-H···O hydrogen bonds are shown by dashed lines (see Table 1 for details; H atoms not involved in hydrogen bonding have ... Secondary atom site location: difference Fourier map. R[F2 > 2σ(F2)] = 0.045. Hydrogen site location: inferred from ... Hydrogen-bond geometry (Å, º). top. Cg is the centroid of the C1-C6 ring. ... Hydrogen-bond geometry (Å, º) top. Cg is the centroid of the C1-C6 ring. ...
  http://journals.iucr.org/e/issues/2013/10/00/su2645/index.html
*  IUCr) Poly[[(μ2-4,4′-bi-pyridyl-κ2N:N′)bis--{μ2-N-[2-(2-hy-dr-oxy-benzo-yl)carbamo-thio-yl]acetamidato-κ4O,N,O′:S}bis--(nitrato...
... and intramolecular hydrogen bonds (purple dashed lines). H atoms not involved in hydrogen bonding are omitted. ... An intra-molecular N-H⋯O hydrogen bond occurs. The crystal structure also features N-H⋯O and O-H⋯O hydrogen bonds, leading to ... Hydrogen-bond geometry (Å, º). top. D-H···A. D-H. H···A. D···A. D-H···A. ... Hydrogen-bond geometry (Å, º) top. D-H···A. D-H. H···A. D···A. D-H···A. ...
  http://journals.iucr.org/e/issues/2013/12/00/rz5087/index.html
*  IUCr) Di-ethyl 3,4-di-methyl-thieno[2,3-b]thio-phene-2,5-di-carboxyl-ate
2. View of the packing and hydrogen bonding of (I) down the a axis. H atoms not involved in hydrogen bonds have been omitted ... For bond lengths and bond angles in similar compounds, see: Umadevi et al. (2009. ); Gunasekaran et al. (2009. ); Wang et al. ( ... Secondary atom site location: difference Fourier map. R[F2 > 2σ(F2)] = 0.045. Hydrogen site location: inferred from ... Hydrogen-bond geometry (Å, º). top. Cg2 is the centroid of the S2/C1-C4 ring. ...
  http://journals.iucr.org/e/issues/2012/12/00/tk5168/index.html
*  E)-2-{3-[4-(Diphenyl-amino)styr-yl]-5,5-dimethyl-cyclo-hex-2-enyl-idene}-malono-nitrile
Secondary atom site location: difference Fourier map. R[F2 , 2σ(F2)] = 0.046. Hydrogen site location: inferred from ... The bond lengths of C13-N1 are shorter than the single C-N distance (1.47-1.50 Å) and longer than double C=N bond distance ( ... All H atoms were positioned geometrically, and allowed to ride on their parent atom with C-H = 0.93 (aromatic), 0.96 (methyl) ... Because of long conjugation length, all atoms are roughly coplanar (Kia et al., 2009). However, the cyclohexene group shows an ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2977807/
*  Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations - Baumketner - 2011 - Protein...
A hydrogen bond between nitrogen atom of G457 and Pγ atom of ATP is the hallmark signature of the post-recovery step ... The chemical bonds in water molecules were held constant by the SETTLE42 algorithm. The bonds involving hydrogen atoms in the ... An obvious choice is the distance between hydrogen bonding atoms G457:N and ATP:Pγ. But with only a handful of SWII closing ... 6(b)], the hydrogen bond between G457:N-ATP: Pγ and the salt bridge between R238:Cz-E459:Cδ can dissociate at different times. ...
  http://onlinelibrary.wiley.com/doi/10.1002/pro.737/full?globalMessage=0
*  What Is "protic Solvent"? | Reference.com
Some examples of protic solvents include water, ethanol, methanol, ammonia, formic acid and hydrogen... ... A protic solvent is a solvent containing a hydrogen bonded to an electronegative atom. ... A protic solvent is a solvent containing a hydrogen bonded to an electronegative atom. Some examples of protic solvents include ... Instead, they contain a C=O bond. Examples of aprotic solvents include acetone and ethyl acetate. ...
  https://www.reference.com/science/protic-solvent-ec2d237b47f0b202
*  Patent US7727727 - Pretreatment method for extraction of nucleic acid from biological samples ... - Google Patents
Aprotic solvents do not donate suitable hydrogen atoms to form labile hydrogen bonds with anions. Nucleophilic substitution by ... However, unlike water, the more common polar solvent, aprotic solvents do not ionize to form hydrogen ions, which confers ...
  http://www.google.com/patents/US7727727?dq=7565338
*  Genes | Free Full-Text | Functional Capabilities of the Earliest Peptides and the Emergence of Life | HTML
These functions tend to be performed with the assistance of the main chain CONH atoms rather than the more variable or limited ... side chain atoms of the peptides presumed to exist then. ... The atoms hydrogen bonded to NH groups of the nest are ... Commonly the second NH group points away and is not hydrogen-bonded and the pattern of hydrogen bonding varies somewhat, but in ... Many nests occur as part of other hydrogen-bonded motifs in which the egg atom bound to the nest is a carbonyl oxygen not far ...
  http://www.mdpi.com/2073-4425/2/4/671/htm
*  Automated site-directed drug design : the prediction and observation of ligand point positions at hydrogen-bonding regions on...
These regions would represent positions for hydrogen-bonding acceptor and donor atoms. In this paper the prediction of the ... the position of hydrogen-bonded atoms in methotrexate and NADPH co-crystallized with dihydrofolate reductase, and in ... surveys of experimental data for water-molecule positions in protein crystals and with the positions of hydrogen-bonding atoms ... Automated site-directed drug design : the prediction and observation of ligand point positions at hydrogen-bonding regions on ...
  http://rspb.royalsocietypublishing.org/content/236/1283/115
*  Molsoft L.L.C.: Protein Structure Analysis
Select hydrogen bond atom pairs.. Change the representation of hyrdrogen bonds (e.g. dotted line, spheres, solid line, ... Color hydrogen bond by energy (red strong-->blue weak). Change the representation of hydrogen bond style based on energy or ... Superimpose by 3D strucure using visible atoms, C-Alpha, backbone or heavy atoms. ... Superimpose multiple protein structures by alignment, residue number, exact match and by visible atoms, C-Alpha, backbone or ...
  http://www.molsoft.com/protein_structure_analysis.html
*  Chapter 1: Biological Molecules Flashcards by Anna Calvert | Brainscape
High ratio of energy storing carbon-hydrogen bonds to carbon atoms and so a good source of energy. -Low mass to energy ratio so ... Shape due to hydrogen bonding. Polypeptide chain is twisted into an alpha helix coil or beta pleated sheets. ... High ratio of hydrogen to oxygen atoms, when oxidised they can therefore provide water. ... Chains run parallel to each other and hydrogen bonds add collective strength. -Molecules are grouped to form microfibrils which ...
  https://www.brainscape.com/flashcards/chapter-1-biological-molecules-6630625/packs/10525218