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Topic: Aromatic interaction

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	Stacking (chemistry) - Wikipedia, the free encyclopedia
		In supramolecular chemistry, an aromatic interaction (or π-π interaction) is a noncovalent interaction between organic compounds containing aromatic moieties.
		Through aromatic interactions, the pi bonds, extending from atoms participating in double bonds, overlap with pi bonds of adjacent bases.
		Aromatic stacking interaction, sometimes called phenyl stacking, is a phenomenon in organic chemistry that affects aromatic compounds and functional groups.
	en.wikipedia.org /wiki/Pi-pi_interaction (464 words)

	Aromaticity - Wikipedia, the free encyclopedia
		Aromaticity is a chemical property in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.
		Aromatic molecules are able to interact with each other in so-called π-π stacking: the π systems form two parallel rings overlap in a "face-to-face" orientation.
		Aromatic molecules are also able to interact with each other in an "edge-to-face" orientation: the slight positive charge of the substituents on the ring atoms of one molecule are attracted to the slight negative charge of the aromatic system on another molecule.
	en.wikipedia.org /wiki/Aromatics (1471 words)

	Research Projects (Site not responding. Last check: 2007-10-11)
		We are investigating the influence of sequence, sheet propensities, and sidechain-sidechain interactions on beta-hairpin stabilities.
		In proteins, this type of interaction includes, for example, edge-face interactions between two aromatic sidechains, the interaction of a lysine sidechain with an aromatic group, and the interaction of the axial hydrogens of carbohydrates with the Pi-cloud of an aromatic ring in carbohydrate binding proteins.
		Aromatic interactions (pi-pi stacking, cation-pi interactions) have been proposed to provide facial selectivity in numerous asymmetric reactions by blocking one face of a pro-chiral substrate, such as in acyl transfer catalysis.
	www.chem.unc.edu /people/faculty/watersml/mlwgroup/ProjectsTable.htm (942 words)

	Encyclopedia :: encyclopedia : Human-computer interaction (Site not responding. Last check: 2007-10-11)
		Interaction between users and computers occurs at the user interface (or simply interface), which includes both hardware (i.e.
		A basic goal of HCI is to improve interaction between user and computers, by making computers more user-friendly and easier to use.
		However, researchers and practitioners now refer to their field of study as HCI (pronounced as an initialism), which perhaps rose in popularity partly because of the notion that the human, and the human's needs and time, should be considered first, and are more important than the machine's.
	www.hallencyclopedia.com /Human-computer_interaction (1262 words)

	Aromatic clusters: a determinant of thermal stability of thermophilic proteins -- Kannan and Vishveshwara 13 (11): 753 ...
		Aromatic interactions are known to be important in the structural
		mutation of Tyr93 and Tyr151 to Ile94 and Asn152, the aromatic
		aromatic clusters emanate from helices, 32% from strands, 21%
	peds.oxfordjournals.org /cgi/content/full/13/11/753 (3969 words)

	The Aromatic-(i+2) Amine Interaction in Peptides (Site not responding. Last check: 2007-10-11)
		The interaction between aromatic ring and an amine group has been proposed to be important for the behavior of proteins and peptides.
		A special case, notable in the folding pathway of BPTI, is the interaction of the aromatic side chain of the i-th residue with the amine group in the peptide link to the (i+2)-th residue.
		In this geometry, the aromatic-amine interaction energy is dominated by the interaction energy of the (i+2) amine group with solvent and the rest of the (i+2)-th residue with the aromatic ring.
	projects.villa-bosch.de /mcm/abs/20.html (274 words)

	Ludi - Theory (Site not responding. Last check: 2007-10-11)
		To generate the interaction sites, Ludi uses a set of rules that are intended to cover the complete range of energetically favorable orientations for hydrogen bonds and hydrophobic contacts.
		Interactions between a protein and ligand are usually formed through favorable nonbonded contacts such as hydrogen bonds or hydrophobic interactions.
		The use of atom pairs for H-donor and H-acceptor interaction sites makes subsequent fragment fitting straightforward although some fragments will not use both positions (e.g., if a fragment containing an ether moiety is fitted onto an H-acceptor site, the ether oxygen is fitted onto the position A and the adjacent position Y is not used).
	www-bio.unizh.ch /docu/acc_docs/doc/ludi/2-Theo.doc.html (1747 words)

	Hyperbranched Polymer (Site not responding. Last check: 2007-10-11)
		The effect on the host-guest type interaction by hydrophobic binding in these cavities was investigated for polymer compatibility and other possible applications.
		A model study using aromatic hyperbranched polymers showed a weak but conclusive interaction of small aromatic molecules with these polymers.
		Blends of hyperbranched aromatic polymers with polystyrene showed improvements in flow characteristics, stability and in some mechanical properties.
	flux.aps.org /meetings/YR97/BAPSMAR97/abs/S5255006.html (155 words)

	Structural investigation of inhibitor binding to carbonic anhydrases II and IV using crystallographic and computational ...
		We have manipulated the electrostatics of this interaction by systematically substituting fluorine atoms for the benzyl ring hydrogens of SBB.
		Additionally, aromatic interactions between two inhibitors are probed within the scaffolding of the Phe131→Val CAII crystal lattice, where 2 inhibitor molecules bind to one protein.
		These interaction geometries are analyzed with regard to van der Waals, electrostatic, and charge-transfer effects.
	repository.upenn.edu /dissertations/AAI3003645 (388 words)

	The cisproline(i - 1)-aromatic(i) interaction: Folding of the Ala-cisPro-Tyr peptide characterized by NMR and ... (Site not responding. Last check: 2007-10-11)
		The cisproline(i-1)-aromatic(i) interaction: Folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches
		The former have the tyrosine ring interacting with the alanine alpha proton and are enthalpically stabilised.
		The latter have the aromatic ring interacting with the proline side chain and are entropically stabilised.
	projects.villa-bosch.de /mcm/abs/jbnmr00.html (332 words)

	Ran's C-terminal, Basic Patch, and Nucleotide Exchange Mechanisms in Light of a Canonical Structure for Rab, Rho, Ras, ...
		Residues homologous to R39 (mainly arginine, glutamine, or serine), though inconsistently conserved at the sequence level, conserve hydrogen bonding interactions with the SA region.
		Canonical interactions between the SA and Switch I regions within the Ras, Rho, and Ran families.
		Canonical interactions between the NK.D and SA regions within the Ras, Rho, and Ran families.
	www.genome.org /cgi/content/full/13/4/673 (7253 words)

	Investigation of the nature of the methionine-{pi} interaction in {beta}-hairpin peptide model systems -- Tatko and ...
		interacts with the aromatic ring to the greatest extent (Tatko and Waters 2004).
		All of the observed diagonal interactions are stabilizing in
		Cheney, B.V., Schulz, M.W., and Cheney, J. Complexes of benzene with formamide and methanethiol as models for interactions of protein substructures.
	www.proteinscience.org /cgi/content/full/13/9/2515 (3512 words)

	Alcoholic beverage - Wikipedia, the free encyclopedia
		Ethanol is a moderately good solvent for many "fatty" substances and essential "oils", and thus facilitates the inclusion of several coloring, flavoring, and aromatic compounds to alcoholic beverages, especially to distilled ones.
		In many cultures, both contemporary and historical, alcoholic beverages — mostly because of their neurological effects — have also played an important role in various kinds of social interaction, providing a form of "liquid courage" (those who consume it "gain" confidence and lose discretion).
		While other psychoactive drugs (such as opium, coca, khat, cannabis, kava-kava, etc.) also have millennial traditions of social use, only coffee, tea and tobacco have been as universally used and accepted as ethanol is today.
	en.wikipedia.org /wiki/Alcoholic_beverage (3901 words)

	Study of the Interaction of Aromatic Compounds with Coals by Inverse Liquid Chromatography (Site not responding. Last check: 2007-10-11)
		Study of the Interaction of Aromatic Compounds with Coals by Inverse Liquid Chromatography
		The capacity factors of substituted anthracenes (methyl-, ethyl-, tert-butyl, phenyl-, and diphenylanthracenes) were found to decrease with an increase in their bulkiness, suggesting that the substituted groups on an anthracene ring hinder the access of the anthracenes to the interacting sites in coals.
		The extraction residue with a higher extraction yield showed a larger difference in the capacity factors between benzene, naphthalene, and anthracene than that with lower extraction yield from the same coal.
	www.anl.gov /PCS/bib/REF721.HTML (134 words)

	N-(Piperidin-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide (SR141716A) Interaction ...
		N-(Piperidin-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide (SR141716A) Interaction with LYS 3.28(192) Is Crucial for Its Inverse Agonism at the Cannabinoid CB1 Receptor -- Hurst et al.
		The conformationally constrained compound VCHSR (2), a vinylcyclohexyl analog of SR141716, was synthesized by Wittig
		The R state is characterized by a salt bridge between K3.28(192) and D6.58(366) and two patches of aromatic residues that form clusters in the TMH 3-4-5-6 region of CB1, W5.43(279)/F3.36(200)/W6.48(356), and Y5.39(275)/W4.64(255)/F5.42(278).
	molpharm.aspetjournals.org /cgi/content/full/62/6/1274 (8341 words)

	Thermodynamics of Interactions between Amino Acid Side Chains: Experimental Differentiation of Aromatic-Aromatic, ...
		interactions of aromatic residues with the Phe MSP are entropically
		Dadlez, M. Hydrophobic interactions accelerate early stages of the folding of BPTI.
		Energetics of interactions of aromatic hydrocarbons with water.
	www.biophysj.org /cgi/content/full/76/5/2319 (5612 words)

	Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model -- Ding et al. 88 (1): 147 -- ...
		and backbone interactions are assigned by analyzing the corresponding
		Although the salt-bridge interaction is assigned to be the strongest
		The aromatic-proline interaction is commonly observed to stabilize
	www.biophysj.org /cgi/content/full/88/1/147 (5027 words)

	Molecular-Level Investigation of Monoaromatic Compound Sorption to Suspended Soil Particles by Deuterium Nuclear ...
		Sorption of aromatic compounds is driven by the hydrophobic
		C NMR studies of the interaction of acetone, carbontetrachloride and trichloroethylene with soil components.
		Sediment porewater partitioning of polycyclic aromatic hydrocarbons in 3 cores from Boston Harbor, Massachusetts.
	jeq.scijournals.org /cgi/content/full/32/1/232 (4246 words)

	Energy Citations Database (ECD) - Energy and Energy-Related Bibliographic Citations (Site not responding. Last check: 2007-10-11)
		The objective of the present study is to clarify the role of OH-{pi} interaction in selective recognition of aromatic rings by Morwell brown coal.
		The interaction between coal and aromatic penetrants was evaluated with an interaction index, S{sub ar}, that was determined by an inverse liquid chromatography technique.
		However, excessively strong hydrogen bond between OH groups and the solvent interfered with the interaction of aromatic molecules with OH groups.
	www.osti.gov /energycitations/product.biblio.jsp?osti_id=181683 (430 words)

	Holistic Health Articles
		Aromatherapy is the therapeutic use of essential oils derived from aromatic plants.
		The oils are highly concentrated and represent the blood and soul of the plant and are used through the sense of smell.
		Aromatic molecules travel no further than the nose and are mostly on the subconscious level.
	www.healingisessential.com /holisticarticles.htm (8209 words)

	Aromatic-Aromatic Interactions (Site not responding. Last check: 2007-10-11)
		About 60% of the aromatic side chains (Phe, Tyr, and Trp), found in proteins are involved in aromatic pairings.
		Studies with model compounds suggest that the optimal geometry is perpendicular, such that the partially positively charged hydrogens on the edge of one ring can interact favourably with the pi electrons and partially negatively charged carbons of the other.
		Carter, 1984; Horovitz and Fersht, 1990) indicates that the interaction energy between the two aromatic groups contributes only 1.3 kcal/mol to the protein stability.
	www.cryst.bbk.ac.uk /PPS2/projects/day/TDayDiss/AromaticInteractions.html (282 words)

	Cation-Pi Interactions in Protein Explorer
		Gallivan and Dougherty conclude "When a cationic sidechain is near an aromatic sidechain, the geometry is biased toward one that would experience a favorable cation-pi interaction", and "cation-pi interactions should be considered alongside the more conventional hydrogen bonds, salt bridges, and hydrophobic effects in any analysis of protein structure".
		Cation-pi interactions are usually energetically important when the ligand has either positive charge or an aromatic ring, and are involved in control of ion channels, G-protein-coupled receptors, transporters, and enzymatic catalysis.
		A number of nearby sidechains that potentially could interact appear to be blocked by other noncovalent bonding interactions, and the peptide lysine sidechains are generally pointing away from the protein.
	www.umass.edu /microbio/chime/beta/molslides/june1/pe2.73/protexpl/cationpi.htm (3167 words)

	Interaction of aromatic molecules with the acid site in zeolites
		The interaction of aromatic molecules with the acid site in zeolite H-Beta as observed through a newly discovered Fano resonance at the Al K edge
		A new tool to study the interaction of aromatic molecules with the acid sites in zeolites is described yielding both geometric and electronic information simultaneously.
		The diffuse character of this latter orbital results in an overlap with the π* of the aromatics and enables the CT.
	stacks.iop.org /0953-8984/13/10383 (516 words)

	[No title]
		We suggest, based on experimental and bioinformatical analysis, that aromatic stacking interactions may provide energetic contribution as well as order and directionality in the self-assembly of ordered amyloid structures.
		This is in line with the well-known central role of aromatic stacking interactions in self-assembly of many supramolecular structures.
		The aim of the project is to study this new operon -its function, interactions, and structure and Stability parameters.
	www.tau.ac.il /lifesci/departments/biotech/members/gazit/gazit.html (2979 words)

	[No title] (Site not responding. Last check: 2007-10-11)
		The adsorption of aromatic molecules on metallic surfaces is not only of fundamental interest as a model system, but often also a precursor to catalytic reactions like hydrogenation and hydrogenolysis, relevant for a wide range of petrochemical processes.
		Reactions following a Langmuir-Hinshelwood mechanism are based on the adsorption of the reactants, hence this project is dedicated to an analysis of the interaction of aromatic molecules with transition metal surfaces.
		In the case of pyridine the adsorption is driven by the interaction of the nitrogen with the surface, resulting in the formation of an covalent bond.
	www.univie.ac.at /qccd/hpsc/2003/Kresse/mitten/report.html (222 words)

	Presentation Days 2000 Program and Abstracts
		We are pursuing the synthesis of two different model structures to further evaluate the potential of aromatic residues in N-ribohydrolases for stabilizing a cationic transition state.
		The cation-p interaction is an electrostatic attraction between a cation and the electron-rich p face of an aromatic ring.
		Because cationic and aromatic side groups are found in natural amino acids, the interaction should influence protein folding.
	www2.dof.hmc.edu /Presdays/2000/wednesday.html (3656 words)

	Aromatic-aromatic interactions in and around {alpha}-helices -- Bhattacharyya et al. 15 (2): 91 -- Protein Engineering ...
		The average number of aromatic residues in a helix containing a given number of residues (helix length).
		Lines signify aromatic planes (the longer one is for the residue with the smaller sequence number in an interacting pair) perpendicular to the paper.
		of interacting hydrophobic residues that straddles the helix
	peds.oxfordjournals.org /cgi/content/full/15/2/91 (4071 words)

	Ecological Engineering Group
		It is this symbiotic relationship between soil microbes that is responsible for the accelerated degradation of soil contaminants.
		The interaction between plants and microbial communities in the rhizosphere is complex and has evolved to the mutual benefit of both organisms.
		Sustainability is "a process of responsible consumption, wherein waste is minimized, and buildings interact in balanced ways with natural environments and cycles, balancing the desires and activities of humankind within the integrity and carrying capacity of nature, and achieving a stable, long-term relationship within the limits of their local and global environment." (Rocky Mountain Institute)
	www.ecological-engineering.com /defs.html (5940 words)

	Olefinic vs Aromatic -H Interaction: A Theoretical Investigation of the Nature of Interaction of First-row Hydrides ... (Site not responding. Last check: 2007-10-11)
		Olefinic vs Aromatic -H Interaction: A Theoretical Investigation of the Nature of Interaction of First-row Hydrides with Ethene and Benzene
		In either case, the contribution of dispersion energies is vital to obtain an accurate estimate of the binding energy.
		We also elaborate on the correlation of various interaction energy components with changes in geometries and vibrational frequencies.
	pubs.acs.org /cgi-bin/abstract.cgi/jacsat/2001/123/i14/abs/ja0013531.html (300 words)

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