Synthesis and conformational analysis of novel N(OCH3)-linked disaccharide analogues

N(OMe)-linked disaccharide analogues, isosteric to the corresponding natural disaccharides, have been synthesized by chemoselective assembly of unprotected natural monosaccharides with methyl 6-deoxy-6-methoxyamino-alpha-D-glucopyranoside in an aqueous environment. The coupling reactions were found to be chemo- and stereoselective affording beta-(1-->6) disaccharide mimics when using Glc and GlcNAc; in the case of Gal, the beta-anomer was prevalent (beta:alpha=7:1). An iterative method for the synthesis of linear N(OMe) oligosaccharide analogues was demonstrated, based on the use of an unprotected monosaccharide building block in which an oxime functionality at C-6 is converted during the synthesis into the corresponding methoxyamino group. The conformational analysis of these compounds was carried out by using NMR spectroscopy, ab initio, molecular mechanics, and molecular dynamics methods. Optimized geometries and energies of fourteen conformers for each compound have been calculated at the B3LYP/6-31G* level. Predicted conformational equilibria were compared with the results based on NMR experiments and good agreement was found. It appears that N(OMe)-linked disaccharide analogues exhibit a slightly different conformational behavior to their parent natural disaccharides.     

1H, 1 3C,and 1 5N Chemical shifts and 1H-1 5N and 1 3C-1 5N heteronuclear spin-spin coupling constants in the NMR spectra of 5-substituted furfural oximes

The ¹H, ¹³C, and ¹⁵N NMR spectra of ¹⁵N-enriched 5-substituted furfural oximes were investigated. It was shown that the chemical shifts of the ring atoms and the oxime group correlate satisfactorily with the F and R substituent constants, whereas their sensitivity to the effect of the substituents is lower than in monosubstituted furan derivatives. The constants of spin-spin coupling between the ring protons and the oxime group were determined. An analysis of the ¹H-¹H spin-spin coupling constants (SSCC) on the basis of their stereospecificity indicates that the E isomers have primarily an s-trans conformation in polar dimethyl sulfoxide, whereas the Z isomers, on the other hand, have an s-cis conformation. The signs of the direct and geminal ¹³C-¹⁵N SSCC were determined for 5-trimethylsilylfurfural oxime.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1172–1177, September, 1985.The authors thank N. O. Saldabol, L. M. Ignatovich, and N. P. Erchak for providing us with the investigated compounds.     

C?H···N and C?H···O intramolecular hydrogen bonding effects in the 1H, 13C and 15 N NMR spectra of the configurational isomers of 1‐vinylpyrrole‐2‐carbaldehyde oxime substantiated by DFT calculations

According to the ¹H, ¹³C and ¹⁵N NMR spectroscopic data and DFT calculations, the E‐isomer of 1‐vinylpyrrole‐2‐carbaldehyde adopts preferable conformation with the anti‐orientation of the vinyl group relative to the carbaldehyde oxime group and with the syn‐arrangement of the carbaldehyde oxime group with reference to the pyrrole ring. This conformation is stabilized by the C? H···N intramolecular hydrogen bond between the α‐hydrogen of the vinyl group and the oxime group nitrogen, which causes a pronounced high‐frequency shift of the α‐hydrogen signal in ¹H NMR (～0.5 ppm) and an increase in the corresponding one‐bond ¹³C–¹H coupling constant (ca 4 Hz). In the Z‐isomer, the carbaldehyde oxime group turns to the anti‐position with respect to the pyrrole ring. The C? H···O intramolecular hydrogen bond between the H‐3 hydrogen of the pyrrole ring and the oxime group oxygen is realized in this case. Due to such hydrogen bonding, the H‐3 hydrogen resonance is shifted to a higher frequency by about 1 ppm and the one‐bond ¹³C–¹H coupling constant for this proton increases by ～5 Hz. Copyright © 2008 John Wiley & Sons, Ltd.     

Solution- and bound-state conformational study of N,N',N"-triacetyl chitotriose and other analogous potential inhibitors of hevamine: application of trNOESY and STD NMR spectroscopy

The solution-state conformations of N,N',N"-triacetyl chitotriose (1) and other potential chitinase inhibitors 2-4 were studied using a combination of NMR spectroscopy (NOESY) and molecular mechanics calculations. Determination solely of the global energy minimum conformation was found to be insufficient for an agreement with the NMR results. An appropriate consistency between the NMR experimental data and theoretical calculations was only reached by assessing the structures as population-weighted average conformers based on Boltzmann distributions derived from the calculated relative energies. Analogies, but also particular differences, between the synthetic compounds 2-4 and the naturally-occurring N,N',N"-triacetyl chitotriose were found. Furthermore, the conformation of compounds 1 and 2 when bound to hevamine was also studied using transferred NOESY experiments and the binding process was found to impart a level of conformational restriction on the ligands. The preferred conformation as determined for 1 in the bound state to hevamine belonged to one of the conformational families found for the compound when free in solution, although full characterisation of the bound-state conformations was impeded due to severe signal overlap. Saturation transfer difference NMR experiments were also employed to analyse the binding epitopes of the bound compounds. We thus determined that it is mainly the acetyl amido groups of the trisaccharide and the heterocyclic moiety which are in close contact with hevamine.     

Solvatochromic analysis of some N-nitroso oxime derivatives--Taft and Catalan approach

Some novel N-nitroso oxime derivatives were synthesized and characterized by (1)H, (13)C, (1)H-(1)H and (1)H-(13)C COSY NMR spectra. The spectra of all these N-nitroso oximes reveal the presence of two isomers labelled as E (-NOH group is anti to N-N=O moiety) and Z (-NOH group is syn to N-N=O moiety) in solution and the coupling constants ruled out the possibility of normal chair conformation. From the theoretical studies and coupling constant values it was found that both E (major) and Z (minor) isomers of N-nitroso oximes exist as an equilibrium mixture of CA and boat conformation (B(1)) and this was also supported by DFT calculation. The photophysical properties of these oxime derivatives were studied and the observed lower fluorescence quantum yield may be due to an increase in the non-radiative deactivation rate constant. This is attributed due to the presence of non-chair conformation of N-nitroso oxime derivatives.     

The origin of the conformational preference of N,N'-diaryl-N,N'-dimethyl ureas

Poly aromatic ureas and poly aromatic amides are important classes of foldamers-oligomers with well defined conformations. We have explored the origins of the conformational preference of some N,N'-diaryl-N,N'-dimethyl ureas by a combination of NMR spectroscopy and electronic structure calculations using both a recently developed density functional (M06-2X) and a DFT approach (DFT-D) having empirical corrections for dispersive interactions. We have validated the DFT-D approach for structures of this type using high level wavefunction calculations, (CCSD(T)), of the unsubstituted N,N'-diphenyl-N,N'-dimethyl urea. For the N,N'-diaryl-N,N'-dimethyl ureas we have identified a number of 'endo' conformers (i.e. having an E,E geometrical conformation about the two urea C-N bonds), both π- and tert-butyl-stacked, as well as 'exo' structures (having a Z geometrical conformation about at least one of the C-N bonds), and have computed the relative energies of these conformers as well as the barriers for their interconversion. We find that the relative energies of the 'endo' structures closely follow the relative values of the dispersive interactions. The calculations have allowed us to associate different conformers with the various peaks in the NMR spectra, which point to relatively small differences in energy between the conformers. Somewhat larger energy differences are predicted by the two computational approaches, with the M06-2X functional performing the better of the two. It is suggested that the continuum model employed may not be sufficiently accurate to reflect the solvation of the various conformers.     

The structure of azines derived from C‐formyl‐1H‐imidazoles in solution and in the solid state: tautomerism,configurational and conformational studies

The structures of three azines derived from 2‐formylimidazole, 4(5)‐formylimidazole, and 4(5)‐formyl‐5(4)‐methylimidazole have been determined in solution and in the solid state. Density Functional Theory (DFT) Polarizable Continuum Model (PCM) calculations (geometries, energies, and chemical shifts), NMR [solution and cross polarization magic‐angle spinning (CPMAS)], and X‐ray crystallography [azine of 4(5)‐formylimidazole] have been used. The configuration around the central C = N bonds has been determined and some insights about prototropic tautomerism and conformation have been gained. Copyright © 2013 John Wiley & Sons, Ltd.     

Approaches to the synthesis of some tyrosine-derived marine sponge metabolites: synthesis of verongamine and purealidin N

The oxidation of tyrosine ethyl ester (7) with Na(2)WO(4)/H(2)O(2) in ethanol, dimethyldioxirane in acetone, or methyltrioxorhenium/H(2)O(2) in EtOH gave the corresponding tyrosine oxime (8) in high yield. Controlled bromination of the aromatic ring gave the monobromo oxime (9), the dibromo oxime (10), or the spiroisoxazoline (11) depending upon reaction conditions. Synthesis of the known metabolite verongamine (15) was achieved by oxidation of O-methyl bromotyrosine methyl ester and amidation of the resulting oxime ester (14) with histamine. The mono- and di-bromotyrosine oxime derivatives (9 and 10) were further transformed into the naturally occurring nitriles (16 and 17) by base hydrolysis of the ester and acid-catalyzed decarboxylation. Wadsworth-Emmons olefination of the dibromobenzaldehyde (20b) with phosphonate (18) gave the pyruvate silylenolether (21b). Deprotection and in situ oxime formation gave the oxime ester (23b). Attempted purification of the pyruvate ester resulted in a homoaldol condensation yielding butenolide (22). Amidation of the oxime ester (23b) with histamine, followed by deprotection of the MOM ether gave the first synthesis of purealidin N (28). Oxidative spirocyclization of the phenolic oxime ester (23d) with a polymer-bound iodosyl diacetate gave the spiroisoxazoline (24) and represents a formal synthesis of aerothionin (26a), homoaerothionin (26b), and aerophobin-1 (25).     

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

Preceding NMR experiments show that the conformation of tandem GA base pairs, an important recurrent non-canonical building block in RNA duplexes, is context dependent. The GA base pairs adopt "sheared" N3(G)-N6(A), N2(G)-N7(A) geometry in the r(CGAG)(2) and r(iGGAiC)(2) contexts while switching to "imino" N1(G)-N1(A), O6(G)-N6(A) geometry in the r(GGAC)(2) and r(iCGAiG)(2) contexts (iC and iG stand for isocytosine and isoguanine, respectively). As base stacking is likely to be one of the key sources of the context dependence of the conformation of GA base pairs, we calculated base stacking energies in duplexes containing such base pairs, to see if this dependence can be predicted by stacking energy calculations. When investigating the context dependence of the GA geometry two different conformations of the same duplex were compared (imino vs. sheared). The geometries were generated via explicit solvent MD simulations of the respective RNA duplexes, while the subsequent QM energy calculations focused on base stacking interactions of the four internal base pairs. Geometrical relaxation of nucleobase atoms prior to the stacking energy computations has a non-negligible effect on the results. The stacking energies were derived at the DFT-D/6-311++G(3df,3pd) level. We show a rather good correspondence between the intrinsic gas-phase stacking energies and the NMR-determined GA geometries. The conformation with more favorable gas-phase stacking is in most cases the one observed in experiments. This correlation is not improved when including solvent effects via the COSMO method. On the other side, the stacking calculations do not predict the relative thermodynamic stability of duplex formation for different sequences.     

N’-苄基酰腙分子的氮-氮键旋转位阻及分子构象

采用动态核磁共振波谱(DNMR)和密度泛函理论(DFT)对N'-苄基酰腙化合物进行构象研究. 实验和理论计算表明, 1H NMR图谱中三组不同质子的双峰裂分是由N—N键旋转位阻造成的, 而这三个双峰裂分的化学位移差异随温度升高而减小. 通过模拟化学位移差异与温度的关系, 得到了交换速率常数, 采用Eyring方程计算出N—N键旋转位阻. 提出顺式和反式共存的模型来分析酰胺质子信号分裂的原因, 并利用DFT计算得出优化的异构体构象及其最低能量. 端甲基质子和次甲基质子信号裂分也来源于N—N键旋转受阻. N'-苄基酰腙通过缩合反应转变成1,3,4-二唑化合物, 消除了甲基空间取向的差异, 其信号变为单峰.     

Synthesis and Crystal Structure of [VO2（C17H11N3O2） ] [VO （C4H13N3）（C6H5N3O） ]（C2H5OH）

The reaction of VO（acac）2 with 2-hydroxyl-1-naphthaldehyde isonicotinyl hydrazone and amines （ethylenediamine or diethylenetriamine） in CH3OH yields crystals of novel vanadium compounds characterized by IR, NMR spectroscopic methods and X-ray single-crystal structure determination. Two different vanadium units exist in the crystal cell of [VO2（C17H11N3O2）][VO- （C4H13N3）（C6H5N3O）]（C2H5OH） which crystallizes in the triclinic system, space group P1 with a = 8.0104（17）, b = 13.898（3）, c = 14.955（3）A, α = 89.103（4）, β = 79.551（4）, γ = 78.352（4）°, V = 1603.3（6）A^3, Mr = 723.54, Dc = 1.499 g/cm^3, Z = 2, λ（MoKα） = 0.71073 ]A,μ= 0.644 mm^-1, F（000） = 748, the final R = 0.0547 and wR = 0.0997 for 8920 observed reflections with I 〉 2σ（I）. According to structure analysis, two different molecules are arranged in the lattice and the two vanadium atoms adopt octahedral and square pyramidal coordination geometries, respectively. The interactions between DNA and vanadium complexes have been investigated by UV-Vis absorption spectro- photometry.     

Synthesis and Crystal Structure of a N,N,N′-tri(2-hydroxy-5-methylbenzyl)-1,2-ethanediamine

An aminophenol ligand, N,N,N′-tri(2-hydroxy-5-methylbenzyl)-1,2-ethanediamine, was prepared through the Mannich reaction, and structurally characterized by NMR, IR, MS and single-crystal X-ray diffraction. The title compound (C26H32N2O3, Mr = 420.54) belongs to the monoclinic system, space group P21/n with a = 8.6233(14), b = 10.2655(16), c = 26.017(4) ′, β = 95.797(2)o, V = 2291.3(6) ′3, Z = 4, the final R = 0.0461 and wR = 0.1139 for 4267 unique reflections (Rint = 0.028) with 11691 observed ones (I > 2σ(I)).     

2-环己氧羰基乙基三氯化锡及其N,N-二乙基二硫代氨基甲酸配合物的合成与结构表征

合成了2-环己氧羰基乙基三氯化锡及其N,N-二乙基二硫代氨基甲酸配合物,通过元素分析、IR、¹H和 ¹³C NMR及X-射线单晶衍射对其结构进行了表征。化合物2属于单斜晶系,C2/c空间群,晶胞参数为a=1.90867(17)nm,b=0.67885(8)nm,c=3.1902(3)nm,β=97.311(7)°,Z=8,μ=1.715mm^-1,R=0.0334。中心锡原子为含有分子内羰基氧原子和N,N-二乙基二硫代氨基甲酸配体的两个硫原子配位的畸变八面体构型。波谱数据表明化合物1和2存在着分子内羰基氧原子对锡原子的配位,而在化合物3和4中这一配位则被两个或三个双齿二硫代氨基甲酸配体所替代。化合物2的理论研究表明AM1半经验计算可以成功预测这类有机锡化合物的几何构型。     

二苄基锡N,N-二甲基氨荒酸酯的合成及晶体结构

利用二苄基二氯化锡和N, N-二甲基氨荒酸钠反应, 合成了二苄基锡N, N-二甲基氨荒酸酯(C20H26N2S4Sn, Mr = 541.36)。通过元素分析、红外光谱、核磁共振氢谱和质谱对其结构进行了表征。用X-射线单晶衍射测定了该化合物的晶体结构。化合物为单斜晶系, 空间群P21/n, a = 1.3926(5), b = 0.9832(4), c = 1.7080(7) nm, b = 103.541(6), V = 2.274(2) nm3, Z = 4, Dc = 1.581 g/cm3, m(MoKa) = 1.500 mm-1, F(000) = 1096, R = 0.0482, wR = 0.1162. 在化合物的晶体中, 锡原子为六配位的畸变八面体构型。     

Geometries and electronic structures of metastable C2N4 and its ions

We carried out the computational studies on the geometric and electronic properties of electronic states of metastable C(2)N(4) (m-C(2)N(4)) and corresponding ions using the CASSCF and DFT(B3LYP)/CCSD(T) techniques. The optimized geometries of electronic states, vibrational frequencies, Mulliken populations, bond orders, and average polarizabilities are computed at the DFT level while the relative energies of the electronic states, ionization energy, electron affinity, binding energy of m-C(2)N(4) are calculated at the CCSD(T) level. The anion photoelectron spectra of m-C(2)N(4)(-) are also predicted. It is interesting to find that the relative energies of the electronic states of m-C(2)N(4) cluster linearly correlate with the amount of charge transfer between N and C atoms and that, however, there is no charge transfer between C and N atoms upon electron ionization or electron attachment.     

Convenient synthesis and NMR spectral studies of variously substituted <Emphasis Type="Italic">N</Emphasis>-methylpiperidin-4-one-<Emphasis Type="Italic">O</Emphasis>-benzyloximes

Abstract  A series of variously substituted N-methylpiperidin-4-one-O-benzyloximes were synthesized by three different methods. Among them, the direct conversion of 2,6-diarylpiperidin-4-ones into the corresponding oxime ethers (method A) was proved to be better than the other two methods in the sense of good yield, convenience, easy work-up and quick reaction time. All the synthesized compounds are characterized by IR, Mass and NMR (¹H NMR, ¹³C NMR, ¹H-¹H COSY, ¹H-¹³C COSY and HMBC) spectral studies. The conformational preference of the synthesized oxime ethers with/without alkyl and aryl substituents at C-3/C-5 and C-2/C-6 is discussed using the spectral data. The observed chemical shifts and coupling constants suggest that the synthesized oxime ethers adopt chair conformation with equatorial orientation of all the substituents, whereas 1-methyl-3-isopropyl-2,6-diphenylpiperidin-4-one-O-benzyloxime also exists in boat conformation. Based on the NMR data, the effects of oximination on ring carbons and their associated protons and alkyl substituents are discussed. In addition, the effect of NMe group on the 2,6-diarylpiperidin-4-one-O-benzyloximes was also studied. Graphical abstract        

1H, 13C and 15N NMR assignments of phenazopyridine derivatives

Phenazopyridine hydrochloride (1), a drug in clinical use for many decades, and some derivatives were studied by one- and two-dimensional (1)H, (13)C and (15)N NMR methodology. The assignments, combined with DFT calculations, reveal that the preferred protonation site of the drug is the pyridine ring nitrogen atom. The chemoselective acetylation of phenazopyridine (2) and its influence on the polarization of the azo nitrogen atoms were evidenced by the (15)N NMR spectra. Molecular calculations of the phenazopyridines 2-4 show that the pyridine and phenyl groups are oriented in an antiperiplanar conformation with intramolecular hydrogen bonding between the N-b atom and the C-2 amino group preserving the E-azo stereochemistry.     

Study of conformations and hydrogen bonds in the configurational isomers of pyrrole‐2‐carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis

The ¹H, ¹³C and ¹⁵N NMR studies have shown that the E and Z isomers of pyrrole‐2‐carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole‐2‐carbaldehyde oxime is stabilized by the N? H···N and N? H···O intramolecular hydrogen bonds, respectively. The N? H···N hydrogen bond in the E isomer causes the high‐frequency shift of the bridge proton signal by about 1 ppm and increase the ¹J(N, H) coupling by ～3 Hz. The bridge proton shows further deshielding and higher increase of the ¹J(N, H) coupling constant due to the strengthening of the N? H···O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by ～3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of ¹H shielding and ¹J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N? H···N and N? H···O hydrogen bondings to be estimated. The NBO analysis suggests that the N? H···N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N? H bond through the N? H···O hydrogen bond occurs in the Z isomer. Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis and Crystal Structure of 4,4'-(4-(1-Naphthyl)-4-phenyl-1,3-butadienylidene)-bis[N,N-diethylbenzenamine]

1 INTRODUCTION Organic photo-conductors (OPCs), due to their great advantages over inorganic ones, have been widely used in xerography and holography and aroused considerable interest in the past several de- cades. Recently, almost all OPCs are of a layered structure with a thin charge generation layer (CGL) and a charge transport layer (CTL). Current resear- ches are directed to both improving the chara- cteristics of existing OPCs and developing new ma- terials for future applicati…     

Structural and spectral studies on N-(4-chloro)benzoyl-N′-(4-tolyl)thiourea

The crystal and molecular structure of the N-(4-chloro)benzoyl-N′-(4-tolyl)thiourea (C₁₅H₁₃N₂OSCl, M_r=304.79) is determined by X-ray diffraction. The crystal structure is monoclinic, space group: P2₁/n, a=16.097(6), b=4.5989(2), c=19.388(7) Å and β=89.299(6)° V=1434.7(9)ų, Z=4. FTIR and NMR spectra have been characterized. The interactions of intramolecular and intermolecular hydrogen bonds have been discussed. Density functional theory (DFT) (B3LYP) methods have been used to determine the structure and energies of stable conformers. Minimum energy conformations are calculated as a function of the torsion angle θ (C13–N1–C14–N2) varied every 30°. The optimized geometry corresponding to crystal structure is the most stable conformation. This has partly been attributed to intramolecular hydrogen bonds. With the basis sets of the 6-311G* quality, the DFT calculated bond parameters and harmonic vibrations are predicted in a very good agreement with experimental data.