PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 22731388-3 2012 The syn oxygen atom of the carboxylic group attacks the alpha-phosphorous atom (alphaP) of ATP in all class I aaRSs (except TrpRS) investigated, while the anti oxygen atom attacks in the case of class II aaRSs. Oxygen 8-14 synemin Homo sapiens 4-7 22731388-3 2012 The syn oxygen atom of the carboxylic group attacks the alpha-phosphorous atom (alphaP) of ATP in all class I aaRSs (except TrpRS) investigated, while the anti oxygen atom attacks in the case of class II aaRSs. Oxygen 160-166 synemin Homo sapiens 4-7 22731388-6 2012 The result shows that the strength of the interaction of syn oxygen and alphaP is stronger than the interaction with the anti oxygen for class I aaRSs. Oxygen 61-67 synemin Homo sapiens 57-60 22731388-7 2012 This indicates that the syn oxygen is the most probable candidate for the nucleophilic attack in class I aaRSs. Oxygen 28-34 synemin Homo sapiens 24-27 22731388-8 2012 The result is further supported by the computation of the variation of the nonbonded interaction energies between alphaP atom and anti oxygen as well as syn oxygen in class I and II aaRSs, respectively. Oxygen 157-163 synemin Homo sapiens 153-156 16506768-4 2006 Use of PCy(3) or P[(4-MeO)C(6)H(4)](3) as the ligand for Pd leads to syn-addition of the arene and the oxygen atom across the double bond, whereas use of (+/-)-BINAP or DPP-benzene affords products that result from anti-addition. Oxygen 103-109 synemin Homo sapiens 69-72 20481591-2 2010 The annulation is believed to proceed via (1) oxidative addition of the aryl iodide to Pd(0), (2) syn-addition of the resulting arylpalladium complex to the 1,3-diene, (3) intramolecular coordination of the phenolic oxygen to the Pd center, (4) hydrolysis of the acetyl group, and (5) reductive elimination of Pd(0), which regenerates the catalyst. Oxygen 216-222 synemin Homo sapiens 98-101 19630374-3 2009 The resulting alkenylrhodium(I) intermediate undergoes beta-oxygen elimination to open the oxirane ring in a syn-selective fashion. Oxygen 60-66 synemin Homo sapiens 109-112 19569635-10 2009 We found that the most active enantiomer is (S) tabun with the cyano group syn to the oxygen of Ser203. Oxygen 86-92 synemin Homo sapiens 75-78 12868878-3 2003 These [4 + 2] cycloadditions proceed with a strong kinetic bias for bonding to the dienophile from the direction syn to the tetrahydrofuranyl oxygen and consequently hold value in stereoselective synthesis. Oxygen 142-148 synemin Homo sapiens 113-116 15516766-0 2004 Preparation of enantiopure norbornane ligands bearing both (2S,3S)-bis(phosphinomethyl) and 7-syn-oxygen functional groups and an application to rhodium-catalyzed asymmetric hydrogenation. Oxygen 98-104 synemin Homo sapiens 94-97 15845009-12 2005 This preference was found to be reversed in the monoformyl-substituted systems (50a,b, 51a,b), where the syn conformer (when formyl oxygen is near the selenium) is energetically more favorable than the anti conformer. Oxygen 132-138 synemin Homo sapiens 105-108 15612717-0 2004 Stereoselectivity control by oxaspiro rings during Diels-Alder cycloadditions to cross-conjugated cyclohexadienones: the syn oxygen phenomenon. Oxygen 125-131 synemin Homo sapiens 121-124 15612717-3 2004 In all cases, the preferred [4+2] cycloaddition pathway consisted of bonding from that pi-surface syn to the oxygen atom. Oxygen 109-115 synemin Homo sapiens 98-101 12788450-8 2003 Syn-conformers of dU are stabilized by the intramolecular hydrogen bond O5"H...O2 and the dominant conformation of the ribose ring is C2"-endo. Oxygen 79-81 synemin Homo sapiens 0-3 12384583-8 2002 In addition, the amino group of C formed a hydrogen bond with the phosphate oxygen of A. G adopted a syn orientation about the glycosidic bond, while the sugar puckers of A and C were either C2"-endo or flexible. Oxygen 76-82 synemin Homo sapiens 101-104 12617670-8 2003 Solvent-induced topological isomerism of these 3-D hydrogen-bonded networks of 1 arises from (i) the guest inclusion ability based on a radially functionalized hexagonal structure of 1, (ii) the correlation between the hydrogen bond donor ability of the syn and anti protons of the primary amide group in host 1 and the hydrogen bond acceptor ability of the oxygen atoms of 1 and guest solvents, and (iii) the polarity of the bulk crystallization solvents. Oxygen 358-364 synemin Homo sapiens 254-257 11846651-3 2002 The addition of dimethylacetylene dicarboxylate (DMAD) is influenced by the electrostatic repulsion arising from the interaction of an electron pair orbital on the acetal oxygen and the orthogonal pi-orbital of the acetylene unit in DMAD in the syn-to-oxygen addition of the latter. Oxygen 171-177 synemin Homo sapiens 245-248 11878963-4 2002 The epimerization is likely initiated by the formation of Zn-enolate that is stabilized by intramolecular chelation to the pyranose ring-oxygen to form a syn chair-boat structure. Oxygen 137-143 synemin Homo sapiens 154-157 11846651-5 2002 The enhanced and accelerated syn-to-oxygen addition in lithium perchlorate in nitromethane is interpreted as a consequence of the coordination of Li+ to both the acetal oxygen and a heteroatom in the dienophile that brings them in close proximity to facilitate a reaction. Oxygen 169-175 synemin Homo sapiens 29-32 11846651-3 2002 The addition of dimethylacetylene dicarboxylate (DMAD) is influenced by the electrostatic repulsion arising from the interaction of an electron pair orbital on the acetal oxygen and the orthogonal pi-orbital of the acetylene unit in DMAD in the syn-to-oxygen addition of the latter. Oxygen 252-258 synemin Homo sapiens 245-248 11846651-6 2002 The Li+-oxygen combination, however, also exerts some steric effect that results in reduced syn-to-oxygen addition of dienophiles having large substituents such as N-phenylmaleimide. Oxygen 8-14 synemin Homo sapiens 92-95 11846651-6 2002 The Li+-oxygen combination, however, also exerts some steric effect that results in reduced syn-to-oxygen addition of dienophiles having large substituents such as N-phenylmaleimide. Oxygen 99-105 synemin Homo sapiens 92-95 11846651-4 2002 This repulsion is offset on coordination of Li+ to the said oxygen electron pair orbital, and the addition thus proceeds syn to oxygen. Oxygen 60-66 synemin Homo sapiens 121-124 11846651-4 2002 This repulsion is offset on coordination of Li+ to the said oxygen electron pair orbital, and the addition thus proceeds syn to oxygen. Oxygen 128-134 synemin Homo sapiens 121-124 11846651-5 2002 The enhanced and accelerated syn-to-oxygen addition in lithium perchlorate in nitromethane is interpreted as a consequence of the coordination of Li+ to both the acetal oxygen and a heteroatom in the dienophile that brings them in close proximity to facilitate a reaction. Oxygen 36-42 synemin Homo sapiens 29-32 11325277-3 2001 The stereochemical outcome of the IMDAF cycloaddition has the sidearm of the tethered alkenyl group oriented syn with respect to the oxygen bridge. Oxygen 133-139 synemin Homo sapiens 109-112 11375681-8 2001 The molecule possesses syn-syn conformation (both C=O bonds synperiplanar to the O-O bond) with O-O = 1.426(10) A and dihedral angle phi(C-O-O-C) = 86.5(32) degrees. Oxygen 81-84 synemin Homo sapiens 23-26 11375681-8 2001 The molecule possesses syn-syn conformation (both C=O bonds synperiplanar to the O-O bond) with O-O = 1.426(10) A and dihedral angle phi(C-O-O-C) = 86.5(32) degrees. Oxygen 81-84 synemin Homo sapiens 27-30 11262101-5 2001 The rotational rate and syn/anti ratio, which indicate the orientation between carbonyl oxygen and hydrogen at the 4-position, are significantly affected by addition of magnesium ion. Oxygen 88-94 synemin Homo sapiens 24-27 11262118-3 2001 The stereochemical outcome of the IMDAF cycloaddition has the side arm of the tethered alkenyl group oriented syn with respect to the oxygen bridge. Oxygen 134-140 synemin Homo sapiens 110-113 10774023-3 2000 Free enthalpies, calculated by using electronic energy at the higher theory level and with inclusion of solvent effects, indicates that syn, exo TSs, where the olefinic OH group hydrogen bonds the peroxy oxygens of the peroxy acid, outweigh syn, endo TSs, where the peroxy acid carbonyl oxygen is involved in hydrogen bonding. Oxygen 204-211 synemin Homo sapiens 136-139 11076611-5 2000 For dioxa cages, the structural facial difference around the reaction center is minor, but the electronic difference of syn and anti faces generated by the two remote oxygen atoms is clearly demonstrated via frontier orbital and MEP analyses. Oxygen 167-173 synemin Homo sapiens 120-123 10843633-6 2000 The most favorable pathway takes place along an endo/syn approach of the furan ring relative to the bridged oxygen atom of the oxanorbornadiene system, with participation of the substituted double bond. Oxygen 108-114 synemin Homo sapiens 53-56 10790841-3 2000 Protonation at the terminal oxygen atoms in methyl nitrate was less exothermic; the calculated proton affinities were 725, 722, and 712 kJ mol-1 for the formation of the syn-syn, anti-syn, and syn-anti ion rotamers 3a+, 3b+, and 3c+, respectively. Oxygen 28-34 synemin Homo sapiens 170-173 10790841-3 2000 Protonation at the terminal oxygen atoms in methyl nitrate was less exothermic; the calculated proton affinities were 725, 722, and 712 kJ mol-1 for the formation of the syn-syn, anti-syn, and syn-anti ion rotamers 3a+, 3b+, and 3c+, respectively. Oxygen 28-34 synemin Homo sapiens 174-177 10790841-3 2000 Protonation at the terminal oxygen atoms in methyl nitrate was less exothermic; the calculated proton affinities were 725, 722, and 712 kJ mol-1 for the formation of the syn-syn, anti-syn, and syn-anti ion rotamers 3a+, 3b+, and 3c+, respectively. Oxygen 28-34 synemin Homo sapiens 174-177 10790841-3 2000 Protonation at the terminal oxygen atoms in methyl nitrate was less exothermic; the calculated proton affinities were 725, 722, and 712 kJ mol-1 for the formation of the syn-syn, anti-syn, and syn-anti ion rotamers 3a+, 3b+, and 3c+, respectively. Oxygen 28-34 synemin Homo sapiens 174-177 10774023-3 2000 Free enthalpies, calculated by using electronic energy at the higher theory level and with inclusion of solvent effects, indicates that syn, exo TSs, where the olefinic OH group hydrogen bonds the peroxy oxygens of the peroxy acid, outweigh syn, endo TSs, where the peroxy acid carbonyl oxygen is involved in hydrogen bonding. Oxygen 204-211 synemin Homo sapiens 241-244 10774023-3 2000 Free enthalpies, calculated by using electronic energy at the higher theory level and with inclusion of solvent effects, indicates that syn, exo TSs, where the olefinic OH group hydrogen bonds the peroxy oxygens of the peroxy acid, outweigh syn, endo TSs, where the peroxy acid carbonyl oxygen is involved in hydrogen bonding. Oxygen 204-210 synemin Homo sapiens 136-139 10774023-3 2000 Free enthalpies, calculated by using electronic energy at the higher theory level and with inclusion of solvent effects, indicates that syn, exo TSs, where the olefinic OH group hydrogen bonds the peroxy oxygens of the peroxy acid, outweigh syn, endo TSs, where the peroxy acid carbonyl oxygen is involved in hydrogen bonding. Oxygen 204-210 synemin Homo sapiens 241-244 11674531-3 1999 The stereochemical outcome of the IMDAF cycloaddition has the sidearm of the tethered alkenyl group oriented syn with respect to the oxygen bridge. Oxygen 133-139 synemin Homo sapiens 109-112 10813959-2 2000 Interaction between the silicon in the trialkylsilyl group and the carbonyl oxygen in nucleophiles was postulated to stabilize the transition state, leading preferably to the syn diastereisomers. Oxygen 76-82 synemin Homo sapiens 175-178 9585973-2 1997 From CD and NOE spectra, anomalous syn orientation of Urd-5"-NH2 might be caused by specific interaction between borates and Urd-5"-NH2, which promote the formation of hydrogen bonding between 2-carbonyl oxygen and hydrogen of 5"-amino group. Oxygen 204-210 synemin Homo sapiens 35-38 11672368-5 1998 This implies that the alkoxy oxygen in anti-3 is a much poorer hydrogen bond acceptor than the carbonyl oxygen in syn-3, most likely because of a combination of steric and electrostatic factors. Oxygen 29-35 synemin Homo sapiens 114-117 11672368-5 1998 This implies that the alkoxy oxygen in anti-3 is a much poorer hydrogen bond acceptor than the carbonyl oxygen in syn-3, most likely because of a combination of steric and electrostatic factors. Oxygen 104-110 synemin Homo sapiens 114-117 11671726-3 1997 Interestingly, syn stereoselectivity is eroded and reactions proceed more rapidly when the steric bulk of the oxygen substituent is reduced as in the hydroxy and methoxy derivatives. Oxygen 110-116 synemin Homo sapiens 15-18 34838423-2 2022 Experiments and ab initio calculations revealed that the 1,4-pentadien-3-ol monomer prefers a configuration with one vinyl being syn to the hydroxyl oxygen and the hydroxyl hydrogen toward the skew arranged vinyl, which therefore makes possible simultaneous CH O and OH pi interactions. Oxygen 149-155 synemin Homo sapiens 129-132 34399025-2 2021 Crystal structure analysis revealed that each of these molecules adopts a conformation in which the azide and oxygen groups orient syn to each other with a short O N b contact. Oxygen 110-116 synemin Homo sapiens 131-134 30813573-4 2019 While the C-C bond formation involving the beta-conjugated carbon of alpha-santonin derivative is more favorable than the C-O one, which is responsible for the ortho regioselectivity, the favorable electronic interactions taking place between the oxygen of the nitrile oxide and two axial hydrogen atoms of the alpha-santonin derivative are responsible for the syn diastereofacial selectivity. Oxygen 247-253 synemin Homo sapiens 361-364 34399025-8 2021 A CSD search indicated the frequent and consistent occurrence of this interaction and its role dictating the syn conformation of azide and oxygen in molecules where these groups are separated by 2-4 bonds. Oxygen 139-145 synemin Homo sapiens 109-112 32329533-2 2020 The higher catalytic performance in an oxygen reduction reaction (ORR) was achieved by anti -Me 2 P with higher turnover number (TON = 250 for 30 min) than that by syn -Me 2 P (TON = 218 for 60 min). Oxygen 39-45 synemin Homo sapiens 164-167 32628026-2 2020 Among the four possible conformers of this species, predicted by theory within the energy window of 3 kcal/mol, only the lowest-energy conformer, the syn-trans form was detected in a discharged jet of a 1,3-diiode-but-2-ene (either in Z- or E-conformation) and O2 mixture diluted in Ar. Oxygen 261-263 synemin Homo sapiens 150-153 32255634-8 2020 Those identified from the unimolecular decay of syn-MACR-oxide and subsequent reaction of O2 are acetaldehyde (37 +- 7%), vinyl alcohol (9 +- 1%), methylketene (2 +- 1%), and acrolein (52 +- 5%). Oxygen 90-92 synemin Homo sapiens 48-51 34383986-5 2021 All the results are compared to the benzothiophene-fused analogues and show that the increased electronegativity of oxygen in the syn -fused derivatives leads to enhancement of the antiaromatic core causing greater paratropicity. Oxygen 116-122 synemin Homo sapiens 130-133 35459481-4 2022 By carefully heating the triplet carbene CF3CH in an O2-doped Ar-matrix to 35 K, the elusive carbonyl oxide CF3C(H)OO in syn- and anti-conformations has been generated and characterized with infrared (IR) and ultraviolet-visible (UV-vis) spectroscopy. Oxygen 53-55 synemin Homo sapiens 121-124 26138361-2 2015 This process allows syn substituents to be established stereospecifically on the 2-carbon bridge connecting the ketone carbonyl carbons, and the formation of one carbon-carbon and two carbon-oxygen bonds. Oxygen 191-197 synemin Homo sapiens 20-23 30693322-2 2019 Metalloenzymes activate O2 by employing earth-abundant metals and exhibit diverse reactivities in oxidation reactions, including epoxidation of olefins, functionalization of alkane C-H bonds, arene hydroxylation, and syn-dihydroxylation of arenes. Oxygen 24-26 synemin Homo sapiens 217-220 27439950-3 2016 The strongly-fluorescent syn-bimane chelates the Pd(ii) center via its carbonyl oxygen atoms, affording a non-fluorescent complex. Oxygen 80-86 synemin Homo sapiens 25-28 26646468-3 2015 Experimental results revealed that the alachlor oxidation enhancement in the syn-FeS2 Fenton system was attributed to the molecular oxygen activation induced by more surface-bound ferrous ions on syn-FeS2. Oxygen 132-138 synemin Homo sapiens 77-80 26646468-3 2015 Experimental results revealed that the alachlor oxidation enhancement in the syn-FeS2 Fenton system was attributed to the molecular oxygen activation induced by more surface-bound ferrous ions on syn-FeS2. Oxygen 132-138 synemin Homo sapiens 196-199 26646468-4 2015 The molecular oxygen activation process could generate superoxide anions to accelerate the Fe(II)/Fe(III) cycle on the syn-FeS2 surface, which favored the H2O2 decomposition to generate more hydroxyl radicals for the alachlor oxidation. Oxygen 14-20 synemin Homo sapiens 119-122 28972756-6 2017 The other vibrational frequencies for HOSO are reduced relative to the corresponding frequencies in SO2, H2SO4, and the HOS radical making the infrared features of syn-HOSO likely red-shifted in mixed spectral observation, where oxygen, hydrogen, and sulfur are all found. Oxygen 229-235 synemin Homo sapiens 164-167 28846830-4 2017 In addition, syn-selective carbosilylation was achieved through stereoswitching, by using a silylborane having oxygen functionality on the silyl group. Oxygen 111-117 synemin Homo sapiens 13-16 26427992-4 2015 A computational search for low energy geometries revealed that the syn isomer favors a six-membered ring hydrogen bond to nitrogen and the anti isomer favors a five-membered ring hydrogen bond to oxygen. Oxygen 196-202 synemin Homo sapiens 67-70 25119431-2 2014 Syn adducts emerge with regard to the vicinal nitrogen and oxygen heteroatom substituents. Oxygen 59-65 synemin Homo sapiens 0-3 25959902-4 2015 Here we report the transient infrared spectrum of syn- and anti-CH3CHOO, produced from CH3CHI + O2 in a flow reactor, using a step-scan Fourier-transform spectrometer. Oxygen 96-98 synemin Homo sapiens 50-53 24745224-17 2014 The population analysis of the substrate AA shows that a non-negligible difference exists between the attacking oxygens of AA in class I (syn) and in class II (anti) which is one reason for the lower value of delta(q) in class II relative to class I. Oxygen 112-119 synemin Homo sapiens 138-141 24410212-4 2014 High-level ab initio calculations which reproduce the experimentally determined values well indicate that the in-plane C-H bond in the methyl moiety is trans to the C-O bond, and other two protons are directed to the terminal oxygen atom for the most stable structure of syn-CH3CHOO. Oxygen 226-232 synemin Homo sapiens 271-274 24410212-5 2014 The torsional barrier of the methyl top is fairly large in syn-CH3CHOO, implying a significant interaction between the terminal oxygen and the protons of the methyl moiety, which may be responsible for the high production yields of the OH radical from energized alkyl-substituted Criegee intermediates. Oxygen 128-134 synemin Homo sapiens 59-62 24244317-3 2013 Conformationally constrained phenethylamine analogs have demonstrated that for optimal activity the free lone pair electrons of the 2-oxygen must be oriented syn and the 5-oxygen lone pairs anti relative to the ethylamine moiety. Oxygen 134-140 synemin Homo sapiens 158-161