C-methyl Groups Research Articles

Reaction mechanism of the cation radicals of thymine and thymine derivatives in aqueous solution: A theoretical study

Mechanisms of decomposition reaction of thymine cation radicals (T[Formula: see text]), 1-methyl substituted T[Formula: see text] (1-MeT[Formula: see text]), and 1,3-dimethyl substituted T[Formula: see text] (1,3-Me2T[Formula: see text]) generated by ionizing radiation or one-electron oxidation to thymine, 1-methylthymine and 1,3-dimethylthymine in aqueous solution have been investigated by theoretical calculations. Seven reaction paths including H2O or OH[Formula: see text] addition, and deprotonation were considered. The most likely reaction for T[Formula: see text] decomposition is N1 deprotonation forming T(-N1H)[Formula: see text]. When N1 hydrogen is replaced by methyl, T[Formula: see text] would deprotonate from C5 methyl group generating 1-methyl substituted UCH[Formula: see text] in neutral solution, and reaction with OH[Formula: see text] producing 1-methyl substituted T6OH[Formula: see text] in basic solution. When N1 and N3 hydrogens are both replaced by methyl, T[Formula: see text] decomposition reaction is similar to 1-MeT[Formula: see text], indicating that N3 hydrogen barely influences the subsequent reaction of 1-MeT[Formula: see text]. These results can provide theoretical support for experimental observations.

Synthesis of C3-Methyl-Substituted Pyrroloindolines and Furoindolines via Cascade Dearomatization of Indole Derivatives with Methyl Iodide.

A highly efficient method for constructing C3-methyl-substituted pyrroloindolines and furoindolines via cascade dearomatization reaction of indole derivatives with methyl iodide was developed. This protocol offers a direct approach to a wide range of C3 methyl substituted pyrroloindolines under mild conditions. The utility of this method was further demonstrated in the concise synthesis of (±)-esermethol.

A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration.

Increasing drought and diminishing freshwater supplies have stimulated interest in developing small molecules that can be used to control transpiration. Receptors for the plant hormone abscisic acid (ABA) have emerged as key targets for this application, because ABA controls the apertures of stomata, which in turn regulate transpiration. Here, we describe the rational design of cyanabactin, an ABA receptor agonist that preferentially activates Pyrabactin Resistance 1 (PYR1) with low nanomolar potency. A 1.63 Å X-ray crystallographic structure of cyanabactin in complex with PYR1 illustrates that cyanabactin's arylnitrile mimics ABA's cyclohexenone oxygen and engages the tryptophan lock, a key component required to stabilize activated receptors. Further, its sulfonamide and 4-methylbenzyl substructures mimic ABA's carboxylate and C6 methyl groups, respectively. Isothermal titration calorimetry measurements show that cyanabactin's compact structure provides ready access to high ligand efficiency on a relatively simple scaffold. Cyanabactin treatments reduce Arabidopsis whole-plant stomatal conductance and activate multiple ABA responses, demonstrating that its in vitro potency translates to ABA-like activity in vivo. Genetic analyses show that the effects of cyanabactin, and the previously identified agonist quinabactin, can be abolished by the genetic removal of PYR1 and PYL1, which form subclade A within the dimeric subfamily III receptors. Thus, cyanabactin is a potent and selective agonist with a wide spectrum of ABA-like activities that defines subfamily IIIA receptors as key target sites for manipulating transpiration.

Independent Generation and Reactivity of Thymidine Radical Cations.

Thymidine radical cation (1) is produced by ionizing radiation and has been invoked as an intermediate in electron transfer in DNA. Previous studies on its structure and reactivity have utilized thymidine as a precursor, which limits quantitative product analysis because thymidine is readily reformed from 1. In this investigation, radical cation 1 is independently generated via β-heterolysis of a pyrimidine radical generated photochemically from an aryl sulfide. Thymidine is the major product (33%) from 1 at pH 7.2. Diastereomeric mixtures of thymidine glycol and the corresponding 5-hydroxperoxides resulting from water trapping of 1 are formed. Significantly lower yields of products such as 5-formyl-2'-deoxyuridine that are ascribable to deprotonation from the C5-methyl group of 1 are observed. Independent generation of the N3-methyl analogue of 1 (NMe-1) produces considerably higher yields of products derived from water trapping, and these products are formed in much higher yields than those attributable to the C5-methyl group deprotonation in NMe-1. N3-Methyl-thymidine is, however, the major product and is produced in as high as 70% yield when the radical cation is produced in the presence of excess thiol. The effects of exogenous reagents on product distributions are consistent with the formation of diffusively free radical cations (1, NMe-1). This method should be compatible with producing radical cations at defined positions within DNA.

Fluorine at the C5 Position of 2′‐Deoxyuridine Enhances Repair of a O4‐Methyl Adduct by O6‐Alkylguanine DNA Alkyltransferases

Alkylation damage at the O6‐ and O4‐atoms of 2′‐deoxyguanosine (dG) and thymidine (T), respectively, can be removed by O6‐alkylguanine‐DNA alkyltransferases (AGTs). Previous studies have shown that human AGT (hAGT) repairs small adducts poorly at the O4‐atom of T, in comparison to the E. coli variants (OGT and Ada‐C). The C5 methyl group of the thymine nucleobase is suspected to contribute to hAGT repair proficiency possibly due to steric effects in the protein active site. In the present study, repair of oligonucleotides containing a 5‐fluoro‐O4‐methyl‐2′‐deoxyuridine (dFU‐Me) insert by hAGT, E. coli AGT variants (OGT and Ada‐C) and a chimeric hAGT/OGT protein was evaluated. All AGT variants, particularly hAGT and the hAGT/OGT chimera, demonstrated improved proficiency at removing the O4‐methyl group from substrates containing dFU‐Me, relative to the thymidine and 2′‐deoxyuridine counterparts.

C2-Functionalized 1,3-dialkylimidazolium ionic liquids for efficient cellulose dissolution

Novel C2-functionalized 1,3-dialkylimidazolium-based ionic liquids (ILs) are prepared, in which the acidic hydrogen at the 2-position of 1,3-dialkylimidazolium is replaced with the oxygen-containing methoxymethyl (CH3OCH2-, MOM) and (2-methoxyethoxy)methyl (CH3OCH2CH2OCH2-, MEM) groups to increase their hydrogen bonding interactions with cellulose. While the chloride salts of these C2-functionalized imidazolium cations are unable to dissolve cellulose, the formate and acetate salts exhibit moderate to excellent solvation of high molecular weight cellulose with a degree of polymerization (DP) of 850. Cellulose undergo a decrease in molecular weight with temperature during dissolution in the 1,2,3-trisubstituted imidazolium acetates devoid of the acidic C2 hydrogen, which is similar to that in 1,3-dialkylimidazolium acetates. Deuterium exchange studies suggest that the cellulose degradation is caused by the increased acidity of the hydrogens at C4 and C5 as well as at C2 methylene of the imidazolium cation. The addition of N-methylimidazole as an organic base suppresses the degradation of cellulose.

Preparation and structures of nickel(II) compounds of 2,9-meso-7,14-rac-2,5,5,7,9,12,12,14-octamethyl-1,4,8,11-tetraazacyclotetradecane

Preparations and structures are reported for compounds of 2RS,7RS,9SR,14RS-[(2,5,5,7,9,12,14,14-octamethyl-1,4,8,11-tetrazacyclotetradecane)nickel(II)]2+: trans-octahedral [Ni(mr-III-L)(NCS)2], cis-octahedral [Ni(mr-V-L)(OAc)]ClO4 (and –H2O) with asymmetrical chelate acetato, [Ni(mr-V-L)(acac)]ClO4 and [Ni(mm1-III L)]·2[Ni(mr-V-L)(acac)](ClO4)4 with chelate pentane-2,4-dionato, trigonal pyramidal [Ni(mr-V-L)Cl]ClO4 and [Ni(mr-V-L)(NCS)]ClO4 and square-planar [Ni(mr-V-L)](ClO4)2, where III and V indicate the nitrogen configurations 1R,4S,8S,11R and 1R,4S,8R,11S respectively and mm1-L is the 2R,7S,9S,14R isomer of the amine. The preparations of [Ni(mr-V-L)(A)](ClO4), where A−=chelate nitrato, nitrito and μ-oxalato are reported.

Preparations and structures of some nickel(II) compounds of 2RS,7SR,9SR,14RS- and 2RS,7RS,9SR,14SR-2,5,5,7,9,12,12,14-octamethyl-1,4,8,11-tetraazacyclotetradecane

Reduction of the imine functions of meso-[(3,5,7,7,10,12,14,14-octamethyl-1,4,8,11-tetraazacyclotetradec-4,11-diene)nickel(II)] by NaBH4 yields the complex nickel(II) cations of three stereo-isomers of 2,5,5,7,9,12,14,14-octamethyl-1,4,8,11-tetrazacyclotetradecane (L): 2RS,7SR,9SR,14RS (mm1-L), 2RS,7RS,9SR,14SR (mm2-L) and 2RS,7RS,9SR,14RS (mr-L), in ca. 16, 37 and 23% yields respectively. The preparation and structure of [Ni(mm1-L)](ClO4)2 has been reported, but no metal-ion compounds of mm2-L have been reported. The preparations and structures are reported for square-planar singlet ground state salts: [Ni(mm1-L)]ZnCl4, [Ni(mm2-L)]ZnCl4, [Ni(mm2-L)](ClO4)2, [Ni(mm1-L)]Cl2·2H2O and [Ni(mm1-L)](CNS)2. Preparations and structures are reported for the triplet ground state octahedral compounds trans-[Ni(mm2-L)X2], X−=Cl−, N3−, ONO−, and CH3CO2−, trans-[Ni(mm2-L)(OH2)2](NO3)2, trans-[Ni(mm1-L)(N3)2] and trans-[Ni(mm1-L)(NCS)2]·0.5H2O, all with the nitrogen configuration 1R,4S,8S,11R. The mm1-L compounds are all centrosymmetrical with the C2 and C9 methyl substituents axially oriented. The mm2-L compounds, except for [Ni(mm2-L)]–ZnCl4 and –(ClO4)2, have centrosymmetrical octahedral molecules/cations with the C2 and C9 methyl substituents equatorially oriented. The structure of 2RS,7RS,9SR,14SR-2,5,5,7,9,12,12,14-octamethyl-1,4,8,11-tetraazacyclotetradecane dihydrate, mm2-L·2H2O, released from the nickel(II) compound by reaction with cyanide, is reported. Structures are also reported for trans-[Ni(teta)X2] (teta=meso-5,5,7,12,12,14-hexamethyl-1,4,8,11-tetrazacyclotetradecane, X=NO2− and CH3CO2−.

Synthesis of glucuronic acid derivatives via the efficient and selective removal of a C6 methyl group

This investigation is related to the development of a general strategy for the synthesis of certain glucuronic acid derivatives. In particular, we report exceptionally selective conditions for removing the C6 methyl protecting group by potassium hydroxide without affecting the benzoyl protecting groups on the C2, C3 and C4 hydroxyl groups in high yields (95–99%). The present method proves to be efficient and environmentally friendly in terms of short reaction time, high yield and the single product.

Theoretical studies on the hydrogen abstraction reactions of methyl esters with HO2radical and the following β-scission reactions

Unsaturated fatty acid methyl esters are ubiquitous in biodiesel fuels. The C = C double bond greatly affects the combustion characteristics of biodiesel, especially its ignition behavior at low temperatures. In this work, we report detailed theoretical study on the mechanism and kinetics of the hydrogen abstraction reactions of linear unsaturated C6 methyl esters with hydroperoxy radical (HO2), which play a critical role in the low-temperature combustion of biodiesel. Reaction profiles are obtained via intrinsic reaction coordinate (IRC) analysis including the formation of reactant complexes and product complexes at the entrance and exit channels, respectively. The potential energy surfaces are explored at the CBS-QB3 level. The following β-scission reactions of the forming radicals are also investigated at the same level of theory. The high-pressure limit rate constants for all the reactions in the temperature range from 500 to 2000 K are calculated via conventional transition-state theory with quantum tunneling effect and fitted to the modified Arrhenius expression.

Continuous Upgrading of Fast Pyrolysis Oil by Simultaneous Esterification and Hydrogenation

A mixture of fast pyrolysis oil (FPO) and methanol (1/1 v/v) was continuously converted to methyl levulinate (ML), methyl acetate (MA), and C3 or greater methyl esters using metal-acid functionalized zeolites (Ni and Ru/HZSM-5) and an iron oxide catalyst with both acid and base sites (250 °C, 600 psig). Fractional conversion of FPO components was 60% or greater using the iron oxide catalyst, and space time yields approached 150 and 30–50 g/L cat/h for MA and C3 methyl esters, respectively, at 250 °C (W/F = 0.4 h, liquid hourly space velocity = 5–11.2 h–1). Product yield and concentration using the iron oxide catalyst were comparable to those of the Ni and Ru/HZM-5 catalysts and achieved performance levels higher than those of SiO2-Al2O3 and HZSM-5. Two potential pathways for acetic acid conversion (ketonization and esterification) and ML formation from levoglucosan were observed. Using the bifunctional catalysts in the presence of hydrogen resulted in significant coke reduction (60–80%) and the production...

Enantioselective Synthesis of Both Epimers at C-21 in the Proposed Structure of Cytotoxic Macrolide Callyspongiolide.

Both epimers at C-21 in the proposed structure of (+)-callyspongiolide have been synthesized in a convergent and enantioselective manner. The 14-membered macrolide with a sensitive C2-C3 cis-olefin functionality was installed by a Yamaguchi macrolactonization of hydroxyl alkynoic acid followed by hydrogenation over Lindlar's catalyst. The C5 methyl stereocenter was constructed by a ring-closing olefin metathesis followed by addition of methyl cuprate to an α,β-unsaturated δ-lactone. Other key reactions are chiral Corey-Bakshi-Shibata (CBS) reduction and Sonogashira coupling to conjoin the macrocyclic core and side chain.

Studies directed toward synthesis of taepeenin D: construction of the C4 stereogenic center and the CD benzofuran rings

Taepeenin D is a meroterpenoid isolated from roots and stems of Caesalpinia crista, showing inhibitory activity of Hedgehog signaling pathway. Herein we report selective and short-step construction of two fragments of taepeenin D. First, we demonstrated alkoxy radical-mediated selective functionalization at C19 methyl group for construction of the C4 quaternary carbon stereogenic center. Second, the CD benzofuran rings were constructed in 6 short steps from decalone. The synthesis described herein is not only applicable to total synthesis, but also used for study of the structure–activity relationships of taepeenin D.

Six polycyclic pyrimidoazepine derivatives: syntheses, molecular structures and supramolecular assembly.

A versatile synthetic method has been developed for the formation of variously substituted polycyclic pyrimidoazepine derivatives, formed by nucleophilic substitution reactions on the corresponding chloro-substituted compounds; the reactions can be promoted either by conventional heating in basic solutions or by microwave heating in solvent-free systems. Thus, (6RS)-6,11-dimethyl-3,5,6,11-tetrahydro-4H-benzo[b]pyrimido[5,4-f]azepin-4-one, C14H15N3O, (I), was isolated from a solution containing (6RS)-4-chloro-8-hydroxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepine and benzene-1,2-diamine; (6RS)-4-butoxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-8-ol, C18H23N3O2, (II), was formed by reaction of the corresponding 6-chloro compound with butanol, and (RS)-4-dimethylamino-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-8-ol, C16H20N4O, (III), was formed by reaction of the chloro analogue with alkaline dimethylformamide. (6RS)-N-Benzyl-8-methoxy-6,11-dimethyl-6,11-dihydro-5H-benzo[b]pyrimido[5,4-f]azepin-4-amine, C22H24N4O, (IV), (6RS)-N-benzyl-6-methyl-1,2,6,7-tetrahydropyrimido[5',4':6,7]azepino[3,2,1-hi]indol-8-amine, C22H22N4, (V), and (7RS)-N-benzyl-7-methyl-2,3,7,8-tetrahydro-1H-pyrimido[5',4':6,7]azepino[3,2,1-ij]quinolin-9-amine, C23H24N4, (VI), were all formed by reaction of the corresponding chloro compounds with benzylamine under microwave irradiation. In each of compounds (I)-(IV) and (VI), the azepine ring adopts a conformation close to the boat form, with the C-methyl group in a quasi-equatorial site, whereas the corresponding ring in (V) adopts a conformation intermediate between the twist-boat and twist-chair forms, with the C-methyl group in a quasi-axial site. No two of the structures of (I)-(VI) exhibit the same range of intermolecular hydrogen bonds: different types of sheet are formed in each of (I), (II), (V) and (VI), and different types of chain in each of (III) and (IV).

Preparations and structures of nickel(II) compounds of 2,9-rac-2,5,5,7,9,12,12,14-octamethyl-1,4,8,11-tetraazacyclotetradecane

The imine functions of 3,10-rac-[(3,5,7,7,10,12,14,14-octamethyl-1,4,8,11-tetraazacyclotetradec-4,11-diene)nickel(II)]2+ are reduced by NaBH4 in water forming the 2RS,7SR, 9RS,14SR-, [Ni(rac-rac-1-L)]2+, and 2RS,7SR,9RS,14RS-[Ni(rac-meso-L)]2+, isomeric [(2,5,5,7,9,12,12,14-octamethyl-1,4,8,11-tetraazacyclotetradecane)nickel(II)] cyclic tetraamine cations. The structures of [Ni(rac-rac-1-L)](ClO4)2, [Ni(rac-rac-1-L)]ZnCl4, [Ni(rac-rac-1-L)(acac)]ClO4 and [Ni(rac-meso-L)](ClO4)2·H2O were determined by X-ray diffractometry. The perchlorate and tetrachlorozincate salts of the cation [Ni(rac-rac-1-I-L)]2+ have near twofold symmetry about the nickel(II) ion, normal to the NiN4 plane, with “basket” cyclam nitrogen configuration I (1RS,4RS,8RS,11RS). The C2 and C9 methyl substituents are axially oriented to the same side of the plane as the four NH groups, with the axially oriented components of the C5 and C12 gem-dimethyl groups oriented to the other side. The salt [Ni(rac-rac-1-L)](NCS)2 has uncoordinated thiocyanate ions. The compound [Ni(rac-rac-1-V-L)(acac)]ClO4, with pentane-2,4-dionate chelate, has the macrocycle in configuration 1RS,2SR,4RS,7RS,8RS,9SR,11RS,14RS, folded along N4–Ni–N11, with methyl substituents on C2 and C9 equatorially oriented. The [Ni(rac-meso-L)]2+ cation was isolated as the trans-dithiocyanato compound, [Ni(rac-meso-III-L)(NCS)2], which was converted into the square-planar perchlorate salt [Ni(rac-meso-III-L)](ClO4)2H2O, with configuration 1RS,2SR,4SR,7SR,8SR,9SR,11RS,14RS. This cation has the C2 methyl substituent axially and the C9 substituent equatorially oriented.

Theoretical and kinetic study of the hydrogen atom abstraction reactions of unsaturated C6 methyl esters with hydroxyl radical

This work reports a systematic ab initio and chemical kinetic study of the rate constants for hydrogen atom abstraction reactions by hydroxyl radical (OH) on typical isomers of unsaturated C6 methyl esters at the CBS/QB3 level of theory. The high-pressure limit rate constants at different reaction sites for all the methyl esters in the temperature range from 500 to 2000K are calculated via transition-state theory with the Wigner method for quantum tunneling effect and fitted to the modified three parameters Arrhenius expression using least-squares regression. Further, a branching ratio analysis for each reaction site has been performed.

Reversible Photohydration of Trenbolone Acetate Metabolites: Mechanistic Understanding of Product-to-Parent Reversion through Complementary Experimental and Theoretical Approaches.

Photolysis experiments (in H2O and D2O) and quantum chemical calculations were performed to explore the pH-dependent, reversible photohydration of trenbolone acetate (TBA) metabolites. Photohydration of 17α-trenbolone (17α-TBOH) and 17β-trenbolone (17β-TBOH) occurred readily in simulated sunlight to yield hydrated products with incorporated H(+) at C4 and OH(-) at either C5 (5-OH-TBOH) or C12 (12-OH-TBOH) in the tetracyclic steroid backbone. Although unable to be elucidated analytically, theory suggests preferred orientations of cis-12-OH-TBOH (relative to C13 methyl) and trans-5-OH-TBOH, with the former most thermodynamically stable overall. Both experiment and theory indicate limited stability of trans-5-OH-TBOH at acidic pH where it undergoes concurrent, carbocation-mediated thermal rearrangement to cis-12-OH-TBOH and dehydration to regenerate its parent structure. Experiments revealed cis-12-OH-TBOH to be more stable at acidic pH, which is the only condition where its reversion to parent TBA metabolite occurred. At basic pH cis-12-OH-TBOH decayed quickly via hydroxide/water addition, behavior that theory attributes to the formation of a stable enolate resistant to dehydration but prone to thermal hydration. In a noteworthy deviation from predicted theoretical stability, 17α-TBOH photohydration yields major trans-5-OH-TBOH and minor cis-12-OH-TBOH, a distribution also opposite that observed for 17β-TBOH. Because H(+) and OH(-) loss from adjacent carbon centers allows trans-5-OH-TBOH to dehydrate at all pH values, the presumed kinetically controlled yield of 17α-TBOH photohydrates results in a greater propensity for 17α-TBOH reversion than 17β-TBOH. Additional calculations explored minor, but potentially bioactive, trenbolone analogs that could be generated via alternative rearrangement of the acidic carbocation intermediate.

N,N,N′,N′,N′′,N′′,N′′′,N′′′-Octamethyl(but-2-yne)bisamidinium bis(tetraphenylborate)

The asymmetric unit of the title salt, C12H24N42+.2C24H20B−, comprises half a cation and one tetraphenylborate ion. An inversion centre is situated at the mid-point of the triple C[triple-bond]C bond in the cation. The bisamidinium C—N bonds [1.3249 (11) and 1.3267 (11) Å] have double-bond character and both positive charges are delocalized between the dimethylamino groups. The bonds between the N atoms and the terminal C-methyl groups all have values characteristic for a typical single bond [1.4656 (12)–1.4687 (12) Å]. The acetylenic bond length [1.1889 (18) Å] is consistent with a triple C[triple-bond]C bond and the butyne carbon chain is almost linear. C—H...π interactions between the bisamidinium methyl H atoms and the phenyl C atoms of the tetraphenylborate ions are present. The phenyl rings form aromatic pockets, in which the cations are embedded. This leads to the formation of a two-dimensional supramolecular pattern in theabplane.

Biophysical Mechanism of Sequence-Dependent Attraction between Double-Stranded DNAS and its Biological Significance

The chromosome spends most of its lifetime in the interphase in which it is only loosely condensed and hence viewed as a dynamic polymer. The physical properties of DNA in vitro have been rigorously studied but its structural organization in a living cell and the role of such structure in epigenetics have only started to be explored, leaving the physical mechanism behind largely unknown. From our recent studies combining molecular dynamics simulations and single molecule experiments, we suggest that polycation-driven electrostatic inter-DNA attraction might play a crucial role in determining the overall condensed structure of DNA. We found that the C5 methyl group of thymines, which methylated cytosines also have, induces sequence-dependent attraction between double stranded DNAs. Such behavior is consistent with the large scale structure of chromosomes from Hi-C measurements and the observed compactness of hyper-methylated chromosomes. In this talk, I will present our recent efforts to test the hypothesis from the molecular to the cellular level that may reveal the physical mechanism of controlling the chromosome structure and dynamics for epigenetic gene regulation.

Retinal Chromophore Structure in Meta-II Rhodopsin Revealed by Solid-State 2H NMR and Molecular Modeling

Knowledge of the structural dynamics of retinal bound to rhodopsin is crucial for understanding its activation mechanism [1]. Recent X-ray structures of rhodopsin mutants in the active state and opsin with bound all-trans retinal have reported different orientations of the chromophore. Here we investigate the structure of all-trans retinal bound to the active Meta-II photointermediate by 2H NMR spectroscopy. Rhodopsin was regenerated with retinal containing 2H-labeled methyl groups, and was reconstituted with POPC/DOPE bilayers, followed by alignment of membranes on glass slides. Rhodopsin was then bleached and trapped in the Meta-II state [2] at temperatures below -‍60 °C. Solid-state 2H NMR spectra were acquired for different tilt angles of the aligned samples. The methyl group orientations relative to the membrane normal were calculated by fitting the experimental 2H NMR spectra using a static uniaxial distribution [3] for the protein embedded within lipid bilayers. We found that the orientation of the C9-methyl group obtained from 2H NMR spectroscopy was similar to that from X-ray data. By contrast, the orientations of the C5- and C13- methyl groups were different versus the X-ray crystal structures. The retinal structure was analyzed using the three-plane model, as in previous studies of rhodopsin in the dark and the Meta-I states [4]. Moreover, a new approach was tested that combines 2H NMR and X-ray restraints for retinal together with the rhodopsin binding-pocket using simulated annealing. Our results yield new insights into formation of the activated state of the receptor in lipid membranes. [1] A.V. Struts et al. (2011) Nat. Struct. Mol. Biol. 18, 392-394. [2] A.V. Struts et al. (2015) Meth. Mol. Biol. 1271, 133-158. [3] A.A. Nevzorov et al. (1999) JACS 121, 7636-7643. [4] G.F.J. Salgado et al. (2006) JACS 128, 11067-11071.