Syn Structure Research Articles

Vibrational spectra and gas phase structure of N-trifluoroacetylimidosulfurous difluoride, CF 3C(O)NSF 2

The conformational and structural properties of N-trifluoroacetylimidosulfurous difluoride, CF 3C(O)NSF 2, have been studied by vibrational spectroscopy (IR(gas) and Raman(liquid)), by gas electron diffraction and by quantum chemical calculations (HF, MP2 and B3LYP with 6-31G ∗ and 6-311G ∗ basis sets). Only a single conformer with a syn– syn structure and C S symmetry was observed in the gaseous and liquid states. The CF 3C(O) group is oriented syn relative to the SF 2 group and the CO and NS double bonds are synperiplanar to each other. The preference of this conformation has been rationalized based on a natural bond orbital analysis. Conformations with anti orientations around the NS and N–C bonds correspond to stable structures according to quantum chemical calculations, but are higher in energy by 2.4 kcal/mol or more. The skeletal parameters, N S=1.481(7) A ̊ , N– C=1.406(16) A ̊ , S– F=1.585(2) A ̊ , C–NS=128.2(16)°, NS–F=110.4(12)° and F–S–F=89.3(11)° ( r a values with 3 σ uncertainties), are very similar to those in other imidosulfurous difluorides. Whereas the HF approximation reproduces the geometric parameters satisfactorily, the MP2 and B3LYP methods predict some bonds too long by up to 0.07 Å.

Bis(dimethylamido) complexes of alkyl- and phenylgallium. Useful precursors to the RGa(2+) synthon.

Alkyl- and phenylbis(dimethylamido)gallium, [RGa(NMe(2))(2)](2) [R = Me (1), Et (2), (n)Bu (3), (n)Hx (4), and Ph (5)], were synthesized by reactions of LiNMe(2) with (RGaCl(2))(2). The crystal structure of compound 1 was a disordered mixture of anti and syn isomers, with the ratio of anti/syn being 64:36, which was consistent with the ratio (57:43) found in the (1)H NMR spectrum. The Ga(2)N(2) cores of the anti and syn structures were nonplanar. (1)H NMR spectra indicated the presence of both anti and syn isomers for all of the other substituents. (1)H NMR and mass spectra indicated that a species with the general formula of R(3)Ga(2)(NMe(2))(3) was formed when these compounds were heated at high temperatures.

Solution structure of a trans-opened (10S)-dA adduct of (+)-(7S,8R,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully complementary DNA duplex: evidence for a major syn conformation.

Two-dimensional NMR was used to determine the solution structure of an undecanucleotide duplex, d(CGGTCACGAGG).d(CCTCGTGACCG), in which (+)-(7S,8R,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene is covalently bonded to the exocyclic N(6)() amino group of the central deoxyadenosine, dA(6), through trans addition at C10 of the epoxide (to give a 10S adduct). The present study represents the first NMR structure of a benzo[a]pyrene (10S)-dA adduct in DNA with a complementary T opposite the modified dA. Exchangeable and nonexchangeable protons of the modified duplex were assigned by the use of TOCSY (in D(2)O) and NOESY spectra (in H(2)O and D(2)O). Sequential NOEs expected for a B-type DNA conformation with typical Watson-Crick base pairing are observed along the duplex, except at the lesion site. We observed a strong intraresidue NOE cross-peak between H1' and H8 of the modified dA(6). The sugar H2' and H2' ' of dC(5) lacked NOE cross-peaks with H8 of dA(6) but showed weak interactions with H2 of dA(6) instead. In addition, the chemical shift of the H8 proton (7.51 ppm) of dA(6) appears at a higher field than that of H2 (8.48 ppm). These NOE and chemical shift data for the dA(6) base protons are typical of a syn glycosidic bond at the modified base. Restrained molecular dynamics/energy minimization calculations show that the hydrocarbon is intercalated from the major groove on the 3'-side of the modified base between base pairs A(6)-T(17) and C(7)-G(16) and confirm the syn glycosidic angle (58 degrees ) of the modified dA(6). In the syn structure, a weak A-T hydrogen bond is possible between the N3-H proton of T(17) and N7 of dA(6) (at a distance of 3.11 A), whereas N1, the usual hydrogen bonding partner for N3-H of T when dA is in the anti conformation, is 6.31 A away from this proton. The 10(S)-dA modified DNA duplex remains in a right-handed helix, which bends in the direction of the aliphatic ring of BaP at about 42 degrees from the helical axis. ROESY experiments provided evidence for interconversion between the major, syn conformer and a minor, possibly anti, conformer.

Ab initio study of syn and anti structures of N-nitroso compounds containing a carbonyl group

A variety of ab initio molecular orbital methods, RHF, MP2 and B3LYP, have been applied to N-methyl- N-nitrosourea ( 1), N-methyl- N-nitrosoacetamide ( 2) and N-methyl- N-nitrosomethylcarbamate ( 3) and the anti and syn structures and the transition state (TS) structures connecting them have been examined. In each of these compounds, the anti structure was predicted to be more stable than the syn structure and the relative energy of the TS structure was considerably higher than those of the anti and syn structures. The energy difference between anti and syn of 1 is slightly smaller than those of 2 and 3 owing to the existence of hydrogen bonding between O in the nitroso group and H in the NH 2 group.

Photochemical syn-anti isomerization reaction in N4-hydroxycytosine. An experimental matrix isolation and theoretical study.

Infrared spectra of N4-hydroxycytosine isolated in argon and nitrogen low-temperature matrixes are reported. The compound was found to adopt the syn structure of the imino-oxo tautomeric form exclusively. A photoreaction (lambda > 250 nm) converting this form into the anti isomer was observed. The reaction is reversible and leads to a photostationary point. The initial infrared spectrum and the spectrum of the photoproduct were assigned to the syn and anti isomers, respectively. This assignment is based on a close agreement between the experimental spectra and the spectra theoretically simulated at the DFT(B3LYP)/6-31++G** level of theory.

Proton affinity of peroxyacetyl nitrate. A computational study of topical proton affinities.

The structure and energetics of the peroxyacetyl nitrate conformers syn- and anti-PAN and several cations formed by PAN protonation were investigated by a combination of density functional theory and ab initio calculations. syn-PAN is the more stable conformer that is predicted to predominate in gas-phase equilibria. The acetyl carbonyl oxygen was found to be the most basic site in PAN, the oxygen atoms of the peroxide and NO(2) groups being less basic. The 298 K proton affinity of syn-PAN was calculated as 759-763 kJ mol(-1) by effective QCISD(T)/6-311 + G(3df,2p) and 771-773 kJ mol(-1) by B3-MP2/6-311 + G(3df,2p). The calculated values are 25-39 kJ mol(-1) lower than the previous estimate by Srinivasan et al. (Rapid Commun. Mass Spectrom. 1998; 12: 328) that was based on competitive dissociations of proton-bound dimers (the kinetic method). The calculated threshold dissociation energies predicted the formation of CH(3)CO(+) + syn - HOONO(2) and CH(3)COOOH + NO(2)(+) to be the most favorable fragmentations of protonated PAN that required 83 and 89 kJ mol(-1) at the respective thermochemical thresholds at 298 K. The previously observed dissociation to CH(3)COOH + NO(3)(+) was calculated by effective QCISD(T)/6-311 + G(3df,2p) to require 320 kJ mol(-1). The disagreement between the experimental data and calculated energetics is discussed.

Asymmetric Addition of Dimethylzinc to Benzaldehyde Catalyzed by (2S)-3-exo-(Dimethylamino)isobornenol. A Theoretical Study on the Origin of Enantioselection

The asymmetric reaction of dimethylzinc and benzaldehyde in the presence of (2S)-3-exo-(dimethylamino)isobornenol ((2S)-DAIB) proceeds via a methylzinc aminoalkoxide/dimethylzinc/benzaldehyde mixed-ligand complex. Molecular orbital and density functional calculations revealed that the asymmetric bias is generated in the intramolecular methyl-transfer step by differences in the stabilities of the four diastereomeric transition structures. The anti-configured 5/4/4 tricyclic structures are favored over the syn tricyclic transition states that exhibit electrostatic repulsion between the 1,3-syn-oriented Zn−CH3 groups. The steric origins of enantioselectivity are (1) the high stereodifferentiating ability of the bornane skeleton of DAIB and (2) nonbonded repulsion between the unreactive Zn−CH3 spectator and the aldehyde phenyl group (anti structure) or between the DAIB N-CH3 group and the migrating methyl group and/or carbonyl substituent (syn structure). The ground-state Zn complexes and transition states in...

Bi-, Tri-, and Tetranuclear Metallomacrocycles Constructed by Metal-Directed Reactions Involving Resorcinol or Hydroquinone or by Addition of Octahedral Metal Centers to Tetrahexylcalix[4]resorcinarene: X-ray Crystal Structure of syn,syn-[Mo{HB(3,5-Me(2)C(3)HN(2))(3)}(NO)(1,4-O(2)C(6)H(4))](3).

The reaction between [Mo(NO)(Tp)I(2)] [Tp(-) = hydrotris(pyrazol-1-yl)borate] and tetrahexylcalix[4]resorcinarene (resH(8)) affords a mixture of metalated macrocycles from which [{Mo(NO)(Tp)}(2)(resH(4))], [{Mo(NO)(Tp)}(3)(resH(2))], and [{Mo(NO)(Tp)}(4)(res)] can be isolated. In the solid state the tetrametalated compound can act as a host for CH(2)Cl(2) which forms a weak hydrogen bond to the oxygen of a coordinated nitric oxide: H.O1 2.47 Å, angle C-H.O1 161 degrees. Direct reaction of [Mo(NO)(Tp)I(2)] [Tp(-) = hydrotris(3,5-dimethylpyrazol-1-yl)borate] with resorcinol itself offers a route to the related resorcinol-based tetrametallomacrocycle [Mo(NO)(Tp)(1,3-O(2)C(6)H(4))](4). This reaction also produces the cyclic trimer [Mo(NO)(Tp)(1,3-O(2)C(6)H(4))](3) together with some cyclic dimer. A similar reaction involving 1,4-dihydroxybenzene and [M(NO)(Tp)I(2)] (M = Mo, W) also affords cyclic trimers and cyclic tetramers, but in this case, cyclic dimers are not formed. It has been possible to separate the single isomers syn,syn-[Mo(NO)(Tp)(1,4-O(2)C(6)H(4))](3), anti,syn-[M(NO)(Tp)(1,4-O(2)C(6)H(4))](3) (M = Mo, W), anti,syn-[Mo(NO)(Tp)(1,3-O(2)C(6)H(4))](3), and anti,syn,syn-[Mo(NO)(Tp)(1,3-O(2)C(6)H(4))](4). The crystal structure of syn,syn-[Mo(NO)(Tp)(1,4-O(2)C(6)H(4))](3) has been determined: C(63)H(78)B(3)Mo(3)N(21)O(9); monoclinic space group P2(1)/a; a = 16.269(10), b = 35.31(3), c = 16.056(10) Å; beta = 97.59(2) degrees; Z = 4. The coordination geometry at the molybdenum atoms is essentially octahedral. The trimer does not show 3-fold symmetry, the triangle of molybdenum atoms having two long edges, 8.485(3) and 8.703(3) Å, and one short edge of 7.886(3) Å. These distances are paralleled by the corresponding distances between the nitrosyl oxygen atoms, 6.177(12), 6.526(12), and 3.729(12) Å, respectively. The electrochemical properties of the metallomacrocycles reveal differing patterns of redox potentials depending upon the number and geometric arrangement of metal centers in the macrocyclic structure.

The Preparation, Stereochemistry and Reactions of Some [Co(cyclen)(NH3)X]3+/2+ Complexes (X = OH2, Cl, N3, OH)

A number of new [Co(cyclen)(NH(3))X](3+/2+) complexes have been prepared (X = OH(2), Cl, N(3), OH), and their stereochemistries, interconversions, and substitution reactions have been explored. All have the syn,anti configuration about the two meridional amine centers of the cis-coordinated cyclen ligand (syn(NH(3)),anti(X)- and syn(X),anti(NH(3))-isomers for X = OH(2), Cl, N(3), OH; designated as 1-X and 2-X respectively) but a syn,syn intermediate is proposed for a number of the reactions. OH(-)-catalyzed hydrolysis (base hydrolysis) dominates the substitution chemistry in aqueous solution (k(OH)/M(-)(1) s(-)(1) values reported) and results from deprotonation at one of the relatively very acidic meridional NH centers (k(H)/M(-)(1) s(-)(1) values reported). A syn orientation of the NH proton in the reactant is considered important in these reactions, with the resulting lone pair assisting in the displacement of X, and with this proton being transferred to X = OH to facilitate an unusually fast and spontaneous solvent replacement reaction (k(ex) = 8 +/- 2 s(-)(1), I = 1.0 M (NaClO(4)), 25 degrees C). Anation by N(3)(-) has been studied, and this proceeds largely via 2-OH for both isomers. A crystal structure of syn(NH(3)),anti(N(3))-[Co(cyclen)(NH(3))N(3)]Cl(0.5)(ClO(4))(1.5). H(2)O is reported; monoclinic, P2(1)/n (No. 14), a = 9.008(6) Å, b = 28.690(15) Å, c = 14.528(7) Å, a = 90 degrees, beta = 104.12(7) degrees, gamma = 90 degrees, Z = 8, R = 0.0695.

Structures of anti,Z -4,4-dimethyl-3-thiosemicarbazide, syn,E,Z -2,4-dimethyl-3-thiosemicarbazide and syn,E -1-cyclopentano-3-thiosemicarbazone

The structures of three alkyl derivatives of thiosemicarbazide are described: anti,Z-4,4-dimethyl-3-thiosemicarbazide (1), syn,E,Z-2,4-dimethyl-3-thiosemicarbazide (2), and syn,E-1-cyclopentano-3-thiosemicarbazone (3). Crystal data: for 1: triclinic, P-1 (#2), a = 5.802(1)A, b = 6.935(1)A, c = 8.104(2)A, α = 78.35(1)°, β = 82.13(1)°, γ = 70.71(1)°, and Z = 2; for 2: orthorhombic, Pbca (#61), a = 9.417(3)A, b = 8.624(2)A, c = 15.169(3)A, and Z = 8; for 3: triclinic, P-1 (#2), a = 6.068(3)A, b = 8.145(4)A, c = 8.666(5)A, α = 83.75(4)°, β = 86.16(5)°, γ = 74.07(4)°, and Z = 2. In general, molecules are linked by N–H···S hydrogen bonds with sulfurs accepting two or three hydrogen bonds. Structures 2 and 3, which adopt the syn conformation, form N–H···N intramolecular hydrogen bonds. The solid-state structures are consistent with their infrared and proton nuclear magnetic resonance spectra.

Formation of thesyn-isomer of [Cp*MoO(μ−S)

The structure of the title compound,syn-[Cp*MoO(μ−S)]2,1, has been determined.1 crystallized in the monoclinic space groupC2/c with dimensionsa=11.758(2),b=12.243(2), c = 15.585(3)A, β=104.63(3)°. The reaction of Cp* 2Mo2(S2)(S)(S2O3) with Me2PhP producessyn-[Cp*MoO(μ−S)]2 and Me2PhPO. The compounds [Cp′MoO(μ−S)]2 [Cp′=Cp, CpMe, Cp*] can exist as either thesyn- oranti-isomers. The present structure,syn-[Cp*MoO(μ−S)]2 is compared with the structure of theanti-isomer and with the previously determined structure ofsyn-[Cp*MoO(μ−S)]2 in a different space group.

A Functionalized Dimethyl 1,3-Butadiene-2,3-dicarboxylate

The crystal structure of dimethyl syn-(Z)-2-(4-methylphenylmethylene)-3-(1,5,5-trimethylpyrrolidene-2-ylidene)butanedioate, C21H27NO4, has been determined in order to establish its constitution and configuration, and to characterize the preferred conformation in the solid state. There are notable differences in the conformations of the functional groups; the essential structural features are discussed and compared.

Ab initio conformational study of 2,2′:5′,2″-terthiophene

The conformers of 2,2′:5′,2″-terthiophene were determined through ab initio MO full geometry optimization with a 6-31G * basis set. Different minima were found corresponding to twisted anti, anti, syn, anti and syn, syn structures. An estimate of the interconversion rate between conformers was performed.

ChemInform Abstract: Synthesis, Structure, and Electronic Properties of syn‐(2.2) Phenanthrenophanes: First Observation of Their Excimer Fluorescence at High Temperature.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

1.1]Ferrocenophanes in solution?Anti orsyn isomers?

Carbon-bridged [1.1]ferrocenophanes have generally been assumed to have syn structures, since anti isomers have been considered to be too strained. The recent discovery that such compounds may crystallize as anti isomers raises the question of whether the compounds prefer anti or syn conformations in solution. The synthesis of β-acetyl-[1.1]ferrocenophane (1) and its investigation by 1H,1H-NOESY are reported. Compound 1 was found to be a rapidly equilibrating mixture of syn isomers in CDCl3 at 22 °C.

Shielding effect of carbonyl group and its application to the conformational analysis of 1,1,10,10-tetramethyl[3.3]metacyclophane-2,11-dione

The conformational analysis of the title compound ( 2) using X-ray crystallographic analysis, molecular mechanics calculations, and chemical shift simulation method is presented. Temperature dependent signal behavior of 2 in its 1H NMR spectrum showed that a single anti conformer plays a significant role in its conformational dynamic equilibrium with very small contribution of syn structures. The structure of the anti conformer was analyzed by our newly developed technique using chemical shift simulation. The structure of the anti conformer was thus determined unequivocally in solution, and is identical with the structure found in the crystalline state.

The molecular structure of N-sulfinyl trimethylsilanamine, (CH 3) 3SiNSO

The geometric structure of (CH 3) 3SiNSO in the vapour phase has been determined by gas electron diffraction. The molecule possesses a planar SiNSO skeleton with syn conformation. The Si(CH 3) 3 group staggers the NS double bond. The following skeletal parameters ( r a distances and ∠ α angles with 3σ errors limits) were obtained: SiN 1.750(6)Å, NS 1.508(5)Å, SO 1.444(4)Å, SiNS 133.9(9)°, NSO 122.5(10)°. Ab initio calculations ( HF/3−21 G∗ ) were performed for H 3SiNSO and confirm the planar syn structure for sulfinyl silanamines.

Heterobimetallic indenyl complexes. Synthesis and structure of syn-[Cr(CO) 3(μ, η:η-indenyl)Rh(COD)

The heterobimetallic complex syn-[Cr(CO) 3(μ,η:η-indenyl)Rh(COD)] was obtained of syn-[Cr(CO) 3(μ,η:η-indenyl(Rh(CO) 2] with COD. The stereochemistry was retained in the exchange reaction as confirmed by 1H and 13C NMR measurements and by X-ray diffractometric analysis. In spite of great distortion, the COD complex is quite stable. An unusual bonding interaction between the hybrid CO orbitals of the Cr(CO) 3 group and the s-orbital of methine hydrogen atoms of COD is inferred on the basis of spectroscopic and X-ray structural data.

Cycloheptatrinyl bridged heterobimetallic complexes: synthesis, fluxional behaviour and X-ray crystal structure of syn-[( μ- η3; η2-C 7H 7)Fe(CO) 3Pt( η2, σ1-C 8H 12C 5H 5)

The reaction of [( η 3C 7H 7)Fe(CO) 3] − with [( η 4-C 8H 12)( η 5-C 5 H 5)Pt] + leads to the formation of syn-[( μ- η 3; η 2-C 7H 7)-Fe( CO) 3Pt) η 2, σ 1-C 8H 12-C 5H 5)] ( 1), a bridged cycloheptatrienyl complex with an FePt bond. In solution two structural isomers of 1 are present ini roughly the same concentration, whereas in the solid only one isomer is detected. Both isomers are fluxional and undergo ring whizzing of the C 7H 7 ring. The slow-exchange limiting NMR spectrum of the cycloheptatrienyl unit cannot be reached even at low temperature (∼173 K). The C 7H 7 ring has an uncoordinated double bond and the cyclopentadienyl unit is linked to the C 8H 12 ring through an sp 2 carbon; the resulting cyclooctenyl unit is coordinated η 2, σ 1 to platinum. The C 5H 5 transfer, mediated by platinum, can be of interest in the synthesis of the skeleton of natural occurring products. Crystal data for syn-[( μ- η 3; ν 2-C 7h 7)Fe(CO) 3Pt( ν 2, σ 1-C 8H 12-C 5H 5)]: monoclinic, space grou[ C2/ C (No. 15), a = 45.197(6), b=13.306(1), c=7.509(1) A ̊ , β=92.96(1)°, V=4509.8(9) A ̊ 3, Z=8, R=0.033, R w =0.080 .

Raman and infrared spectra, conformational stability, vibrational assignment, and ab initio calculations of cis-1,3-dichloropropene

The Raman (3200−10 cm−1) and infrared (3200−20 cm−1) spectra of gaseous and solid cis-1,3-dichloropropene, cis-ClHC=CHCH2Cl, have been recorded. Additionally, the Raman spectrum of the liquid with qualitative depolarization data has also been obtained. These spectral data have been interpreted on the basis that the molecule exists predominantly in the gauche (allylic chlorine atom oriented gauche to the double bond) conformation in all physical phases. Some bands in the infrared spectrum of the gas could be due to a second higher energy conformer but the lack of corresponding Raman bands casts doubt on such an assignment. Ab initio Hartree–Fock gradient calculations employing the RHF/6-31G* basis set are consistent with two minima that correspond to the two equivalent gauche forms for the potential surface for the internal rotation about the C—C bond. These minima occur at dihedral angles, [Formula: see text] ClCCC, of 122° and 238° (0° corresponds to the syn conformation) and the gauche to gauche barrier at the 180° transition state, which corresponds to the anti structure, is 342 cm−1. The barrier from the gauche minima to the syn (0°) structure, which is also a transition state, is 2425 cm−1. Complete equilibrium geometries for the gauche structure have been determined with the RHF/3-21G*, RHF/6-31G*, and MP2/6-31G* basis sets. A normal coordinate analysis utilizing a harmonic force field calculation with the RHF/3-21G* basis set has been carried out for the gauche conformer. The results are discussed and compared with the corresponding quantities obtained for some similar molecules.