Rapid identification of common hexapyranose monosaccharide units by a simple TOCSY matching approach

Solution NMR spectroscopy is a well established technique for non-destructive characterization of the structures and conformations of complex oligo- and polysaccharides. One of the key experiments involves the use of 2D TOCSY to collect the 1H spins into groups that can be associated with the individual saccharide units that are present in the molecule under study. It is well known that the magnetization transfer rate through the 1H spin system during the TOCSY spin lock period is sensitive to the intervening 3J(H,H) scalar couplings, and therefore also to the saccharide stereochemistry. Here, we have investigated the potential to extract information on the stereochemistry of hexapyranose monosaccharide units directly from TOCSY spectra. Through a systematic experimental investigation of the magnetization transfer initiated from the anomeric 1H resonance in D-glucose, D-galactose and D-mannose it is shown that a 100 ms spin lock time provides optimal spectroscopic discrimination between these three commonly occurring building blocks. A simple matching scheme is proposed as a new tool for rapid attribution of the TOCSY traces originating from the anomeric 1H resonances towards the underlying monosaccharide type. The scheme appears robust with regard to structural variations and fairly tolerant to incidental overlap. Its application provides useful guidance during the subsequent NMR assignment process, as demonstrated with the PS7F polysaccharide from Streptococcus pneumonia. In addition, we show that our scheme affords a clear-cut distinction between the alpha- and beta-epimers of D-mannose-type units, which can be difficult to discriminate by NMR analysis. Application to the N-glycan 100.2 demonstrates the potential and wide applicability of this new discrimination approach.     

阿魏酸分子结构和振动光谱的理论研究

阿魏酸是一种有效的天然油脂抗氧化剂.采用密度泛函理论(DFT) B3LYP方法和从头算HF两种方法,在6-311++G**基组水平上对阿魏酸分子的几何结构进行全优化,得到其几何结构参数,进一步计算得到阿魏酸的红外和拉曼振动光谱.计算结果表明,采用B3LYP和HF 2种方法优化得到的几何结构及频率值是一致的,对在B3LYP方法下计算得到的红外和拉曼振动频率进行合理的理论归属并与SDBS数据库实验数据进行比较,发现计算得到的红外和拉曼振动频率与实验测定结果符合较好.阿魏酸分子结构和振动光谱的研究,为研究阿魏酸及其衍生物的化学结构与生理活性之间的构效关系提供依据.     

Theoretical investigation on the IR spectra of four‐membered silicon oxide ring

To test the mass effect on the ring vibrational frequencies (SiO₂) shift of the four‐membered silicon oxide ring, the deuterium and the tritium substituted cyclodisiloxanes on the hydrogen positions are examined at the CCSD(T)/cc‐pVTZ level of theory. The SiO₂ ring vibrations for a silicon oxide surface model compound, substituted cyclodisiloxane (Si₃O₅? O₂? Si₃O₅) with two six‐membered ring, are also calculated at the B3LYP/cc‐pVTZ level of theory. Our results of 909 and 920 cm^?1 are in good agreement with the experimental result. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

氨氯地平圆二色谱的理论解析

采用量子化学密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)在B3LYP/6-311++G**水平上对氨氯地平分子的圆二色谱进行理论研究。计算结果表明:振动圆二色谱(VCD)的803、1113、1190、1238、1348、1509、1514、1736、2972、3022和3091 cm-1处存在吸收峰,产生以上吸收峰的振动均涉及到分子手性中心或者所处的基团与分子手性中心形成相关。研究还发现,甲醇溶液使电子圆二色谱(ECD)的吸收峰红移;甲醇溶液中,S-氨氯地平的ECD谱在207、366 nm处存在正性康登效应,223 nm处存在负性康登效应;以上吸收峰均来源于π-π*电子跃迁。这些结论对于深入理解氨氯地平的手征光学性质具有一定的指导意义。     

Electronic CD study of a helical peptide incorporating Z-dehydrophenylalanine residues: conformation dependence of the simulated CD spectra

Electronic circular dichroism (CD) spectra as well as transitions from ground to excited states were predicted for a helical nonapeptide based on alternative sequence--[Z-alpha,beta-dehydrophenylalanine (Delta(Z)Phe)-X]--through semiempirical molecular orbital computation combined with time-dependent (TD) method. The simulation was performed for its various conformers that differ in helix type, helix sense, and Delta(Z)Phe side-chain orientation. These conformational variations have been shown to depend largely on its CD spectra. Comparison between simulated and observed CD profiles reveals that peptide 1 in solution favors a right-handed 3(10)-helix that adopts phenyl (Delta(Z)Phe) planes basically in a vertical orientation with respect to the helix axis. These predictions were essentially supported from CD simulation of a shorter helical analogue at ab inito or density functional TD levels. The theoretical CD-conformation relationship should provide us useful guideline for determination of helix sense in the dehydropeptide, and for estimation of its conformations statistically averaged in solution.     

Theoretical studies on the conformation of saccharides

Conformations of 2-methoxytetrahydropyran as a model for the six-membered ring in aldopyranosides have been calculated by the PCILO method using the algorithm of the conjugated gradient to optimize the geometry. The calculated geometry of the fourteen basic forms of 2-methoxytetrahydropyran was found to be in agreement with the available data obtained by X-ray diffraction of pyranosides. The results indicate differences in the geometry of 2-methoxytetrahydropyran resulting from the change of the axial vs. equatorial position of the methoxyl group. These changes are particularly meaningful in the values of bond angles and they are in agreement with the anomeric and exoanomeric effects. The experimentally found differences in the energies of an axial (⁴ C ₁) and equatorial (¹ C ₄) conformer, G = 2.9–3.7 kJ/mol, and the dipole moment, = 1.20 ± 0.05 D (1D = 3.33 10^–30mAs) agree well with the calculated values E = 3.18 kJ/mol and <> = 1.18 D which, in turn, suggest that the axial conformer is preferred over the equatorial one by a ratio a:e = 78:22.     

Theoretical studies on the conformation of saccharides

The stereochemistry of d-glucopyranose has been studied theoretically in 11 solvents. The stability of the individual conformers in solution has been compared using a method in which the total energy is divided into the energy of an isolated molecule and the solvation energy. The structure and the energy of the isolated molecule have been estimated by geometry optimization using the PCILO quantum chemical method. The solvation energy consists of electrostatic, dispersion, and cavity terms which have been determined from calculated properties of the solute and physiochemical properties of the solvents. The influence of the solvent on rotation of the individual pendant groups and the stability of anomers have been investigated. The calculated composition of the anomeric mixture of d-glucopyranose in various solvents at 25°C (e.g., in pyridine 49% is -anomer, in dimethyl sulfoxide 46%, and in water 32%) is in good agreement with the available experimental data and clearly demonstrates that the solvation properties of - and -d-glucopyranose differ. Based on the calculated abundances of anomers the magnitude of the anomeric effect has been estimated and compared with the results of corresponding calculations on other compounds.     

Theoretical study on dependence of hyperpolarizability of one‐dimensional ring system on the delocalization transition

We calculate the optical properties such as the polarization, the (hyper)polarizabilities, the critical vector potential, etc., in terms of the non‐Hermitian Anderson model of a 6‐site ring model. The dependence of the optical properties on the delocalization transition is investigated. It is found that all the total optical properties nonlinearly increase with the increase of the delocalization. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Theoretical and experimental study of the structure and vibration spectra of 4,4′-carbonyl-di-morpholine

4,4′-Carbonyl-di-morpholine was synthesized and characterized by X-ray diffraction, the FTIR and NMR spectra. The extended MO calculations using density functional theory (DFT) and self-consistent field molecular orbital Hartree-Fock theory were carried out. The results of the calculations were compared with experimental data. The experimental and calculated results were supported each other. The performance of a hybrid B3LYP density functional was compared with the ab initio restricted Hartree-Fock method. With the basis sets of the 6-311G** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.     

几种B环间位取代异黄酮衍生物的核磁共振谱理论研究(英文)

在B3LYP/6-31G**水平下优化了几种B环间位取代异黄酮衍生物的几何构型,在B3LYP/6-311G**水平下计算了该类化合物的核磁共振谱。研究结果表明:在1E!1H和2E～2H中的分子内氢键,其键长为0.1668nm,使整个分子形成一个四环的交叉共轭体系。从9位羟基取代对异黄酮衍生物NMR数据的影响来看,相邻的碳和相邻的氢化学位移的减少是由于电子云密度的增加和屏蔽作用的加强。而相邻碳的化学位移增加更大。此外,从取代基对化学位移的影响进行了讨论。邻对位氢的化学位移与取代基使苯环电子云密度增大的趋势相一致。A环和C环上的氢基本不受取代基的影响。对位碳的化学位移则与取代基使苯环电子云密度增大的趋势相反,邻位碳的化学位移变化趋势不明显。     

From anisole to 1,2,4,5‐tetramethoxybenzene: Theoretical study of the factors that determine the conformation of methoxy groups on a benzene ring

Unhindered ortho‐dimethoxy‐substituted phenyl rings often display a coplanar conformation. A theoretical study of a series of methoxybenzenes consisting of methoxybenzene (anisole), the three dimethoxybenzenes, and 1,2,4,5‐tetramethoxybenzene, at the DFT/B3LYP/6‐311++G** level of theory, allows us to identify the factors influencing the conformational preference and attribute the coplanarity of such methoxy groups to mesomeric effects. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Theoretical study of the structure and vibrational spectra of the Ci(2) conformation of 18-crown-6

Optimized geometries of 18-crown-6 (18ce6) were calculated at the HF/6-31G* and B3LYP/6-31G* levels of theory for the D3d, Ci(1) and Ci(2) conformations. At the B3LYP level, the Ci(2) optimized geometry was higher in energy by 23.3 and 18.8 kcal mol(-1) than the Ci(1) and D3d optimized geometries, respectively. Harmonic force field, vibrational frequencies and IR absorption intensities were calculated at the corresponding optimized geometry at the B3LYP level for the Ci(2) conformation. Scaled Ci(2) frequencies were compared with the experimental frequencies of free 18ce6, Ci(1) conformation, and 18ce6-urea complex, Ci(2) conformation. This comparison showed possible misassignments in the fundamental vibrational frequencies of 18ce6.     

LB膜中NMOB分子构象的研究

利用DFTB3LYP/4-31G^*方法,对2-硝基-5-(N-甲基-N-十八烷基)氨基苯甲酸(NMOB)进行研究。计算结果发现,苯环的5位碳原子、氨基氮原子以及十八烷基链上与其最临近的两个碳原子所组成的两面角(D)约为90ⅲ时,NMOB有最稳构象,在NMOB自交替膜中,NMOB即以这种构象存在;而D=180ⅲ时,体系总能量较最稳构象高出31.57kJ/mol,这种构象存在于NMOB/花生酸镉(CdA)交替膜中,较小的能量差异使NMOB容易在两种构象之间进行转化,在NMOB/花生酸镉(CdA)交替膜中因受到花生酸直立构象紧密排列的诱导作用,NMOB分子以能量相对较高的构象存在。     

The conformation,UV-absorption spectra and photoelectron spectra of phenoxachalcogenins

The analysis of dipole moment data obtained for dibenzo-p-dioxin, phenoxathiin, phenoxaselenin and phenoxatellurin in benzene at 25°C in conjunction with EHT calculations of the ocnformational energies show that these molecules adopt a non-planar conformation in solution. Each of the phenoxachalcogenins is folded along the axis connecting the two heteroatoms. A butterfly flapping motion about the planar conformation canot be excluded. The uv and photoelectron spectroscopic data support the conclusions drawn from the dipole moment studies. The spectroscopic data were interpreted with the help of SCF-PPP-CI calculations.     

Comparative analysis of vibration spectra of dispersive silicas and their components

Comparative analysis has been carried out on a set of partial basis spectra of the doubly amplitude-weighted density of vibration states (AWDS) of four dispersive silica: aerosil A380, silica gels SG20 and SG100 (with pore sizes 20 and 100 Å), and aerogel AG200 with mass density 200 kg/m³. The set of basis spectra includes the vibration spectra of frameworks, and of the hydroxyl and aqueous components of the surface zone of the above compounds. Aerosils, silica gels, and aerogels have been found to be radically different structural forms of amorphous silica, both from the viewpoint of their frameworks and their surface zones. The basis spectra considered represent a collection of fingerprints of the structure-dynamic properties of the compounds studied, which allows us to formulate a qualitatively new approach to computational modeling of dispersive silicas.Russian University of People's Friendship, Institute of Surface Chemistry, Ukrainian Academy of Sciences, Unified Institute of Nuclear Research. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 4, pp. 39–51, July–August, 1993.Translated by L. Smolina     

Probing furanose ring conformation by gas-phase computational methods: energy profile and structural parameters in methyl beta-D-arabinofuranoside as a function of ring conformation

The potential energy surface of methyl beta-D-arabinofuranoside (3) has been studied by ab initio molecular orbital (HF/6-31G) and density functional theory (B3LYP/6-31G) calculations via minimization of the 10 possible envelope conformers. The partial potential energy surface identified that the global minimum and lowest energy northern conformer was E(2). In the HF calculations, (2)E was the most stable southern conformer, while the density functional theory methods identified (4)E as the local minimum in this hemisphere. Additional calculations at higher levels of theory showed that the B3LYP-derived energies of many of the envelope conformers of 3 are dependent upon the basis set used. It has also been demonstrated that B3LYP/6-31+G//B3LYP/6-31G single point energies are essentially the same as those obtained from full geometry optimizations at the B3LYP/6-31+G level. The northern and southern minima of the B3LYP/6-31+G surface are, respectively, the E(2) and (2)E conformers. The B3LYP/6-31G geometries were used to study the relationship between ring conformation and various structural parameters including bond angles, dihedral angles, bond lengths, and interatomic distances.     

Ir spectra and conformation of 2-acetylindoles

On the basis of data from the IR spectra of 2-acetylindoles and their pyrrole-ring-substituted derivatives it is concluded that these substances exist in CCl₄ solution primarily in the s-trans conformation.     

Theoretical study on the lowest-frequency mode of the flavin ring

The dynamic aspects along the normal vibrational motions of the lowest frequencies in the oxidized, radical, and reduced states of flavin (isoalloxazine) have been studied. In comparison with the twist motions in the oxidized state, the butterfly motions in the radical and reduced states turned out to bring more significant variations to the frontier molecular orbital energies and to the charge distributions on the atoms of the pyrazine ring in isoalloxazine. It can be considered that the electron transfers from and to the isoalloxazine ring can be adjusted or controlled by these variations. In the reduced states the electron release from the molecule, and in the radical states the electron release from or acceptance by the molecule, could be impelled by the butterfly motions, while in the oxidized state the electron acceptance by the molecule could be accelerated slightly by the twist motion. Received: 30 September 1998 / Accepted: 20 January 1999 / Published online: 7 June 1999