• 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)
  • The driving force for reversible solid transitions appears to be the formation of hydrogen bonds between the guest and an unsatisfied hydrogen bond acceptor, which is a lone pair of the urea oxygen. (unair.ac.id)
  • The Hydrogen Bond Donor-Acceptor (HBDA) calculates atomic hydrogen bond donor and acceptor inclination. (chemaxon.com)
  • For more information regarding this plugin, see Hydrogen Bond Donor-Acceptor Plugin . (chemaxon.com)
  • Calculates molecular hydrogen bond acceptor multiplicity (the sum of atomic multiplicities). (chemaxon.com)
  • Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. (irbbarcelona.org)
  • 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)
  • Herein, we report a new donor-acceptor system for photo-induced proton-coupled electron transfer (PCET) that leverages an azo linkage as the proton-sensitive component and anthracene as a photo-trigger. (rsc.org)
  • Metal aqua-ions may act as excellent, readily available hydrogen bond donors with limited acceptor properties. (iucr.org)
  • Which column in the psf specifies donor/acceptor status? (charmm.org)
  • so in the example below, one always read along a row with a donor index followed by an acceptor index, donor then acceptor kind of fashion. (charmm.org)
  • so atom 1 and 5, 2 and 1, 3 and 1 are examples of donor/acceptor pairs? (charmm.org)
  • Add DONOr and ACCEptor statements as needed to your RTF and regenerate the PSF - do not play directly with the PSF. (charmm.org)
  • A) Types of hydrogen bonds depending on donor-acceptor distance. (vectorsjournal.org)
  • 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)
  • The most important features considering the 11β-HSD2 selectivity seem to be the hydrogen bond acceptor feature that could interact with the Ser310 and the hydrogen bond donor feature next to it. (helsinki.fi)
  • We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. (bvsalud.org)
  • 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)
  • In these cases, catalysis with hydrogen-bond donors is an attractive strategy since the anionic tetrahedral intermediates are better hydrogen-bond acceptors than the starting compound. (wikipedia.org)
  • Electron bifurcation moves electrons from a two-electron donor to reduce two spatially separated one-electron acceptors. (rsc.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)
  • C and G pair well together because their hydrogen bond donors and acceptors fit together almost like a puzzle piece. (khanacademy.org)
  • Both of the models consisted of six features (hydrogen bond acceptors, hydrogen bond donor and hydrophobic feature) besides the exclusion volumes. (helsinki.fi)
  • Reactions in which electrons tunnel long distances from donors (D) to acceptors (A) pervade solid-state physics, chemistry and biology. (aps.org)
  • In biological systems, hydrogen bonding plays a key role in many enzymatic reactions, both in orienting the substrate molecules and lowering barriers to reaction. (wikipedia.org)
  • However, high dilutions with water can result in a disruption of the supramolecular structure of NADES as water molecules will compete with NADES components for hydrogen bonding. (frontiersin.org)
  • Squaramide (pictured) and its derivatives are rigid planar molecules used as strong hydrogen-bond donors. (chemistryviews.org)
  • Rates of electron-proton transfer within the H-bonded exciplexes are evaluated using the free energy correlation with donor's H-bonding acidity. (rsc.org)
  • 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)
  • In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp2 atoms of amides, aromatics, and other groups occur in protein self-assembly processes including folding, oligomerization, and condensate formation. (bvsalud.org)
  • Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp2O with amide sp2N unified atoms (presumably Câ O···H-N hydrogen bonds) and amide/aromatic sp2C (lone pair π, n-π*) are particularly favorable. (bvsalud.org)
  • These findings are relevant for interactions involving π-bonded sp2 atoms in protein processes. (bvsalud.org)
  • This structure provides CPEs with interacting driving forces of conjugated polymers (pi-pi stacking and hydrophobic interactions) and of polyelectrolytes, such as coordination through electrostatic forces and hydrogen bonding (H-bonding). (utupub.fi)
  • Therefore, the formally negative oxygen engages in a much stronger hydrogen bond than the starting carbonyl oxygen because of its increased negative charge. (wikipedia.org)
  • Hydrogen-bond catalysis is a type of organocatalysis that relies on use of hydrogen bonding interactions to accelerate and control organic reactions. (wikipedia.org)
  • New reactions catalyzed by hydrogen-bond donors are being discovered at an increasing pace, including asymmetric variants of common organic reactions useful for synthesis, such as aldol additions, Diels-Alder cycloadditions and Mannich reactions. (wikipedia.org)
  • Alcohols - organic analog of water Hydrogen bond donor O-Hd+. (powershow.com)
  • Organic decomposition of sulfur compounds in sewers, barns, liquid manure pits, ships' holds, and sulfur springs also produces hydrogen sulfide. (medscape.com)
  • 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)
  • The team attributes this to hydrogen-bond interactions between lactose and the squaramide derivative. (chemistryviews.org)
  • Hydrogen-bonding catalysts are often simple to make, relatively robust, and can be synthesized in high enantiomeric purity. (wikipedia.org)
  • Concepts for the thermodynamically challenging synthesis of weak N-H bonds by photoinduced proton coupled electron transfer are explored. (rsc.org)
  • In these cases, hydrogen sulfide is created by mixing household chemicals (eg, an acidic detergent such as a toilet bowl cleaner, which acts as a proton donor, and a sulfur source such as a pesticide or bath salts), leading to the terms detergent suicide and chemical suicide. (medscape.com)
  • In all cases, the close association of the catalyst molecule to substrate also makes hydrogen-bond catalysis a powerful method of inducing enantioselectivity. (wikipedia.org)
  • Also, a pyrimidine is always H bonded to a purine so that the diameter/width of the DNA molecule is consistent throughout the molecule. (khanacademy.org)
  • 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)
  • Halogen bonding with the electrophilic iodide in pentafluoroiodobenzene can also drive absorption by the host to give a well-ordered host:guest complex. (unair.ac.id)
  • Before removing cruft from old hydrogen/halogen-bond code. (github.com)
  • 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)
  • Poor coupling across nonbonded interfaces produces a strong bias in favor of covalent and hydrogen-bonded pathways between redox sites in proteins. (aps.org)
  • 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)
  • 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)
  • 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)
  • The fundamental, overtone and combination bands involving the donor OH libration and stretching motions were observed in order to extract relevant anharmonicity constants. (goettingen-research-online.de)
  • 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)
  • Hydrogen sulfide forms a complex bond to the ferric moiety causing inhibition of mitochondrial cytochrome oxidase (iron-containing protein), thereby arresting aerobic metabolism in an effect similar to cyanide toxicity. (medscape.com)
  • Catalytic amounts of hydrogen-bond donors can promote reactions through a variety of different mechanisms. (wikipedia.org)
  • With more detailed studies of structure and mechanism in the future, hydrogen-bond catalysis has great potential for enabling new, efficient, selective reactions and promising applications in asymmetric synthesis. (wikipedia.org)
  • 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)
  • There is a clear difference in both C-N bond distances in the pyrazoline ring: N1=C5 shows double-bond character [1.287 (3) Å] while N2-C3 [1.496 (3) Å] is a single bond. (iucr.org)
  • The coordination polyhedron of the Co atom is that of an elongated octahedron defined by an O 6 donor set. (iucr.org)
  • Compstatin (SEQ ID NO:2), a 13-residue peptide, circularized by disulfide bond (Cys-2-Cys-12), displays an inhibitory activity of IC 50 =12 μM. (justia.com)
  • This tactic, however, has been hampered by insufficient methods to introduce thioamide bonds into peptide or protein backbones in a site-specific and stereo-retentive fashion. (bvsalud.org)
  • The coupling disparity between bonded and nonbonded interfaces accounts in large part for the finding that protein electron-transfer rates do not exhibit a uniform dependence on distance, but instead depend critically on the composition of the medium between redox sites. (aps.org)
  • just by looking at the site of H-bonding, can't we say that G can bond with both A and T as they both have three sites where H- bonding can happen? (khanacademy.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)
  • Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. (bvsalud.org)
  • Besides these properties, the isothiouronium cationic functionality in the CITs under study, gives them enhanced hydrogen-bonding (H-bonding) donor capabilities. (utupub.fi)
  • Hydrogen sulfide (H 2 S) is a colorless, flammable gas that has strong odor of rotten eggs. (medscape.com)
  • In the crystal structure, the mol-ecules are connected into chains running in the b -axis direction by O-H⋯N hydrogen bonding. (iucr.org)
  • The interaction pair for this hydrogen bond donor feature was not observed in the homology model. (helsinki.fi)
  • 975 mg/m 3 ) have the potential to cause sudden death, theoretically due to hydrogen sulfide's effect on the brainstem respiratory center. (medscape.com)
  • However, the deliberate mixture of household chemicals to create hydrogen sulfide is increasingly used as means of committing suicide, and these cases pose a potential risk for first responders. (medscape.com)
  • [ 1 ] The petroleum industry is responsible for most cases of hydrogen sulfide toxicity in North America. (medscape.com)
  • For example, in a typical acyl substitution reaction, the starting carbonyl compound is coordinated to the catalyst through one, two or possibly more hydrogen bonds. (wikipedia.org)
  • In the PIL, the [TEA] cation acts as a HB donor, being able to donate a single HB. (rsc.org)
  • In 2019, 761 single exposures to hydrogen sulfide exposure were reported to Poison Control Centers in the United States. (medscape.com)
  • [ 2 ] In addition to deaths, at least 80% of hydrogen sulfide suicides "have resulted in injuries to police officers, firefighters, emergency workers or civilians exposed to the gas. (medscape.com)
  • first look at the backbone-backbone hydrogen bonds coor hbond verbose select type HN .or. (charmm.org)
  • Low-level exposures to hydrogen sulfide usually produce local eye and mucous membrane irritation, while high-level exposures rapidly produce fatal systemic toxicity. (medscape.com)