RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case

Nuclear magnetic resonance (NMR) provides structural and dynamic information reflecting an average, often non-linear, of multiple solution-state conformations. Therefore, a single optimized structure derived from NMR refinement may be misleading if the NMR data actually result from averaging of distinct conformers. It is hypothesized that a conformational ensemble generated by a valid molecular dynamics (MD) simulation should be able to improve agreement with the NMR data set compared with the single optimized starting structure. Using a model system consisting of two sequence-related self-complementary ribonucleotide octamers for which NMR data was available, 0.3 ns particle mesh Ewald MD simulations were performed in the AMBER force field in the presence of explicit water and counterions. Agreement of the averaged properties of the molecular dynamics ensembles with NMR data such as homonuclear proton nuclear Overhauser effect (NOE)-based distance constraints, homonuclear proton and heteronuclear ¹H–³¹P coupling constant (J) data, and qualitative NMR information on hydrogen bond occupancy, was systematically assessed. Despite the short length of the simulation, the ensemble generated from it agreed with the NMR experimental constraints more completely than the single optimized NMR structure. This suggests that short unrestrained MD simulations may be of utility in interpreting NMR results. As expected, a 0.5 ns simulation utilizing a distance dependent dielectric did not improve agreement with the NMR data, consistent with its inferior exploration of conformational space as assessed by 2-D RMSD plots. Thus, ability to rapidly improve agreement with NMR constraints may be a sensitive diagnostic of the MD methods themselves.     

Synthesis and crystal morphology control of AlPO4-5 molecular sieves by microwave irradiation

AlPO₄-5 molecular sieves have been synthesized by the hydrothermal and solvothermal reactions using triethylamine as a template, aluminum isopropoxide and orthophosphate as the aluminum and phosphorus resource under microwave irradiation. The influences of various experimental parameters, such as reaction time, reaction temperature and reaction power, have been systematically investigated. The morphology control of AlPO₄-5 molecular sieves was achieved by changing the dosage of solvent and HF to control the solvent polarity and control the nucleation respectively. The products were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and so on. The results show that the aspect ratio of the AlPO₄-5 molecular sieves increases with the increase of the solvent polarity and with the increasing concentration of HF, the morphology of AlPO₄-5 molecular sieves changes from hexagonal plate to hexagonal rod.     

Oxidative methylation of toluene with methane catalyzed by lithium modified molecular sieves

Lithium modified molecular sieves with different structures (X, Y, ZSM-5 and AlPO₄-5) were studied as catalysts for oxidative methylation of toluene with methane. LiX zeolite was the most active catalyst for attaining best yields of ethylbenzene and styrene. The effects of basicity, crystallinity and type of structure were examined.     

Physicochemical and catalytic properties of CoAPO-5 and CoAPSO-5 molecular sieves

The physicochemical and catalytic properties of cobalt- and silicon-substituted AlPO-5 molecular sieves were studied by means of temperature-programmed reduction, temperature-programmed desorption of ammonia and the reaction of toluene disproportionation.     

NMR and Raman spectral studies of ammonium hydrogen selenites single crystals

The chemical composition and peculiarities of the structure of a salt that precipitates from aqueous solution of NH₄HSeO₃ at the 25 °C was studied by NMR and Raman spectroscopy methods using the single crystal samples with different heavy water contents. It was proved that this salt is actually monohydrate of hydrogen selenite, NH₄HSeO₃H₂O but not trihydrate of pyroselenite, (NH₄)₂Se₂O₅3H₂O as was assumed previously based on the data cited in the literature.     

Bibracchial diazatetralactams. Structure and molecular modeling of calcium complexes

Doubly-armed diazatetralactams constitute a new series of easily synthesized tetralactams. The structural study of the calcium complexes of their N,N′-dimethyl acetamido and (2-pyridylmethyl) derivatives was performed by IR, ¹H, ¹³C NMR spectroscopies and molecular modeling. These complexes showed a C₂ symmetry and a high number (8–9) of coordination around the calcium atom.     

Quantitative determination of formic acid in apple juices by H NMR spectrometry

A quantitative determination method of formic acid in apple juices is proposed by means of the proton nuclear magnetic resonance (¹H NMR) technique. Formic acid gives a singlet signal at the 8.2-8.4 ppm interval of the spectrum, and its area is used to determine the concentration of the acid. 1,3,5-Benzenetricarboxylic acid is added to the juice as an internal standard. Since the chemical shift of both species varies with the pH, ascorbic acid is also added to adjust it at 2.74 and to avoid the overlapping of the signals. Recoveries between 95 and 109% are obtained when the standard addition method is applied to the juices of five different cider apple varieties. The coefficient of variation obtained is 3.9% for intra-day repeatability (n = 5), and 4.6% for inter-day repeatability (n = 10). The limit of detection is 1.49 mg/l, calculated from “3S_y/x + intercept”. The described method is direct and no previous derivatization is needed.     

NQR and NMR study of hydrogen bonding interactions in anhydrous and monohydrated guanine cluster model: A computational study

In this paper extensive systematic computational study has been carried out to justify hydrogen bonding interactions and their influence on the oxygen, nitrogen and hydrogen NQR and NMR parameters of the anhydrous and monohydrated guanine crystal structures at two different levels, B3LYP and MP2, using 6-311++G** and D95** basis sets. These theoretical data have been compared with experimental NMR and NQR measurements. For further investigation, results of cluster calculation have been compared with that of a single molecule. Our theoretical NQR and NMR parameters of ¹⁷O, ¹⁵N and ²H atoms of anhydrous and monohydrated guanine exhibited extreme sensitivity to electron distribution around mentioned nuclei caused by cooperative influences of various types of hydrogen bonding interactions. Fortunately, our calculated isotropic shielding values and CS tensors for the ¹⁷O and ¹⁵N nuclei as well as obtained ¹⁴N-NQR parameters are in excellent agreement with experimental data. Therefore, we can undoubtedly conclude that for anhydrous and monohydrated guanine tetrameric clusters including intermolecular interactions, our theoretical estimates are in better agreement with observed experimental values than those in which these interactions have been ignored.     

Carbon-13 NMR distinction between categories of molecular order and disorder in cellulose

Differences between values of proton rotating-frame spin relaxation time constants can be exploited to separate a solid-state¹³C NMR spectrum of cellulose into subspectra of crystalline and noncrystalline regions. Variations in chemical shifts and¹³C spin-lattice relaxation time constants can then be used to study variations in molecular order and disorder within each of the two broader categories. Mechanical damage during Wiley milling increases the content of noncrystalline cellulose and changes the nature of molecular disorder within that category. Resolution enhancement of the subspectrum assigned to crystalline cellulose reveals pairs of signals at 83.9 and 84.9 ppm (cellulose I) or 86.8 and 88.3 ppm (cellulose II) assigned to C-4 on well-ordered crystal surfaces. A broader peak in the subspectrum of crystalline cellulose I is assigned to poorly-ordered surfaces. Relative proportions in Avicel microcrystalline cellulose were estimated as: 54% in crystal interiors, 22% on well-ordered surfaces, 8% on poorly-ordered surfaces, 16% in domains of disorder extending more than a few nanometres.     

Phase behavior of amphiphiles at liquid crystals/water interface: A coarse-grained molecular dynamics study

We present a coarse-grained molecular dynamics simulation study of phase behavior of amphiphilic monolayers at the liquid crystal （LC）/water interface. The results revealed that LCs at interface can influence the lateral ordering of amphiphiles. Particularly, the amphiphile tails along with perpendicularly penetrated LCs between tails undergo a two-dimension phase transition from liquid-expanded into a liquid-condensed phase as their area density at interface reaches 0.93. While, the liquid-condensed phase of the monolayer never appears at oil/water interface with isotropic shape oil particles. These findings reveal the penetration of anisotropic LC can promote ordered lateral organization of amphiphiles. Moreover, we find the phase transition point is shifted to lower surface coverage of amphiphiles when the LCs have larger affinity to the amphiphile tails.     

Coupling of chromatography and NMR part 5: Analysis of high-boiling gas-chromatographic fractions by on-line nuclear magnetic resonance

Summary A procedure is described for recording¹H NMR spectra of flowing gaseous GC fractions boiling as high as 200°C. The line width of the signals in the NMR spectra is smaller than 2.2Hz.Part 4: J. Buddrus, H. Herzog, Anal. Chem.55, 1611 (1983).     

Issues in the synthesis of crystalline molecular sieves: towards the crystallization of low framework-density structures.

Fundamental and practical interest in crystalline, microporous, molecular sieves is largely a direct consequence of the fact that their bulk properties can be manipulated through variations in atomic structure. This correspondence between the macroscale and the atomic scale is due to the uniformity of these crystalline materials. Control of the atomic structure therefore is of extreme importance, and is the thesis of this Review. Synthesis mechanisms and the parameters that can direct the crystal assembly pathway and the ultimate product formed are discussed and rationalized.     

Solid-state NMR and EPR study of fluorinated carbon nanofibers

Carbon nanofibers were fluorinated in two manners, in pure fluorine gas (direct fluorination) and with a fluorinating agent (TbF₄ during the so-called controlled fluorination). The resulting fluorinated nanofibers have been investigated by solid-state nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). This underlines that the fluorination mechanisms differ since a (CF)_n structural type is obtained, whatever the temperature, with the controlled reaction, whereas, during the direct process, a (C₂F)_n type is formed over a wide temperature range. Through a careful characterization of the products, i.e. density of dangling bonds (as internal paramagnetic centers), structural type (acting on molecular motion) and specific surface area (related to the amount of physisorbed O₂), the effect of atmospheric oxygen molecules on the spin-lattice nuclear relaxation has been underlined.     

Separation of amino acids in glucose isomerase crystal: Insight from molecular dynamics simulations

The separation of amino acids (Arg, Phe and Trp) in a liquid chromatography is investigated using molecular dynamics simulations. A bioorganic nanoporous material – glucose isomerase crystal – is used as the stationary phase and water as the mobile phase. The transport velocities of amino acids decrease in the order Arg > Phe > Trp, consistent with experimental measurement. The elution order is not affected by the solute concentration or by the flowing rate of mobile phase. Arg is highly hydrophilic and charged, interacts with water the most strongly, and thus moves with flowing water the fastest. Trp has the largest van der Waals volume and encounters the largest steric hindrance, leading to the slowest velocity. From the number distributions of amino acids around protein surface, Trp and Phe are found to stay closer to protein than Arg. The solvent-accessible surface areas of amino acids and the numbers of hydrogen bonds between amino acids and water further elucidate the observed velocity difference. The simulation results provide useful microscopic insight into the retention mechanisms in chromatographic separation process and suggest that glucose isomerase crystal has the capability to separate amino acids.     

NMR study of the order-disorder phase transitions of KHCO3 and KDCO3 single crystals

KHCO₃ and its deuterated analogue KDCO₃ are typical materials that undergo order-disorder phase transitions at 318 and 353 K, respectively. The spin-lattice relaxation times, T₁, spin-spin relaxation times, T₂, and the number of resonance lines for the ¹H, ²D, and ³⁹K nuclei of these crystals were investigated using NMR spectrometer. These materials are known to exhibit anomalous decreases in T₁ near T_C, which have been attributed to a structural phase transition. Additionally, changes in the symmetry of the (HCO₃)₂²⁻ (or (DCO₃)₂²⁻) dimers in these materials are associated with large changes in T₁, T₂, and the number of resonance lines. Here we found that the resonance lines for ¹H, ²D, and ³⁹K nuclei decrease in number as the temperature is increased up to T_C, indicating that the orientations of the (HCO₃)₂²⁻ (or (DCO₃)₂²⁻) dimers and the environments of the K ions change at T_C. Moreover, based on number of resonance lines, the results further indicate that the (HCO₃)₂²⁻ (or (DCO₃)₂²⁻) dimers reorientate to approximately parallel to the directions of the hydrogen bonds (or deuteron bonds) and the direction of the a-axis. The transitions at 318 and 345 K of the two crystals are of the order-disorder type. The present results therefore indicate that the orientations of the (HCO₃)₂²⁻ and (DCO₃)₂²⁻ dimers and the environment of the K ion play a significant role in these phase transitions.     

A computer program for the automatic estimation of H NMR chemical shifts

A computer program has been developed for predicting ¹H NMR chemical shifts. It automatically finds the various substructures of a given molecule for which additivity rules are available. Several strategies have been used to widen the range of applicability. with 200 test compounds, over 90% of the assigned chemical shifts of protons bonded to a carbon atom could be predicted. The mean deviation between observed and predicted values was 0.08 ppm with a standard deviation of 0.19ppm.     

Analogues of DIOP. Synthesis, reactivity, and NMR behaviour

The (4R,5R)-4,5-Bis(diphenylphosphinomethyl)-2-(-naphthoxy)-1,3,2-dioxaphospholane (1) and (4R,5R)-4,5-bis(diphenylphosphinomethyl)-2-dimethylamino-2-oxo-1,3,2-dioxaphospholane (2), analogues of the chiral bisphosphine ligand DIOP, have been synthesized. Both compounds have a second phosphorus functionality in the backbone of the chiral bisphosphine. That the reactivities of the various phosphorus atoms in 1 are different was shown for the reaction with BH₃. The complexation behaviour of 1 towards Rh^I was studied with the aid of ³¹P NMR spectroscope.     

Isomorphous substitution of Mn(II), Ni(II) and Zn(II) in AlPO-31 molecular sieves and study of their catalytic performance

Isomorphously substituted molecular sieves, MAPO-31, NAPO-31 and ZAPO-31, were prepared under mild hydrothermal conditions from gels containing sources of aluminium, phosphorus, appropriate metal and dipropylamine (DPA), presumably acting as a structure-directing template. They were characterized by XRD, FTIR, TGA, inductively coupled plasma (ICP), ESR, Brunauer, Emmett, Teller (BET) and diffusion reflectance spectroscopy (DRS) techniques. In the XRD, the peak at 2θ = 16.7° of the metal substituted AlPO-31 is more intense than that of pure AlPO-31 suggesting preferential occupation of the plane corresponding to it as compared to other planes. The O-H stretch in the IR spectra of the metal-substituted molecular sieves is blue-shifted with respect to the parent AlPO-31 molecular sieves possibly due to metal substitution. Theg values obtained from the ESR spectra of MAPO-31 and NAPO-31 also substantiate framework substitution. Ethylation of toluene was carried out between 300 and 450°C over the above catalysts as a model test reaction. The high toluene conversion over metal-substituted molecular sieves proves the isomorphic substitution of metal ions in the AlPO-31 framework.     

An efficient synthesis of 3-cyano-3-benzoyloxyoxindoles via cyanoacylation of isatins in the presence of 4 Å molecular sieves

In the presence of 4 Å molecular sieves in CH₃CN, a process for the cyanobenzoylation and cyanocarbonylation of isatins with benzoycyanides and ethylcyanoformate under mild reaction conditions has been developed. This approach provides easy access to a wide range of 3-cyano-3-benzoyloxyoxindoles and 3-cyano-3-ethoxycarbonyloxyoxindoles in good to excellent yields.     

Nuclear magnetic resonance study of Li and H diffusion in the high-temperature solid phase of LiBH4

In order to study the atomic jump motions in the high-temperature solid phase of LiBH₄, we have measured the ¹H and ¹¹B nuclear magnetic resonance (NMR) spectra and the ¹H, ⁷Li and ¹¹B spin–lattice relaxation rates in this compound over the resonance frequency range of 14–34.4 MHz. In the temperature range 384–500 K, all the spin–lattice relaxation data are satisfactorily described in terms of a thermally activated jump motion of Li ions with the pre-exponential factor τ₀=1.1×10⁻¹⁵ s and the activation energy E_a=0.56 eV. The observed frequency dependences of the spin–lattice relaxation rates in this temperature range exclude a presence of any distributions of the Li jump rate or any other jump processes on the frequency scale of 10⁷–10¹⁰ s⁻¹. The strong narrowing of the ¹H and ¹¹B NMR lines above 440 K is consistent with the onset of diffusive motion of the BH₄ tetrahedra.