Determination of backbone angle psi in proteins using a TROSY-based alpha/beta-HN(CO)CA-J experiment

Transverse relaxation-optimized NMR experiment (TROSY) for the measurement of three-bond scalar coupling constant between (1)H(alpha)(i-1) and (15)N(i) defining the dihedral angle psi is described. The triple-spin-state-selective experiment allows measurement of (3)J(H(alpha)N) from (13)C(alpha), (15)N, and (1)H(N) correlation spectra H(2)O with minimum resonance overlap. Transverse relaxation of (13)C(alpha) spin is minimized by using spin-state-selective filtering and by acquiring a signal longer in (15)N-dimension in a manner of semi-constant-time TROSY evolution. The (3)J(H(alpha))(N) values obtained with the proposed alpha/beta-HN(CO)CA-J TROSY scheme are in good agreement with the values measured earlier from ubiquitin in D(2)O using the HCACO[N] experiment.     

Vibrational spectral studies on charge transfer and ionic hydrogen‐bonding interactions of nonlinear optical material L‐arginine nitrate hemihydrate

The near infrared Fourier‐transform (NIR FT)‐Raman and Fourier‐transform infrared (FT‐IR) spectroscopies supported by HF/6‐31G(d) computations have been employed to derive equilibrium geometry, vibrational wavenumbers and the first hyperpolarizability of the nonlinear optical (NLO) material, L ‐arginine nitrate (LAN) hemihydrate. The reasonable NLO efficiency, predicted for the first time in this novel compound, has been confirmed by Kurtz–Perry powder second harmonic generation (SHG) experiments. The changes in the atomic charge distribution among different groups due to the presence of strong electronegative atoms and the shrinking of N O bonds of nitrate anion and C N bonds of guanidyl group have been analyzed. The splitting of the carboxylate stretching modes, blue shifting of methine vibrations and the electronic effects such as backdonation and induction on the methylene hydrogen atoms have also been examined in detail. The intense low wavenumber H‐bond Raman vibrations due to electron–phonon coupling and nonbonded interactions in making the LAN molecule NLO active have been discussed based on the vibrational spectral features. The natural bond orbital (NBO) analysis and HF computations confirm the occurrence of strong intra‐ and intermolecular N H·O and O H·O ionic hydrogen bonding between charged species providing the noncentrosymmetric structure in the LAN crystal. Copyright © 2008 John Wiley & Sons, Ltd.     

3hJ coupling between C(alpha) and H(N) across hydrogen bonds in proteins

J couplings between (13)C(alpha) and (1)H(N) across hydrogen bonds in proteins are reported for the first time, and a two- or three-dimensional NMR technique for their measurement is presented. The technique exploits the TROSY effect, i.e., the degree of interference between dipolar and chemical shift anisotropy relaxation mechanisms, for sensitivity enhancement. The 2D or 3D spectra exhibit E.COSY patterns where the splittings in the (13)CO and (1)H(N) dimensions are (1)J((13)C(alpha), (13)CO) and the desired (3h)J((13)C(alpha), (1)H(N)), respectively. A demonstration of the new method is shown for the (15)N,(13)C-labeled protein chymotrypsin inhibitor 2 where 17 (3h)J((13)C(alpha), (1)H(N)) coupling constants ranging from 0 to 1.4 Hz where identified and all of positive sign.     

Improved measurement of (3)J(H(alpha)(i),N(i+1)) coupling constants in H(2)O dissolved proteins.

A modification to the recently proposed alpha/beta-HN(CO)CA-J TROSY pulse sequence (P. Permi et al., J. Magn. Reson. 146, 255-259 (2000)) makes it possible to determine (3)J(H(alpha)(i), N(i+1)) coupling constants from a single E.COSY-type cross-peak pattern rather than from two (1)H(alpha) spin-state-edited subspectra. Advantages are increased (15)N resolution, critical to extracting accurate (1)H(alpha)-(15)N coupling constants, and minimized differential relaxation due to nested (13)C(alpha) and (15)N evolution periods. Application of the improved pulse sequence to Desulfovibrio vulgaris flavodoxin results in (3)J(H(alpha)(i), N(i+1)) values being systematically larger than those obtained with the original scheme. Parametrization of the coupling dependence on the protein backbone torsion angle psi yields the Karplus relation (3)J(H(alpha)(i), N(i+1))=-1.00 cos(2)(psi-120 degrees )+0.65 cos(psi-120 degrees )-0.15 Hz, with a residual root-mean-square difference of 0.13 Hz between measured and back-calculated coupling constants. The curve compares with data derived from ubiquitin (A. C. Wang and A. Bax, J. Am. Chem. Soc. 117, 1810-1813 (1995)), although spanning a slightly larger range of J values in flavodoxin. The orientation of the Ala39/Ser40 peptide link, forming a type-II beta-turn in flavodoxin, is twisted against X-ray-derived torsions by approximately 10 degrees in the NMR structure as evident from the analysis of straight phi- and psi-related (3)J coupling constants. The remaining deviation of some experimental values from the prediction is likely to be due to strong hydrogen bonding, substituent effects, or the additional dependence on the adjacent torsions straight phi.     

三维超分子配合物[Zn（C_（12）H_8N_3）_2·H_2O]的水热合成、晶体结构及光致发光1

通过水热法合成了一种三维超分子配合物Zn（C12H8N3）2.H2O,经元素分析、紫外和红外光谱对其进行表征。用X射线单晶衍射测定了其晶体结构,该配合物晶体属单斜晶系,P21/c空间群,晶胞参数为：a=1.25239（10）nm,b=1.30233（11）nm,c=1.33167（11）nm,β=102.6950（10）°,Z=4,[Zn（C12H8N3）2.H2O],Mr=471.81,V=2.1189（3）nm^3,Dc=1.479g·cm^-3,μ=1.189mm^-1,F（000）=968,R1=0.0300,WR2=0.1017,GOF=1.005。该化合物由1个Zn（Ⅱ）离子、2个2-（2-吡啶基）苯并咪唑阴离子和1分子配位水组成。其中2-（2-吡啶基）苯并咪唑的1位氮原子、吡啶环上氮原子及水分子中氧原子与锌（Ⅱ）离子配位,形成五配位的畸变三角双锥结构,单胞分子之间通过氢键O（w）-H…N和π-π堆积作用相互构成三维网状超分子体系。固态荧光测试显示,该配合物具有强的蓝色荧光发射（λmax=456nm）。     

Structural and electronic properties of a single Si chain doped zigzag AlN nanoribbon

The first-principles projector-augmented wave (PAW) potentials within the density function theory (DFT) framework have been used to determine the geometry structures and electronic properties of the zigzag edge AlN nanoribbons (ZAlNNRs) doped with a single Si chain under generalized gradient approximation (GGA). The average Al–Si, Si–Si, Al–N, Si–N, Al–H and N–H bond lengths are 2.39, 2.16, 1.83, 1.74, 1.59 and 1.03 Å, respectively. Pure 7-ZAlNNR is an indirect semiconductor with a large band gap of 2.235 eV, while a semiconductor to metal transformation is taken place after a single Si chain substituting for a single Al–N chain at various positions. In pure 7-ZAlNNR, the HVB and LCB are mainly attributed to the edge N and Al atoms, respectively, while in a single Si chain substituting doped 7-ZAlNNR, the HVB and LCB are mainly attributed to the Si atoms. The Al–N, Al–H and Al–Si bonds are ionic bond, the Si–Si and Si–H bonds are covalent bond, the N–H and N–Si bonds are covalent bond modified ionic bond.     

Proton-detected separated local field spectroscopy

PISEMO, a separated local field experiment that can be performed with either direct (15)N (or (13)C) detection or indirect (1)H detection, is demonstrated on a single crystal of a model peptide. The (1)H signals modulated by (1)H-(15)N heteronuclear dipole-dipole couplings are observed stroboscopically in the windows of the multiple-pulse sequence used to attenuate (1)H-(1)H homonuclear dipole-dipole couplings. (1)H-detection yields spectra with about 2.5 times the signal to noise ratio observed with (15)N-detection under equivalent conditions. Resolution in both the (15)N chemical shift and (1)H-(15)N heteronuclear dipole-dipole coupling dimensions is similar to that observed with PISEMA, however, since only on-resonance pulses are utilized, the bandwidth is better.     

Asymmetric MRI magnet design using a hybrid numerical method

Two-dimensional 1H/13C polarization inversion spin exchange at the magic angle experiments were applied to single crystal samples of amino acids to demonstrate their potential utility on oriented samples of peptides and proteins. High resolution is achieved and structural information obtained on backbone and side chain sites from these spectra. A triple-resonance experiment that correlates the 1H-13Calpha dipolar coupling frequency with the chemical shift frequencies of the alpha-carbon, as well as the directly bonded amide 15N site, is also demonstrated. In this experiment the large 1H-13Calpha heteronuclear dipolar interaction provides an independent frequency dimension that significantly improves the resolution among overlapping 13C resonances of oriented polypeptides, while simultaneously providing measurements of the 13Calpha chemical shift, 1H-13C dipolar coupling, and 15N chemical shift frequencies and angular restraints for backbone structure determination.     

13C high-resolution solid state NMR studies of the structure and dynamics of 1,6:3,4-dianhydro-2-O-tosyl-beta-D-galactopyranose

13C CP/MAS, dipolar dephasing MAS and theoretical GIAO calculations were employed to assign 13C resonances to the molecular structure of 1,6:3,4-dianhydro-2-O-tosyl-beta-D-galactopyranose 1. From spinning sideband intensities, employing the graphical method of Herzfeld and Berger the 13C delta(ii) parameters for aromatic residue were calculated. The experimental data were compared with computed results obtained by means of the B3PW91 hybrid method and 6-311G (df, p) basis set. The X-ray geometry of 1 with the correlated position of hydrogen atoms was taken as input data for theoretical calculations. As concluded from Cambridge Crystallographic Database (CSD) search, there are two reports describing the X-ray studies of 1 that show the slightly different geometry of the compound under investigation. This work shows that such discrepancies in geometry can generate differences between computed 13C delta(ii) parameters up to 6 ppm. 13C T1 and 1H T1rho relaxation times reveal that 1 is very rigid in crystal lattice. This structure is characterized by extremely long 1H T1rho, found to be in range ca. 200 ms.     

Determination of three-bond scalar coupling between 13C' and 1H(alpha) in proteins using an iHN(CA),CO(alpha/beta-J-COHA) experiment

Triple-resonance NMR experiments for measuring three-bond scalar coupling constant between 13C' (i-1) and 1H(alpha)(i) spins, defining the dihedral angle phi, are presented. The novel experiments enable the measurement of 3JC'H(alpha)) from simple two (or three)-dimensional 13C', (15N/13C(alpha)), 1H(N) correlation spectra with minimal resonance overlap, thanks to solely intraresidual coherence transfer pathway and spin-state-selection. The 3J(C'H(alpha)) values measured in human ubiquitin using the proposed intraresidual iHN(CA),CO(alpha/beta-J-COHA) TROSY method were compared with those determined previously utilizing the HCAN[C'] experiment.     

(13)C chemical shift and (13)C-(14)N dipolar coupling tensors determined by (13)C rotary resonance solid-state NMR

This work explores the utility of simple rotary resonance experiments for the determination of the magnitude and orientation of (13)C chemical shift tensors relative to one or more (13)C--(14)N internuclear axes from (13)C magic-angle-spinning NMR experiments. The experiment relies on simultaneous recoupling of the anisotropic (13)C chemical shift and (13)C--(14)N dipole--dipole coupling interactions using 2D rotary resonance NMR with RF irradiation on the (13)C spins only. The method is demonstrated by experiments and numerical simulations for the (13)C(alpha) spins in powder samples of L-alanine and glycine with (13)C in natural abundance. To investigate the potential of the experiment for determination of relative/absolute tensor orientations and backbone dihedral angles in peptides, the influence from long-range dipolar coupling to sequential (14)N spins in a peptide chain ((14)N(i)--(13)C(alpha)(i)--(14)N(i+1) and (14)N(i+1)--(13)C'(i)--(14)N(i) three-spin systems) as well as residual quadrupolar-dipolar coupling cross-terms is analyzed numerically.     

H,O,N,He原子掺杂Al原子的第一性原理研究

采用密度泛函理论框架下的第一性原理平面波赝势方法,对Al中分别加入H,O,N和He原子后的晶体状态进行了研究.通过晶体结构和形成能分析比较了杂质原子占据不同位置的难易程度及对晶体稳定性的影响,并从态密度、电荷密度和电荷布居的角度,分析了其电子结构.结果表明:H、O和N原子占据金属Al的四面体间隙最稳定,而He原子主要占据金属Al的八面体间隙. O和N原子与Al原子具有强烈的共价作用,H原子与Al原子存在共价作用但相对较弱,而He原子与Al原子的相互作用以范德华力为主.进一步揭示了四种原子在金属Al中不同行为的电子机制.     

Characterization of hydrogen bond lengths in Watson-Crick base pairs by cross-correlated relaxation

Hydrogen bond lengths in Watson-Crick base pairs can be characterized by cross-correlated relaxation between 1H chemical shift anisotropy and dipole-dipole coupling of 1H and its hydrogen bond acceptor 15N. As a reference, the cross-correlated relaxation between 1H chemical shift anisotropy and dipole-dipole coupling of 1H and its hydrogen bond donor 15N is used. With the two measured cross-correlated relaxation rates, an apparent hydrogen bond length can be determined, which is composed by the hydrogen bond length multiplied by a term representing the amplitude of inter-base motions. Data are presented for the 15N3-1H3...15N1 hydrogen bonds in A=T base pairs of the Antennapedia homeodomain-DNA complex with a correlation time of global rotational diffusion of 20 ns.     

Can 2‐acylpyrroles form an intramolecular hydrogen bond?

The formation of intramolecular hydrogen bonding by certain N‐substituted 2‐acylpyrroles has been demonstrated by B3LYP/aug‐cc‐pVDZ calculations, the quantum theory of atoms in molecules, and the natural bond orbital method. Total electron energy densities H_BCP at the bond critical point of the H?O bond were applied to analyze the strength of these interactions. The relations between quantum theory of atoms in molecules, carbonyl stretching vibrational modes ν_{C = O}, and natural bond orbital parameters associated with the formation of the C–H?O interaction have been established. The short contacts were found experimentally in the crystal structure of a new 2‐acylpyrrole derivative 5‐chloro‐2‐oxopentyl‐1‐(5‐chloro‐2‐oxopentyl)pyrrolo‐2‐carboxylate. The influence of 2‐ and N‐substitution of 2‐acylpyrroles on C‐H?O interaction energy is discussed. It was found that the methylene group may act as a proton donor leading to a red‐shift or blue‐shift phenomenon of the ν_C–H stretching mode. Copyright © 2015 John Wiley & Sons, Ltd.     

有机分子PTCDA在P型Si单晶(100)晶面的生长机理

对PTCDA的分子结构及其化学键的形成进行了分析,并讨论了晶面指数（100）Si单晶的晶格结构。在此基础上,评述了PTCDA分子在P-Si单晶（100）晶面上生长的机理,并制备了样品PTCDA/P-Si（100）。利用XRD对样品测试得出,在P-Si（100）晶面上沉积的PTCDA薄膜中仅存在α物相。利用XPS对样品测试得出,在其界面层中PTCDA酸酐中的4个羟基O原子与C原子结合,其结合能为532.4 eV;苝核基团外围的8个C、H原子以共价键结合,其结合能为289.0 eV;在界面处,悬挂键上的Si原子与PTCDA酸酐中的C、O原子结合,形成C-Si-O键及C-Si键,构成了界面层的稳定结构。     

Triple resonance solid state NMR experiments with reduced dimensionality evolution periods

Two solid state NMR triple resonance experiments which utilize the simultaneous incrementation of two chemical shift evolution periods to obtain a spectrum with reduced dimensionality are described. The CO N CA experiment establishes the correlation of (13)C(i-1) to (13)C alpha(i) and (15)N(i) by simultaneously encoding the (13)CO(i-1) and (15)N(i) chemical shifts. The CA N COCA experiment establishes the correlation (13)Ca(i) and (15)CO(i) to (13)C alpha(i-1) and (15)N(i-1) within a single experiment by simultaneous encoding of the (13)C alpha(i) and (15)N(i) chemical shifts. This experiment establishes sequential amino acid correlations in close analogy to the solution state HNCA experiment. Reduced dimensionality 2D experiments are a practical alternative to recording multiple 3D data sets for the purpose of obtaining sequence-specific resonance assignments of peptides and proteins in the solid state.     

元素替代对LiNH2储氢材料释氢能力影响的第一性原理研究

采用第一性原理赝势平面波方法,研究了元素替代对 LiNH₂释氢能力影响及作用机理.计算给出了结合能、电子态密度、电荷布居,分析了结构的稳定性和原子间的成键情况.结果表明：金属Ca,Na,Al替代LiNH₂部分Li时,可以使N—H键有所减弱.Mg,Al同时替代Li时,效果最好.在Li（Mg）NH₂中,非金属元素B,C,P替代N时,C的效果最好.预测Mg,Al,C共同替代时,会得到的一种较低释氢温度的储氢材料. 关键词： 2储氢材料')" href="#">LiNH₂储氢材料 密度泛函理论 元素替代行为 释氢能力     

2D—NMR对皂皮酸—3—氧—葡萄糖醛酸^13C,^1H的完全指定—介绍HMBC和HOHAHA

HMBC是一种测定远程偶合~1H—~(13)C相关的十分灵敏的方法,特别适用于检测和甲基质子远程偶合(~2J,~3J)的碳.HOHAHA谱显示出多次Relay信息,选择适当参数可通过一次实验得到独立自旋体系中所有质子相关信息.本文用HMBC和HOHAHA实验结合同核(~1H)COSY和导核(~(13)C-~1H)COSY确认了Qwhaic acid—3—O—glucuronic acid分子中所有~(13)C和~1H的归属.     

Density functional study of uranyl （VI） amidoxime complexes

Uranyl (Ⅵ) amidoxime complexes are investigated using relativistic density functional theory. The equilibrium structures, bond orders, and Mulliken populations of the complexes have been systematically investigated under a generalized gradient approximation (GGA). Comparison of (acet) uranyl amidoxime complexes ([UO 2 (AO) n ] 2 n , 1≤ n ≤4) with available experimental data shows an excellent agreement. In addition, the U-O(1), U-O(3), C(1)-N(2), and C(3)-N(4) bond lengths of [UO 2 (CH 3 AO) 4 ] 2 are longer than experimental data by about 0.088, 0.05, 0.1, and 0.056 A. The angles of N(3)-O(3)-U, O(2)-N(1)-C(1), N(3)-C(3)-N(4), N(4)-C(3)-C(4), and C(4)-C(3)-N(3) are different from each other, which is due to existing interaction between oxygen in uranyl and hydrogen in amino group. This interaction is found to be intra-molecular hydrogen bond. Studies on the bond orders, Mulliken charges, and Mulliken populations demonstrate that uranyl oxo group functions as hydrogen-bond acceptors and H atoms in ligands act as hydrogen-bond donors forming hydrogen bonds within the complex.     

Hydrogen bonding effects on the (15)N and (1)H shielding tensors in nucleic acid base pairs

The results of systematic ab initio calculations of (15)N and (1)H chemical shielding tensors in the GC base pair as a function of hydrogen bond length are presented for the first time. The hydrogen bond length characterized by the distance r(N...N) between purine N1 and pyrimidine N3 was varied between 2.57 and 3.50 A and the chemical shift tensors were calculated by the sum-over-states density functional perturbation theory. It is shown that the hydrogen bond length has a strong effect on the chemical shielding tensor of both imino proton and nitrogen, on their orientation, and, as a consequence, on the relaxation properties of both nuclei. For a nitrogen nucleus not involved in hydrogen bonding, the shielding tensor is nearly axially symmetric and almost collinear with the bond vector. As the length of the hydrogen bond decreases, the least shielding component sigma(11) deflects from the N-H vector and the shielding tensor becomes increasingly asymmetric. The significance of the presented results for the analysis of relaxation data and the efficiency of TROSY effects together with a summary of the relevant shielding parameters are presented and discussed.