Methyl Atoms Research Articles

Unusual C–C bond cleavage of an α-trifloxy Sialic acid hemiacetal under Lattrell-Dax conditions

We describe the novel oxidative fragmentation of methyl (5-acetamido-4,7,8,9-tetra-O-acetyl-5-deoxy-3-O-trifluoromethanesulfonyl-β-D-erythro-L-gluco-2-nonulopyranos)onate 2 on stirring with sodium nitrite in DMF to give the novel 3-acetamido-2,5,6,7-tetra-O-acetyl-d-glycero-d-galacto-heptono-1,4-lactone 3 in excellent yield. Stirring of the same triflate with sodium carbonate on the other hand affords the novel methyl (5-acetamido-7,8,9-tri-O-acetyl-3,6-anhydro-5-deoxy-d-manno-3-ene-2-nonulos)onate 19 also in excellent yield. Reduction of the heptono lactone with sodium borohydride followed by acetylation gives a peracetylated aminodeoxyheptitol 6 that adopts the zig zag conformation of its carbon backbone.

CP MAS 13C NMR SPECTROSCOPY IN DETERMINATION OF SPECIFIC DIFFERENCES IN COMPOSITION OF WOOD

In recent years solid-state 13C NMR spectroscopy using the technique of cross-polarization (CP) and sample rotation at a magic angle (MAS) has been used in the analysis of plant materials, including wood. Knowledge of the composition, structure and behavior of wood components in different conditions is of great importance, since the properties of wood materials depend on this. In this work differences in the composition of various tree species wood in central Russia (birch, aspen, spruce, and larch) were revealed using CP MAS 13C NMR spectroscopy. Assignment of various peaks in CP MAS 13C NMR spectra with the main components of wood was carried out. It was shown that cellulose is presented in amorphous and crystalline forms, the presence of lignin is unambiguously confirmed by signals of aromatic carbon atoms, and hemicellulose is detected by signals from carbon atoms of methyl groups of acetylxylose and L-rhamnose. According to the integral intensities, the total proportion of cellulose and hemicellulose in relation to lignin was determined: the largest amount of lignin was found in coniferous wood (spruce, larch), and the smallest amount of lignin was detected in deciduous species (aspen and birch).

Crystal Structure, Packing, and Analysis of Hirshfeld Surfaces of 3a-(p-tolyl)-3,3a-dihydrobenzo[d]pyrrolo[2,1-b]thiazol-1(2H)-one

Crystal and molecular structures of 3a-(p-tolyl)-3,3a-dihydrobenzo[d]pyrrolo[2,1-b]thiazole-1(2H)-one obtained by condensing 4-oxo-4-(p-tolyl)butane acid with 2-aminothiophenol are studied using XRD spectroscopy. The crystal of compound 1 occurs in the form of two crystallographically independent molecules. The crystal has no hydrogen bonds and stacking interactions, but the analysis of Hirshfeld surfaces shows that the molecules are weakly stabilized by non-covalent interactions between oxygen atoms and hydrogen atoms of methyl groups as well as by the interactions between hydrogen atoms and carbon atoms of the benzothiazole fragment.

Generating methane adsorption under relaxation of molecular structure of coal

Transformation of molecular structure of coal under long-term effect of confining pressure due to strain relaxation is estimated numerically. It is found that both under dynamic deformation, as has been determined earlier, and under relaxation of molecular structure of coal, atoms of methyl group and hydrogen remove from aliphatic fringe, join together and form molecules of methane. It is shown that these molecules immediately form sorbing-based connection with coal. Volumes of methane adsorption generated in coal due to strain relaxation of molecular structure of coal are calculated.

Crystal structure of S,S′-dimethyl-N-nitroimidodithiocarbonate

The molecule of S,S′-dimethyl-N-nitroimidodithiocarbonate has a planar geometry (with the exception of hydrogen atoms of methyl groups), stabilized by the shortened S…O contact. The bond lengths in the >С=N–NO2 nitrimine moiety, in contrast to nitroguanidine derivatives, make it possible to consider the molecular structure of the compound within the traditional valence formula. The crystal structural feature of the compound is a low energy of its crystal lattice.

Di-chlorido-dimethyl-bis-(thio-urea-κS)tin(IV).

The title compound, [Sn(CH3)2Cl2(CH4N2S)2], crystallizes with two half-mol­ecules in the asymmetric unit. Both mol­ecules are completed by inversion symmetry with the two SnIV atoms located on inversion centers. The metal atoms have distorted octa­hedral coordination environments defined by two Cl atoms, two C atoms of methyl groups and two thio­urea S atoms. In the crystal, mol­ecules are linked via N—H⋯Cl and N—H⋯S hydrogen bonds, forming a three-dimensional structure.

Theoretical investigation on the mechanisms and kinetics of OH-initiated photooxidation of dimethyl phthalate (DMP) in atmosphere

The atmospheric OH-initiated degradation mechanisms of dimethy phthalate (DMP) are analyzed at the MPWB1K/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) level of theory. The principal products detected experimentally are confirmed by this study while several major intermediates are reported for the first time. Additionally, the pathway scheme of hydroxylation reaction of DMP is proposed. The results about initial steps indicate that hydroxyl radical is most likely to be added to the ortho-carbon atom among additional reactions, while H atoms in methyl group are the most favorable to be abstracted by the OH radical. The rate constants of the elementary reactions over the temperature of 200–400K were deduced using RRKM theory. The overall rate constant of the title reaction is 1.18×10−12cm3molecule−1s−1 at 298K and 760Torr while H abstraction reactions predominate. According to the rate constants given at different temperatures, the Arrhenius equation is fitted. The atmospheric half life of DMP with respect to OH is estimated to be 6.8days.

Domino Reaction of Iodoglycosides: Synthesis of Carbohydrate‐Based Nitroalkenes

AbstractHerein we describe a tandem fragmentation/Henry reaction of iodoglycosides, which involves formation of a carbon–carbon double bond and a carbon–carbon single bond. If the fragmentation of methyl 5‐iodo‐D‐ribofuranoside is mediated by zinc/catalytic indium in the presence of bromonitromethane, a separable mixture of a 1‐nitro‐5‐hexene and a 1‐bromo‐1‐nitro‐5‐hexene is obtained in moderate yields with good diastereoselectivities. However, if the reaction is mediated by nBuLi in the presence of nitromethane, the corresponding 1‐nitro‐5‐hexene is obtained as the only product in excellent yield and stereoselectivity in a one‐pot synthetic protocol. This is a general methodology that can be applied to iodopyranoses and iodofuranoses with different protecting groups for the efficient preparation of highly functionalized 1‐nitro‐5‐hexenes or 1‐nitro‐6‐heptenes.

New diorganotin(IV) complexes with 3-(2-hydroxy-5-methylphenylamino)-1,3-diphenylprop-2-en-1-one: Synthesis, spectroscopic characterization, structural studies and antibacterial activity

New organotin(IV) complexes, Ph2SnL (1) and Me2SnL (2), have been synthesized from reaction of corresponding diorganotin(IV) dichlorides with a Schiff base, 3-(2-hydroxy-5-methylphenylamino)-1,3-diphenylprop-2-en-1-one (H2L), derived from condensation of 2-amino-4-methylphenol with dibenzoylmethane. The synthesized compounds have been investigated by elemental analysis and IR, 1H NMR, and 119Sn NMR spectroscopy. Spectroscopic studies show that the Schiff base acts as a tridentate dianionic ligand and coordinates via the nitrogen and phenolic and enolic oxygen atoms. The structures of H2L and 2 have been also confirmed by X-ray crystallography. Schiff base exists as the keto-amine tautomeric form in solid state with two intramolecular hydrogen bonds of the NH⋯O type and also intermolecular hydrogen bonds of OH⋯O type that create a dimer. In the structure of 2, tin center is surrounded by two O and one N atoms from the ligand and two C atoms of methyl groups and the sixth coordination site is occupied by phenolic oxygen atom of another molecule, thus a dimeric molecule with a Sn2O2 four-membered ring is formed. The in vitro antibacterial activity of ligand and complexes has been evaluated against Gram-positive (Bacillus cereus and Staphylococcus aureus) and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacteria. H2L showed no activity but the diphenyltin(IV) complex exhibited good activities along with the standard antibacterial drugs.

3,3,3′,3′-Tetramethyl-6,6′-bis[(pyridin-4-yl)methoxy]-1,1′-spirobiindane monohydrate

The asymmetric unit in the title compound, C33H34N2O2·H2O, consists of a V-shaped mol­ecule and a water mol­ecule to which it is hydrogen bonded. The angle between the mean planes of the two spiro-connected indane groups is 77.06 (5)°. The two five-membered rings of the indane groups have envelope conformations with the methyl­ene atoms adjacent to the spiro C atom forming the flaps. They have deviations from the mean plane of the other four atoms in the rings of 0.374 (4) and 0.362 (4) Å. In the crystal, molecules are linked to form inversion dimers via O—H⋯N hydrogen bonds involving the pyridine N atoms and the solvent water mol­ecule. The dimers are linked into a chain along the b axis by π–π stacking inter­actions between a pyridine ring and its centrosymmetrically related ring in an adjacent dimer. The centroid–centroid distance between the planes is 3.7756 (17) Å, the perpendicular distance is 3.4478 (11) Å and the offset is 1.539 Å.

Structural analysis of Pneumocystis carinii dihydrofolate reductase complexed with NADPH and 2,4-diamino-6-[2-(5-carboxypent-1-yn-1-yl)-5-methoxybenzyl]-5-methylpyrido[2,3-d]pyrimidine.

Structural data are reported for 2,4-diamino-6-[2-(5-carboxypent-1-yn-1-yl)-5-methoxybenzyl]-5-methylpyrido[2,3-d]pyrimidine (PY1014) complexed with Pneumocystis carinii dihydrofolate reductase (pcDHFR) refined to 1.8 Å resolution. These data reveal that the carboxylate of the ω-carboxyalkynyl side chain of PY1014, the most pcDHFR-selective analog in this series, forms ionic interactions with the conserved Arg75 in the substrate-binding pocket of pcDHFR. The reversal of the 2',5'-substitution pattern of this analog compared with the highly selective diaminopyrimidine analog PY1011 (i.e. the 5'-pentynylcarboxy-5'-methoxy pattern of PY1014 versus the 3',4'-dimethoxy-5'-pentynylcarboxy pattern of PY1011) is necessary to achieve optimal interaction with Arg75 as observed in other structures. The larger diaminopyrido[2,3-d]pyrimidine ring of PY1014 places the 5'-methoxy group closer to Leu25 and Ser64 than does the diaminopyrimidine ring of PY1011. The 5'-methoxy O atom forms a hydrogen bond to the amide of Leu25 (O···N, 2.7 Å) and the 5'-methoxy methyl group makes a hydrophobic contact of 3.1 Å with C(β) of Ser64. Although the IC(50) values of PY1014 and PY1011 are similar, inhibition data show that the selectivity of PY1011 for pcDHFR is significantly greater. The greater selectivity for pcDHFR compared with mammalian DHFR of these inhibitors is also influenced by the enhanced hydrophobic interactions of the side-chain methylene atoms with Phe69 of pcDHFR compared with Asn64 of mammalian DHFR.

Structure and some properties of [UO2CrO4{CH3CON(CH3)2}2

A new complex [UO2CrO4{CH3CON(CH3)2}2] (I) was studied by thermal analysis, IR spectroscopy, and X-ray crystallography. The crystals are monoclinic: a = 13.8108(11) A, b = 8.6804(7) A, c = 13.0989(10) A, β = 104.777(1)°, V = 1518.4(2) A3, space group P21/c, Z = 4, R = 2.39%. The structure of I contains infinite chains of the [UO2CrO4{CH3CON(CH3)2}2] composition running along [001]; the complex belongs to the AT11M1 2 crystal-chemical group (A = UO 2 2+ , T11 = CrO 4 2− , M1 = CH3CON(CH3)2) of uranyl complexes. The chains are linked into a three-dimensional framework due to hydrogen bonds between oxygen atoms of chromate ions and hydrogen atoms of methyl groups of the dimethylacetamide.

N-(2-Chlorophenyl)-N′-(2-methylphenyl)succinamide

In the title compound, C17H17ClN2O2, the asymmetric unit contains half a mol­ecule with a centre of symmetry at the mid-point of the central C—C bond. The conformations of the amide O atoms are anti to the methyl­ene atoms. Further, the N—H bonds in the amide fragments are anti to the ortho-chloro/methyl groups in the adjacent benzene rings. The dihedral angle between the benzene ring and the NH—C(O)—CH2 segment in the two halves of the mol­ecule is 62.0 (2)°. In the crystal, a series of N—H⋯O inter­molecular hydrogen bonds link the mol­ecules into column-like infinite chains along the a axis. The methyl and Cl groups are disordered with respect to the ortho positions of the benzene ring, with site-occupation factors of 0.5 each.

Methyl fluoroperoxide와 fuoromethyl fluoroperoxides의 conformers와 isomers 구조에 대한 이론연구

Methyl hydro-peroxide의 methyl group과 O-H에 F를 치환 시킨 fluoromethyl fluoroperoxide(<TEX>$CH_nF_{3-n}OOF$</TEX>)의 안정한 conformers와 isomers에 대하여 MP2/6-311G(d,p) 방법과 B3LYP/6-311++G(d,p) 방법으로 최적화 계산을 수행하였고 vibrational frequencies를 구하였다. <TEX>$CH_3OOF$</TEX>와 <TEX>$CH_2FOOF$</TEX>, <TEX>$CHF_2OOF$</TEX>, <TEX>$CF_3OOF$</TEX> 분자 모두 가장 안정한 형태는 skew 구조로 나타났으며 <TEX>$CH_3OOH$</TEX>와 비교할 때 대단히 짧은 O-O 결합길이를 갖는다. Trans, cis conformers의 경우 skew 형태보다 8-12 kcal/mol 정도 높은 에너지를 갖으며 O-O 결합길이는 훨씬 길어진다. <TEX>$CH_2FOOF$</TEX>, <TEX>$CHF_2OOF$</TEX>, <TEX>$CF_3OOF$</TEX> 분자들은 methyl group의 F에 의한 induction 효과로 짧은 C-O 결합길이를 갖고 O-F 결합길이는 길어지나 치환된 F 원자의 수에 따른 구조변화는 그리 크지 않다. The ab initio calculations for fluoromethyl fluoroperoxides have been carried out using MP2/6-311G(d,p) and B3LYP/6-311++G(d,p) method. The structural optimizations were performed for several isomers and conformers of methyl fluoroperoxide, <TEX>$CH_3OOF$</TEX> and the vibrational frequencies were calculated. The most stable conformer of <TEX>$CH_3OOF$</TEX> is skew form and has fairly short O-O bond distance. The trans and cis conformers have 8-12 kcal/mol higher energies than skew form and the other isomers are very unstable. The structures of <TEX>$CH_2FOOF$</TEX>, <TEX>$CHF_2OOF$</TEX> and <TEX>$CF_3OOF$</TEX> are also optimized and vibrational frequencies were calculated. These molecules also have skew forms as the lowest energy conformers. The O-O bond distances are longer and C-O bond distances are shorter than <TEX>$CH_3OOF$</TEX>, but the structural parameters are almost independent of the number of fluorine atoms in methyl group.

Requirements for mammalian carboxylesterase inhibition by substituted ethane-1,2-diones

Carboxylesterases (CE) are ubiquitous enzymes found in both human and animal tissues and are responsible for the metabolism of xenobiotics. This includes numerous natural products, as well as a many clinically used drugs. Hence, the activity of these agents is likely dependent upon the levels and location of CE expression. We have recently identified benzil is a potent inhibitor of mammalian CEs, and in this study, we have assessed the ability of analogues of this compound to inhibit these enzymes. Three different classes of molecules were assayed: One containing different atoms vicinal to the carbonyl carbon atom and the benzene ring [PhXC(O)C(O)XPh, where X = CH 2, CHBr, N, S, or O]; a second containing a panel of alkyl 1,2-diones demonstrating increasing alkyl chain length; and a third consisting of a series of 1-phenyl-2-alkyl-1,2-diones. In general, with the former series of molecules, heteroatoms resulted in either loss of inhibitory potency (when X = N), or conversion of the compounds into substrates for the enzymes (when X = S or O). However, the inclusion of a brominated methylene atom resulted in potent CE inhibition. Subsequent analysis with the alkyl diones [RC(O)C(O)R, where R ranged from CH 3 to C 8H 17] and 1-phenyl-2-alkyl-1,2-diones [PhC(O)C(O)R where R ranged from CH 3 to C 6H 13], demonstrated that the potency of enzyme inhibition directly correlated with the hydrophobicity ( c log P) of the molecules. We conclude from these studies that that the inhibitory power of these 1,2-dione derivatives depends primarily upon the hydrophobicity of the R group, but also on the electrophilicity of the carbonyl group.

Molecular structure of trimethyl[(3-indole)ethoxy]silane cooled in a supersonic jet

Conformations of He-jet-cooled trimethyl[(3-indole)ethoxy]silane (TIES) have been studied using a laser spectroscopy technique in combination with quantum-chemical computations. Six probable conformers of the molecule were computed, of which only two conformations were observed. Based on an analysis of fluorescence excitation spectra, fluorescence spectra, shapes of rotational band contours at the electronic S0–S1 transition of TIES, and theoretical computations, the above conformers were assigned to steric structures. Twisted structures have the lowest energy due to intramolecular hydrogen bonds $$ C - H \cdots O <_C^{Si} $$ between hydrogen atoms of methyl groups and an oxygen atom and C–H···π between H and the π-electron cloud of the indole ring.

Tert-Butyl 2-benzoyl-2-methylpropanoate

The title compound, C15H20O3, is bent with a dihedral angle of 67.28 (9)° between the mean planes of the phenyl ring and a group encompassing the ester functionality (O=C—O—C). In the crystal, mol­ecules related by inversion symmetry are connected by weak C—H⋯O inter­actions into infinite chains. On one side of the mol­ecule there are two adjacent inter­actions between neighbouring mol­ecules involving the H atoms of methyl groups from the dimethyl groups and the O atoms of the ketone; on the other side, there are also two inter­actions to another adjacent mol­ecule involving the H atoms on the phenyl rings and the carbonyl O atoms of the ester functionality.

2,3,5-Trimethyl-1,4-hydroquinone

The mol­ecule of the title compound, C9H12O2, is approximately planar (mean atomic deviation = 0.0346 Å) and disposed about a crystallographic centre of symmetry. The H atom of the benzene ring is disordered over four orientations, with occupancies of 0.100 (3) and 0.401 (3) at the C atoms in the 2- and 3-positions and the same at their symmetric location. The H atoms of methyl group at the 2-position are disordered over two positions of equal occupancy. In the crystal structure, adjacent mol­ecules are linked through O—H⋯O hydrogen bonds, forming a two-dimensional network.

Theoretical study of the molecular and electronic structure of methanol on aTiO2(110)surface

We present density-functional-theory calculations of the molecular and electronic structure of methanol adsorption on stoichiometric TiO2(110) surface. We have investigated 11 different molecular and dissociated adsorption structures of CH3OH at 1 monolayer coverage. The relative stabilities of different structures depend on the chemisorption-induced charge transfer, the relative strengths of different types of hydrogen bonds, the steric hindrance between methyl groups and the surface stress. We found the intermolecular hydrogen bonding to play an important role in stabilizing the overlayer. We also investigated the occupied and unoccupied surface electronic structure, and the adsorbate-induced surface dipole moment and work-function changes. The electronic structures show that the highest-occupied molecular orbital of CH3OH is near the valance-band maximum, which reflects the character of CH3OH as a hole scavenger on TiO2 surfaces. The unoccupied partially solvated or “wet” electron states for CH3OH on TiO2 are primarily distributed on H atoms of methyl groups. Despite many different structural motifs, the wet-electron-state energy primarily correlates with the surface dipole moment.

2-Bromo-5-iodo-1,3-dimethylbenzene

In the mol­ecule of the title compound, C8H6BrI, the H atoms of methyl groups are disordered; site-occupation factors were fixed at 0.50. The non-H atoms all lie on a crystallographic mirror plane. Weak intra­molecular C—H⋯Br hydrogen bonds result in the formation of two non-planar five-membered rings.