Calculation Of NMR Spectra Research Articles

Solvent role in molecular structure level, structural and topology investigations, molecular docking and antimicrobial activity studies on sulpha drug derivative

The Schiff base (5FSATH) was synthesized and characterized by different experimental techniques. In the context of local energy decomposition analysis (LED), the binding energy of 5FSATH-water interaction is determined to be -15.63 kcal/mol, while the bond distance between the two objects is measured to be 1.9781 A°. The absorption spectrum was recorded using different solvents like DMSO, water, and chloroform. The experimental absorption spectrum wavelengths 206, 220, and 300 nm, were recorded from DMSO solvent. In the emission (fluorescence) spectrum we observed three different wavelengths such as 352, 510, and 609 nm. For the calculated NMR spectrum, used the standard GIAO method and DMSO as the solvent. The HOMO-LUMO analysis indicates the charge transfer within the molecule, it is calculated by different solvents. NBO confirms the synthesized compound stability, hyper conjugative interaction, and charge delocalization. To test for antibacterial and antifungal activity, an agar disc well diffusion method is utilized. Synthesized compound tested against Escherichia coli, Candida albicans, Staphylococcus aureus, and Streptococcus pneumoniae microorganisms. Amoxicillin was used as the reference drug for testing antibacterial and antifungal activity. According to the findings of the antimicrobial activity, the result of the molecular docking experiment showed that the compound 5FSATH had an extremely high binding affinity score.

New promising generation of phosphates α-aminophosphonates: Design, synthesis, in-vitro biological evaluation and computational study

A novel category of phosphate-phosphonate compounds is synthesized by a sequence multicomponent reactions strategy of Kabachnik-Fields and Atherton-Todd reactions. All the designed products are obtained with good chemical yields in short reaction times, and confirmed by spectroscopy analyses. The diethyl [(4-diethylphosphate phenyl) (4-trifluoromethyl phenylamino) methyl] phosphonate 6g is characterized by single-crystal X-ray analysis. These compounds exhibited a strong antifungal effect, a low inhibition of AChE, and no inhibitory activity on BChE, with interesting antioxidant capacity. Results make them promising candidates as original organophosphorus pesticides. The DFT calculations concerning relative stability of various conformers, besides the comparison of the measured and calculated NMR spectra of selected compounds; suggest that conformational interconversion can quite easily occur in this type of molecules, so that many structures of the same compound can coexist in solution.

Construction of Buertai Coal Macromolecular Model and GCMC Simulation of Methane Adsorption in Micropores.

With the increase in high gas mines in the low coal rank mining area in the northwestern part of China, high gas mines in the low-rank coal mining area have caused many gas emission accidents. Coal is a porous material, containing a large number of micropores (<2 nm), which can absorb large amounts of methane, so it is necessary to explore methane adsorption in micropores of low-rank coal. In this work, FTIR, HRTEM, and 13C-NMR were used to test the macromolecular structural parameters of Buertai coal, which was a kind of low-rank Jurassic coal in northwestern China. The results showed that the aromatic structural units in the Buertai coal structure mainly consist of naphthalene, anthracene, and phenanthrene. The fat structure mainly occurs in the form of aliphatic side chains, cycloalkanes, and other compounds. The oxygen atoms are present in the form of carbonyl groups, ether bonds, and phenol groups with a ratio of about 6:4:9. The nitrogen atoms are present in the form of pyrrole and pyridine compounds. Finally, the macromolecular structure model of Buertai coal was built, and the calculated NMR spectrum from the model was very consistent with the experimental NMR spectrum of Buertai coal. The relationship between the macromolecular density and energy of Buertai coal was explored using the Amorphous Cell module in the simulation software, Materials Studios 8.0 (MS 8.0), and the density value at the lowest energy was determined to be about 1.23 g/cm3. The pore structure parameters of Buertai coal were also calculated. It was found that both pore volume and void fraction decreased evenly as the diameter of the probe molecule increased, but the surface area decreased rapidly when the diameter of the probe molecule was 3.46 Å. All pore sizes were found to be smaller than 10 Å from the pore size distribution (PSD) curve of Buertai coal, which provided a lot of adsorption sites for methane (CH4). The results of the CH4 adsorption simulation from Grand Canonical Monte Carlo (GCMC) showed that CH4 is adsorbed inside the micropores of coal, and the adsorption capacity of CH4 depends on the diameters of micropores when the micropores are less than 8.5 Å. There are many micropores where CH4 did not appear because these micropores are closed and did not provide a channel for CH4 to enter. The results of experimental methane adsorption indicate that the excess adsorption capacity from the GCMC simulation was very close to the experimental results of Buertai coal. This work provides a new perspective to study the methane adsorption behavior in micropores of coal.

Gas hydrate formation by allyl alcohol and CH4: Spectroscopic and thermodynamic analysis

We discovered a new structure II (sII) hydrate forming agent, allyl alcohol (AA), in the presence of methane (CH4) for the first time, and characterized the crystal structure, guest distribution, and phase equilibria of the (AA+CH4) hydrate. Using solid-state 13C NMR and Raman spectroscopy, the crystal structure of the (AA+CH4) hydrate was confirmed to be a sII hydrate, and the CH4 molecule was found to be encapsulated in both the large and small cages of the sII hydrate. In addition, AA was found to be included in the large cages of the sII hydrate in the Gauche-Gauche form based on the measured- and calculated-NMR spectra. Notably, we investigated the free OH signal of AA in the Raman spectra to determine whether hydrogen bonding occurred between host and guest molecules; however, we could not determine whether the existence of the free OH signal was consistent with this host-guest interaction. To clearly identify the crystal structure and possible host-guest interactions, a high-resolution powder X-ray diffraction (HRPD) pattern of our (AA+CH4) hydrate sample was analyzed using Rietveld analysis with the direct space method. The crystal structure of the (AA+CH4) hydrate was assigned as the cubic Fd3m structure with a lattice constant of 17.1455 A. In particular, the shortest distance between the AA molecule in the hydrate cages and an oxygen atom in the host water was estimated to be 2.55 A; thus, we concluded that the hydroxyl group of the AA molecule was hydrogen-bonded to the host water framework. Finally, we measured the phase equilibrium conditions of the binary (AA+CH4) hydrate and found that the equilibrium pressure conditions of the binary (AA+CH4) hydrate were slightly higher than those of the pure CH4 hydrate.

Assessment of Mixtures by Spectral Superposition. An Approach in the Field of Metabolomics.

A recent field of metabolomic applications is the analysis of mixtures, for example, in food science or the early recognition of diseases. Particularly in large-scale studies, the number of intermediate states or mixtures tends to expand significantly and in practice, a manual analysis is extremely difficult if not nearly impossible. In this study, we present a model in which the NMR spectra of mixtures are calculated based on the spectral superposition of corresponding pure samples. Instead of using real spectra, where chemical shifts may be influenced by matrix effects, the linear combination of reduced data (buckets) was applied for the calculation. Starting from a set of 262 hazelnut samples of five Eurasian countries we obtained more than 160 000 NMR spectra with mixed geographic origin. Using these as a basis we calculated assessment curves to estimate to which extent admixtures are recognized within a multivariate classification model. Subsequently the calculated data were compared with the measured spectra of tangible mixtures to validate and assess the suitability of this method. The calculated spectra are very similar to the acquired data, and the resulting deviations are on a similar scale to the errors of current metabolomic measurements. Thus, with a suitable sample basis, various different mixtures can be simulated and limitations of the model can be described. This approach reduces time and resource consumption and allows valid predictions based on calculated NMR spectra. In addition to the first example dealing with the admixtures classification of single commodity foods, this approach may also be applied to simulate metabolic progression in other areas.

One‐Pot, Two‐Step Hydroxylation of the Macrocyclic Diterpenoid β‐Cembrenediol Catalyzed by P450 BM3 Mutants

AbstractCytochrome P450 monooxygenases (P450s) are involved in the biosynthesis of a wide range of bioactive secondary metabolites. They often introduce several oxy functionalities at different positions of a substrate through multiple steps and produce a range of oxidized derivatives. Herein, we describe a one‐pot two‐step hydroxylation of the diterpenoid β‐cembrenediol isolated from the plant Nicotiana tabacum. This 14‐membered macrocycle shows neuroprotective effects and is, along with its oxidized derivatives, of pharmaceutical interest. Sequential hydroxylations catalyzed by the regioselective P450 BM3 mutants F87A/I263L and V78A/F87G yielded the epimeric (9S,10R/S)‐β‐cembrenetetraols with a diastereomeric ratio of 48:52. The replacement of the mutant V78A/F87G with L75A/V78A/F87G in the second step improves the diastereomeric ratio up to 10:90. Absolute configurations of the newly introduced hydroxy groups were determined by quantum‐mechanical calculations of NMR spectra.

Evaluating the accuracy of density functional theory for calculating 1H and 13C NMR chemical shifts in drug molecules

The accuracy of different DFT methodologies for calculating 1H and 13C NMR chemical shifts in (R)-ispinesib, a complex drug molecule with multiple chemical groups and one stereocentre, has been evaluated. The accuracy of 6 basis sets and 16 different XC functionals was tested. In addition, we present a detailed study on the role of geometry optimisation (in gas and solution phase using a chloroform polarisable continuum model) on the accuracy of the calculated NMR spectra. NMR calculations using the double-ζ basis sets DGDZVP and 6-31++G(d,p) were found to be more accurate (and computationally more efficient) than those using larger triple-ζ basis sets. The O3LYP/DGDZVP methodology in solution phase using a geometry optimised at the same level of theory was found to be the most accurate method with mean absolute errors (MAEs) for 1H and 13C chemical shifts of 0.174ppm and 3.972ppm, respectively. Irrespective of the choice of XC or basis set used, complete geometry optimisation in either gas or solvent phase was found to be essential for attaining the highest accuracy in both 1H and 13C calculated chemical shifts. Finally, the role of molecular conformation was examined by calculating the Boltzmann-weighted 1H and 13C chemical shifts. Overall, we demonstrate that DFT shows exceptional promise for use in calculating the NMR chemical shifts in complex drug molecules. In the future, DFT calculations of NMR parameters are set to play an increasingly important role in drug discovery and chemical optimisation.

ChemDoodle 6.0.

ChemDoodle 6.0 is an advanced software suite for drawing chemical structure diagrams. The program's capabilities extend far beyond mere structures, however, including the ability to calculate NMR spectra, generate IUPAC names and line notations for structures, manipulate structures imported from the Internet, interpret and interconvert files generated by other chemical drawing software programs, illustrate glassware and equipment setups, and draw TLC plates. This latest version supports full round-trip editing, so that structures produced with the program can be used in standard office software and reimported into ChemDoodle if modifications are needed. These features and more are included in the basic package, which is very affordable.

Computational studies of the unusual water adduct [Cp2TiMe(OH2)](+): the roles of the solvent and the counterion.

The recently reported cationic titanocene complex [Cp2TiMe(OH2)](+) was subjected to detailed computational studies using density functional theory (DFT). The calculated NMR spectra revealed the importance of including the anion and the solvent (CD2Cl2) in order to calculate spectra which were in good agreement with the experimental data. Specifically, two organic solvent molecules were required to coordinate to the two hydrogens of the bound OH2 in order to achieve such agreement. Further elaboration of the role of the solvent led to Bader's QTAIM and natural bond order calculations. The zirconocene complex [Cp2ZrMe(OH2)](+) was simulated for comparison.

The dynamic motion of a M (M = Ca, Yb) atom inside the C74 (D 3h) cage: a relativistic DFT study

The interaction between M (M = Ca, Yb) atom and C74 (D 3h) has been investigated by all electron relativistic density function theory. With the aid of the representative patch of C74 (D 3h), we studied the interaction between C74 (D 3h) and M (M = Ca, Yb) atom and obtained the interaction potential. Optimized structures show that there are three equivalent stable isomers and there is one transition state between every two stable isomers. According to the minimum energy pathway, the possible movement trajectory of M (M = Ca, Yb) atom in the C74 (D 3h) cage is explored. The calculated energy barrier for Yb atoms moving from the stable isomer to the transition state is 10.4 kcal mol(-1) and the energy barrier for Ca atoms is 6.1 kcal mol(-1). The calculated NMR spectra of M@C74 (M = Ca, Yb) are in good agreement with the experimental data. There are nine lines in the spectra: one 1/6 intensity signal, four half intensity signals and four full intensity signals.

Structure and tautomerism of tenuazonic acid – A synergetic computational and spectroscopic approach

All reasonable tautomers and rotamers of tenuazonic acid, which is considered to be of the highest toxicity amongst the Alternaria mycotoxins, were investigated by DFT calculations at different levels of theory in gas phase and in solution to obtain optimized geometries for further examinations. Calculated NMR spectra of tautomeric structures are being presented and compared to experimental data to finally achieve a synergetic computational and spectroscopic approach for structure elucidation of 3-acetyltetramic acids, affording the predominant tautomer of tenuazonic acid in aqueous solution. Furthermore we were able to simulate the less hindered rotation of the exocyclic acetyl group, which occurs after dissociation of tenuazonic acid in protic solvents.

11B-NMR study on Shastry-Sutherland system TbB4

11B-NMR experiments were performed in high magnetic fields applied along a-axis up to 17.5T to investigate the field-induced magnetic phase transitions and the magnetic structure in high magnetic fields microscopically for the single crystalline TbB4, Shastry-Sutherland-type frustrated antiferromagnet. It was found that the field-swept 11B-NMR spectra observed at low magnetic field changes drastically at HC = 15.9 T, where the magnetization jump occurs. Based on a simple model of four-spin cluster and the classical dipole-dipole interaction, we have calculated NMR spectra, which qualitatively reproduced the observation below HC but the one above HC showed discrepancy.

Complete analysis of the 1H and 13C NMR spectra of diastereomeric mixtures of (R,S‐ and S,S‐)‐3,6‐dimethoxy‐2,5‐dihydropyrazine‐substituted indoles and their conformational preference in solution

Complete analysis of the (1)H and (13)C NMR spectra obtained with and without a chemical shift reagent (Eu(fod)(3)), of bis-lactim ether 1 (Schöllkopf auxiliary) and monosubstituted 3- or 2-{(2R,5S or 2S,5S)-5-isopropyl-3,6-dimethoxy-2,5-dihydropyrazin-2-yl]methyl}-1H-indoles is presented using gradient-selected one-dimensional (1D) and two-dimensional NMR techniques, such as 1D TOCSY, 1D NOESY (DPFGSE NOE), gCOSY, NOESY, ROESY gHETCOR, gHSQC and gHMBC. The contour plot of the gCOSY spectrum of 1-10 revealed cross peaks arising from the five-bond coupling between the H2 and H5 resonances of the dihydropyrazine ring for syn- ((5)J(H2, H5) = 4-5.7 Hz) and for anti-isomers ((5)J(H2, H5) = 3.4-3.8 Hz). The magnitude of the coupling constant was utilized to distinguish between the syn- and the anti-isomers (diastereomers). The precise values of (n)J(HH) (n = 3, 4, 5, 6) coupling constants for the indole and 2,5-dihydropyrazine moieties deduced from the calculated NMR spectra were supported by 1D TOCSY and gCOSY experiments and gauge invariant atomic orbital (GIAO) calculations. The magnitude of the coupling constants ((5)J(H2, H5)) indicates that the dihydropyrazine ring exists in a boat conformation. In both isomers, the indole group adopts a 'folded' conformation in which one diastereotopic face is effectively shielded by the aromatic benzene ring of the indole. This is supported by gradient-selected 1D NOESY and 2D NOESY experiments. Theoretical calculations of the conformation were performed to support the through-space shielding effect of the aromatic indole moiety based on the DFT/GIAO calculated (1)H NMR data (chemical shifts and coupling constants) for 2-syn- and 2-anti-diastereomers in CDCl(3).

Quantum mechanics studies of the tautomers of diacetylformoin, an important maillard product and odorant

Diacetylformoin (3,4-dihydroxy-3-hexene-2,5-dione) has 16 tautomers, many with several possible conformations and all have been geometry optimised using quantum mechanics at the HF/6-31+G* level. Eleven structures have been identified with energies within 10 kcal mol −1 of the minimum energy structure. Of these eight are acyclic and three cyclic. Calculations of NMR spectra have clarified the identity of the acyclic and cyclic structures found experimentally. The mechanism for cyclisation has been investigated and transition states obtained. The lowest energy reaction path requires the loss and gain of a proton during cyclisation.

The Liquid Water−Benzene System

The 500 MHz NMR spectra of water-benzene solution near saturation at 303.15, 323.15, and 343.15 K indicate that there is a proton-proton exchange between the water and benzene molecules. In the solution water appears to be present as a dimer attached to the benzene pi cloud on one side of each of the two (initially degenerate) fundamental energy levels, as predicted by the Jahn-Teller effect. This view is reinforced by the fact that one of its hydrogen atoms hovers above one of the carbon atoms and the other three are spread upward around the C6 axis of the benzene molecule. It is also supported by the calculated NMR spectra. Both effects are responsible for the change in the NMR spectra of the water molecules from a single line into four AB signals.

Structure determination of a missing-caged metallofullerene: Yb@C 74 (II) and the dynamic motion of the encaged ytterbium ion

A dynamic motion of the encaged metal in the D 3h cage is proposed for Yb@C 74(II) according its NMR spectrum. In addition, the calculated NMR spectra of D 3h-C 74 and Yb@C 74 with a D 3h cage and the static metal are presented. By comparing Yb@C 74’s dynamic and static NMR spectra, the dynamic metal’s effect on the NMR behavior of the metallofullerene is discussed.

Theoretical investigation of moganite

The structure and properties of two different modifications of moganite have been studied using density functional theory, and the results have been compared to quartz. It is shown that the enthalpy difference between quartz and moganite, whose structure can be understood as Brazil twinning of quartz on a unit cell length scale, is negligible. This explains the significant amount of moganite in fine-grained quartz samples, as well as the frequent occurrence of Brazilian twinning in quartz. The compression mechanism of moganite has been elucidated, and it is argued that moganite is significantly more compressible than quartz. Observed and calculated NMR spectra are compared, and it is found that the bonding in quartz and moganite is very similar, consistent with the results of a Mulliken population analysis. The elastic stiffness coefficients of moganite have been predicted, and it is shown that formal-charge shell model interatomic potentials appear to be more transferable from quartz to moganite than partial-charge rigid ion equivalents.

Solid-state NMR Studies of Al-doped and Al 2O 3-coated LiCoO 2

As a cathode material for commercial lithium rechargeable battery, Al-doped and Al 2O 3-coated LiCoO 2 were structurally characterized and compared by using solid-state 7Li and 27Al magic angle spinning (MAS) NMR. The structural states of lithium and aluminum in those samples were successfully identified by calculation of NMR spectra. 7Li MAS NMR spectra of samples had shown similar features having more than three lithium sites, which were determined as quadrupole coupling constant with the same asymmetric parameter ( η = 0.1); C Q = 1.10 MHz for octahedral site, and C Q = 2.97 MHz and C Q = 3.83 MHz for shoulders. 27Al MAS NMR spectra of samples, however, showed significant difference in two observed aluminum sites. In the simulation of NMR spectrum for Al 2O 3-coated LiCoO 2, the values of C Q and η were obtained; 4.45 MHz and η = 0.86 for tetrahedral site and 4.31 MHz and η = 0.81 for octahedral.

The aperiodic states of zircon: an ab initio molecular dynamics study

We theoretically investigated the local structure of the aperiodic states of zircon (ZrSiO 4 ) using ab initio quantum mechanical calculations. The low and high density liquid and solid glassy phases were obtained by constant volume Car-Parrinello molecular dynamics simulations, using the molar volume of metamict and crystalline zircon, respectively. As in naturally metamict zircons, the polymerization of Si units, the segregation of Zr atoms, and an overall decrease of the Zr coordination were observed. However, the local ordering of our theoretical glasses differs from that of the natural amorphous samples. In the theoretical glasses, the Zr-O distances in the first coordination polyhedra are significantly more distributed and five- and six-coordinated Si species were observed. The relaxation of the glass structure on a time scale exceeding the possibility of molecular modeling is a possible explanation for these discrepancies. The dielectric and 2 9 Si NMR responses of the glassy phases were computed, providing new constraints for the analysis of experimental data recorded from metamict zircons. The calculated NMR spectra are in good agreement with the experimental NMR spectra in the four-coordinated Si region. Our results show that the usual regular systematic decrease of the 2 9 Si chemical shift as a function of the polymerization of Si units (Q n species) cannot be used to interpret the 2 9 Si NMR spectrum of amorphous zircon. In particular, whereas the empirical scale would indicate an average polymerization of Q 3 , the average polymerization of Q 1 . 5 observed in the low density zircon glass can account for the experimental data. In a non-uniform model of the structure of metamict zircon, this lower average polymerization is consistent with a clustering of cations limited to few coordination polyhedra.

Experimental and calculated 1H, 13C and 31P NMR spectra of (hydroxypyridin-3-yl-methyl)phosphonic acid

(Hydroxypyridin-3-yl-methyl)phosphonic acid named also 3-pyridylmethyl(hydroxy)-phosphonic acid, MC5, is biologically active compound and exhibits metal binding ability attributable to the presence of the phosphonic group and the pyridine nitrogen. Its proton NMR data have been previously reported, only. Thus, in this work we offer interpretation of 1H, 13C and 31P NMR spectra of this compound dissolved in D 2O in the pD range between 1.5 and 9.0. Additionally, to support our interpretation of the obtained data, we calculated NMR spectra of all expected forms that are the result of consecutive deprotonation of MC5. Theoretical calculations of the NMR spectra as well as structural parameters of the compounds (cation, zwitteranion, and two anions) were performed at the B3PW91 level with the 6-311G** and 6-311++G**basis sets.