Prediction of the 1H and 13C NMR Spectra of α-d-Glucose in Water by DFT Methods and MD Simulations

The effect of AgNPS bio-functionalization on the cytotoxicity of the yeast Saccharomyces cerevisiae

This work used Sedum praealtum leaf extract to synthesize silver nanoparticles (AgNPs) in a single step. The cytotoxicity of AgNPs was studied with the yeast Saccharomyces cerevisiae W303-1. In addition, the antioxidant activity of the DPPH radical was studied both in the extract of S. praealtum and in the AgNPs. UV-Vis spectroscopy determined the presence of AgNPs by the location of the surface plasmon resonance (SPR) band at 434 nm. TEM and XRD analyzes show AgNPs with fcc structure and hemispherical morphology. Also, AgNPs range in size from 5 to 25 nm and have an average size of 14 nm. 1H NMR, FTIR, and UV-Vis spectroscopy techniques agreed that glycosidic compounds were the main phytochemical components responsible for the reduction and stabilization of AgNPs. In addition, AgNPs presented a maximum of 12% toxicity in yeast attributed to the generation of ROS. Consequently, there was low bioactivity because glycoside compounds cover the biosynthesized AgNPs from S. praealtum. These findings allow applications of AgNPs involving contact with mammals and higher organisms.

Computational 1 H and 13 C NMR in structural and stereochemical studies

Present review outlines the advances and perspectives of computational ¹ H and ¹³ C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational ¹ H and ¹³ C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.

Efficiently Computing NMR 1H and 13C Chemical Shifts of Saccharides in Aqueous Environment

Determining the structure of saccharides in their native environment is crucial to understanding their function and more accurately targeting their utilization. Nuclear magnetic resonance observables such as the nuclear Overhauser effect or spin-spin coupling constants are routinely utilized to study saccharides in their native water environment. However, while highly sensitive to the local environment, chemical shifts are mostly overlooked, despite being commonly measured for compounds identification. Although chemical shifts carry considerable structural information, their direct association with structure is notoriously difficult. This is mostly due to the similarity in the chemical nature of most saccharides causing similar physicochemical environments close to sugar C and H atoms, resulting in comparable chemical shifts. The rise of computational power allows one to compute reliable chemical shifts and use them to determine atomistic details of these sugars in solution. However, any prediction is severely limited by the computational protocol used and its accuracy. In this work, we studied a set of 31 saccharides on which we evaluated various computational protocols to calculate the total number of 375 ¹H and 327 ¹³C chemical shifts of sugars in an aqueous environment. Our study proposes two cost-effective protocols for simulating ¹H and ¹³C chemical shifts that we recommend for further use. These protocols can help with the interpretation of experimental spectra, but we also show that they are also capable of structure prediction independently. This is possible because of the low mean absolute deviations of calculated shifts from the experiment (0.06 ppm for ¹H and 1.09 ppm for ¹³C). We explore different solvation methods, basis sets, and optimization schemes to reach such accuracy. A correct sampling of the conformation phase space of flexible sugar molecules is also key to obtaining accurately converged theoretical chemical shifts. The linear regression method was applied to convert the calculated isotropic nuclear magnetic shielding constants to simulated chemical shifts comparable with the experiment. The achieved level of accuracy can help in utilizing chemical shifts for elucidating the 3D atomistic structure of saccharides in aqueous solutions. All linear regression parameters obtained on our extensive set of sugars for all the tested protocols can be reutilized in future works.

Highly Efficient and Selective Carbon-Doped BN Photocatalyst Derived from a Homogeneous Precursor Reconfiguration

The modification of inert boron nitride by carbon doping to make it an efficient photocatalyst has been considered as a promising strategy. Herein, a highly efficient porous BCN (p-BCN) photocatalyst was synthesized via precursor reconfiguration based on the recrystallization of a new homogeneous solution containing melamine diborate and glucose. Two crystal types of the p-BCN were obtained by regulating the recrystallization conditions of the homogeneous solution, which showed high photocatalytic activities and a completely different CO2 reduction selectivity. The CO generation rate and selectivity of the p-BCN-1 were 63.1 μmol·g−1·h−1 and 54.33%; the corresponding values of the p-BCN-2 were 42.6 μmol·g−1·h−1 and 80.86%. The photocatalytic activity of the p-BCN was significantly higher than those of equivalent materials or other noble metals-loaded nanohybrids reported in the literature. It was found that the differences in the interaction sites between the hydroxyl groups in the boric acid and the homolateral hydroxyl groups in the glucose were directly correlated with the structures and properties of the p-BCN photocatalyst. We expect that the developed approach is general and could be extended to incorporate various other raw materials containing hydroxyl groups into the melamine diborate solution and could modulate precursors to obtain porous BN-based materials with excellent performance.

Towards Elucidating Structure–Spectra Relationships in Rhamnogalacturonan II: Computational Protocols for Accurate 13C and 1H Shifts for Apiose and Its Borate Esters

Apiose is a naturally occurring, uncommon branched-chain pentose found in plant cell walls as part of the complex polysaccharide Rhamnogalacturonan II (RG-II). The structural elucidation of the three-dimensional structure of RG-II by nuclear magnetic resonance (NMR) spectroscopy is significantly complicated by the ability of apiose to cross-link via borate ester linkages to form RG-II dimers. Here, we developed a computational approach to gain insight into the structure–spectra relationships of apio–borate complexes in an effort to complement experimental assignments of NMR signals in RG-II. Our protocol involved structure optimizations using density functional theory (DFT) followed by isotropic magnetic shielding constant calculations using the gauge-invariant atomic orbital (GIAO) approach to predict chemical shifts. We evaluated the accuracy of 23 different functional–basis set (FBS) combinations with and without implicit solvation for predicting the experimental 1H and 13C shifts of a methyl apioside and its three borate derivatives. The computed NMR predictions were evaluated on the basis of the overall shift accuracy, relative shift ordering, and the ability to distinguish between dimers and monomers. We demonstrate that the consideration of implicit solvation during geometry optimizations in addition to the magnetic shielding constant calculations greatly increases the accuracy of NMR chemical shift predictions and can correctly reproduce the ordering of the 13C shifts and yield predictions that are, on average, within 1.50 ppm for 13C and 0.12 ppm for 1H shifts for apio–borate compounds.

Sensomics-Assisted Flavor Decoding of Dairy Model Systems and Flavor Reconstitution Experiments

The whole sensometabolome of a typical dairy milk dessert was decoded to potentially serve as a blueprint for further flavor optimization steps of functional fat-reduced food. By applying the sensomics approach, a wide range of different dairy volatiles, semi and nonvolatiles, were analyzed by ultrahigh-performance liquid chromatography tandem mass spectrometry with or without derivatization presteps. While for volatile sulfur compounds with low odor thresholds, headspace solid-phase microextraction gas chromatography was established, abundant carbohydrates and organic acids were quantified by quantitative ¹H nuclear magnetic resonance spectroscopy. Validated quantitation, sensory reconstitution, and omission studies highlighted eight flavor-active compounds, namely, diacetyl, δ-tetra-, δ-hexa-, and δ-octadecalactone, sucrose, galactose, lactic acid, and citric acid as indispensable for flavor recombination. Furthermore, eight odorants (acetaldehyde, acetic acid, butyric acid, methanethiol, phenylacetic acid, dimethyl sulfide, acetoin, and hexanoic acid), all with odor activity values >1, additionally contributed to the overall flavor blueprint. Within this work, a dairy flavor analytical toolbox covering four different high-throughput methods could successfully be established showing potential for industrial applications.

Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives

This review is written amid a marked progress in the calculation of NMR parameters of carbohydrates substantiated by a vast amount of experimental data coming from several laboratories worldwide. By no means are we trying to cover in the present compilation a huge amount of all available data. The main idea of the present review was only to outline general trends and perspectives in this dynamically developing area on the background of a marked progress in theoretical and computational NMR. Presented material is arranged in three basic sections: (1)-a brief theoretical introduction; (2)-applications and perspectives in computational NMR of monosaccharides; and (3)-calculation of NMR chemical shifts and spin-spin coupling constants of di- and polysaccharides.

The use of MM/QM calculations of 13C chemical shifts in the conformational analysis of some monosaccharides and sucrose

The ¹³C NMR chemical shifts of some common pyranose monosaccharides in D₂O solution were predicted using a combined molecular mechanics (Pcmod 9.1/MMFF94) and ab initio (GIAO (B3LYP/DFT, 6-31G(d))) model.

Diversity of the Hydrogen Bond Network and Its Impact on NMR Parameters of Amylose B Polymorph: A Study Using Molecular Dynamics and DFT Calculations Within Periodic Boundary Conditions

Classical molecular dynamics simulations have been combined with quantum (DFT) calculations of ¹³C NMR parameters in order to relate the experimental spectrum of the double-helix form of the amylose B-polymorph in highly crystalline conditions not only to its 3D structure but also to the arrangement of atoms in the crystal lattice. Structures obtained from these simulations or from geometry optimization procedures at the DFT level have shown the presence of hydrogen bond networks between sugars of the same helix or between residues of the two chains of the double helix. ¹³C NMR parameter calculations have revealed the impact of such a network on the chemical shifts of carbon atoms. In addition, DFT calculations using periodic boundary conditions were compulsory to highlight the presence of two types of sugar within the crystal sample. It allows us to confirm, theoretically, the experimental hypothesis that the existence of two distinct sugar types in the NMR spectrum is a consequence of crystal packing.

NMR Calculations with Quantum Methods: Development of New Tools for Structural Elucidation and Beyond

Structural elucidation is an important and challenging stage in the discovery of new organic molecules. Single-crystal X-ray analysis provides the most unquestionable results, though in practice the availability of suitable crystals limits its broad use. On the other hand, NMR spectroscopy has become the leading and universal technique to accomplish the task. Despite continuous advances in the field, the misinterpretation of NMR data is commonplace, evidenced by the large number of erroneous structures being published in top journals. Quantum calculations of NMR chemical shifts and scalar coupling constants emerged as ideal complements to facilitate the elucidation process when experimental NMR data is inconclusive. Since seminal reports demonstrated that affordable DFT methods provide NMR predictions accurate enough to differentiate among closely related isomers, the discipline has experienced substantial growth. The impact has been felt in different areas, and nowadays the results of such calculations are routinely seen in high impact literature.This Account describes our investigations in the field of quantum NMR calculations, focusing on the development of tools for structural elucidation and practical applications. We pioneered the use of artificial intelligence methods in the development of novel strategies of structural validation. Our first generation of trained artificial neural networks (ANNs) showed excellent ability to identify mistakes at the atom connectivity level, whereas the use of multidimensional pattern recognition pushed the performance to the stereochemical limit. In a conceptually different approach, we developed DP4+, an updated version of the DP4 probability used to determine the most likely structure among two or more candidates when one set of experimental data is available. Increasing the level of theory in NMR calculations and including unscaled data in the formalism improved the performance of the method, further validated to settle the configuration of challenging motifs such as spiroepoxides or Mosher's derivatives. One of the limitations of DP4+ is related to the relatively large computational cost involved in obtaining DFT-optimized geometries, which led to the development of a fast variant including the valuable information provided by coupling constants (J-DP4 method).These tools were explored to suggest the most probable structure of controversial natural or unnatural products originally misassigned, with some predictions further validated by synthesis (as in the case of pseudorubriflordilactone B). The possibility of predicting the structure of a natural product without requiring authentic sample was investigated in collaboration with Prof. Pilli (UNICAMP, Brazil) in the computer-guided total synthesis and stereochemical revisions of several natural products. Despite these advances, there remain considerable challenges, such as the case of configurational assessment of polar systems featuring multiple intramolecular hydrogen bonding interactions because of the poor energy predictions provided by most DFT methods. In our latest work, we tackle this problem by averaging the results provided by randomly generated ensembles, paving the way for a new paradigm in quantum NMR-assisted structural elucidation.

13C NMR Dataset Qualitative Analysis of Grecian Wines

The development of analytical techniques for characterizing food samples, especially for the wine industry, is a main topic of research. Regarding the classification of wines based on their geographical origin, nuclear magnetic resonance (NMR) spectroscopy represents a fast and effective tool for determining chemical fingerprints. Herein, a 13C NMR dataset, which was acquired for classification of Grecian wines through multivariate statistics, is reported and described. Thus, the main qualitative differences between grapes of the same geographical origin, observable by the visual analysis of the 13C NMR data, are discussed.

13C NMR-Based Chemical Fingerprint for the Varietal and Geographical Discrimination of Wines

A fast, economic, and eco-friendly methodology for the wine variety and geographical origin differentiation using ¹³C nuclear magnetic resonance (NMR) data in combination with machine learning was developed. Wine samples of different grape varieties cultivated in different regions in Greece were subjected to ¹³C NMR analysis. The relative integrals of the ¹³C spectral window were processed and extracted to build a chemical fingerprint for the characterization of each specific wine variety, and then subjected to factor analysis, multivariate analysis of variance, and k-nearest neighbors analysis. The statistical analysis results showed that the ¹³C NMR fingerprint could be used as a rapid and accurate indicator of the wine variety differentiation. An almost perfect classification rate based on training (99.8%) and holdout methods (99.9%) was obtained. Results were further tested on the basis of Cronbach's alpha reliability analysis, where a very low random error (0.30) was estimated, indicating the accuracy and strength of the aforementioned methodology for the discrimination of the wine variety. The obtained data were grouped according to the geographical origin of wine samples and further subjected to principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA). The PLS-DA and variable importance in projection (VIP) allowed the determination of a chemical fingerprint characteristic of each geographical group. The statistical analysis revealed the possibility of acquiring useful information on wines, by simply processing the ¹³C NMR raw data, without the need to determine any specific metabolomic profile. In total, the obtained fingerprint can be used for the development of rapid quality-control methodologies concerning wine.

Cooperativity in alkane-1,2- and 1,3-polyols: NMR, QTAIM, and IQA study of O─H… OH and C─H… OH bonding interactions

Proton nuclear magnetic resonance chemical shifts and atom-atom interaction energies for alkanepolyols with 1,2-diol and 1,3-diol repeat units, and for their 1:1 pyridine complexes, are computed by density functional theory calculations. In the 1,3-polyols, based on a tG'Gg' repeat unit, the only important intramolecular hydrogen bonding interactions are O─H^… OH. By quantum theory of atoms in molecules analysis of the electron density, unstable bond and ring critical points are found for such interactions in 1,2-polyols with tG'g repeat units, from butane-1,2,3,4-tetrol onwards and in their pyridine complexes from propane-1,2,3-triol onwards. Several features (OH proton shifts and charges, and interaction energies computed by the interacting quantum atoms approach) are used to monitor the dependence of cooperativity on chain length: This is much less regular in 1,2-polyols than in 1,3-polyols and by most criteria has a higher damping factor. Well defined C─H^… OH interactions are found in butane-1,2,3,4-tetrol and higher members of the 1,2-polyol series, as well as in their pyridine complexes: There is no evidence for cooperativity with O─H^… OH bonding. For the 1,2-polyols, there is a tenuous empirical relationship between the existence of a bond critical point for O─H^… OH hydrogen bonding and the interaction energies of competing exchange channels, but the primary/secondary ratio is always less than unity.

Conformational Analysis of 5,4'-Dihydroxy-7,5',3'-trimethoxyisoflavone in Solution Using 1H NMR: A Density Functional Theory Approach

Among 20 compounds isolated from the extracts of Ouratea ferruginea the 5,4'-dihydroxy-7,5',3'-trimethoxyisoflavone (9) showed the best inhibitory effect on glutathione S-transferase (GST) and so deserves our attention. In this work we investigated the preferred molecular structure of 9 in chloroform solution using the density functional theory (DFT) and molecular dynamics simulation. Comparison between experimental ¹H NMR data in CDCl₃ solution and calculated chemical shifts enabled us to precisely determine the conformation adopted by 9 in solution, which can be used in further theoretical studies involving interaction with biological targets. Moreover, the experimental NMR data were used as reference to assess the ability of DFT based methods to predict ¹H NMR spectrum in solution for organic compounds. Among various DFT functionals the hybrid B3LYP was the most adequate for the calculation of chemical shifts in what CH_n protons are concerned. Regarding the OH hydrogen, inclusion of explicit CHCl₃ solvent molecules adequately placed around the solute led to good agreement with the experimental chemical shifts (in CDCl₃). It is a well-known fact that theoretical prediction of chemical shifts for OH hydrogens poses as a challenge and also revealed that the way the solvent effects are included in the DFT calculations is crucial for the right prediction of the whole ¹H NMR spectrum. It was found in this work that a supermolecule solute-solvent calculation with a minimum of four CHCl₃ molecules is enough to correctly reproduce the ¹H NMR experimental profile observed in solution, revealing that the calculated solvated structure used to reproduce the NMR chemical shifts is not unique.

Computational 1 H NMR: Part 3. Biochemical studies

This is the third and the last part of three closely interrelated reviews dealing with computation of ¹ H nuclear magnetic resonance chemical shifts and ¹ H-¹ H spin-spin coupling constants. Present review deals with the computation of these parameters in biologically active natural products, carbohydrates, and other molecules of biological origin focusing on stereochemical applications of computational ¹ H nuclear magnetic resonance to these objects.

New triterpenoid saponin glycosides from the fruit fibers ofTrichosanthes cucumerinaL

Five new triterpenoid saponin glycosides, trichocucumerisides A–E (1–5), together with eleven known compounds (6–16) were isolated from Trichosanthes cucumerina fruit fibers. The structures of the new compounds were elucidated by detailed analysis of NMR and mass spectroscopic data as well as chemical reactions. The anti-inflammatory study against nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated RAW264.7 cells shows that compounds 7 and 9 exhibited stronger NO inhibitory activity, with IC₅₀ values of 3.0 and 2.7 μM, respectively, with comparison to positive references Celecoxib and aminoguanidine (IC₅₀ values 75.7 and 75.0 μM, respectively). Compounds 7 and 9 also possessed a greater selectivity index (SI) of approximately 3–4-fold activity than that of the positive references.

The new glycosides 1–5, together with eleven known compounds were isolated. Two compounds exhibited more potent anti-inflammatory activity than Celecoxib and aminoguanidine reference compounds.

Hydrogen Bond between Molybdate and Glucose for the Formation of Carbon-Loaded MoS2 Nanocomposites with High Electrochemical Performance

The effects of glucose on the growth and surface properties of MoS₂ with a nanosheet structure were investigated in detail. In the presence of glucose, the hydrothermal reaction of sodium molybdate and thiourea yields carbon-loaded MoS₂ nanocomposites (C/MoS₂). Compared with bare MoS₂ nanosheets with more than six layers obtained in the absence of glucose and carbon spheres with a diameter of 500 nm prepared from the carbonization of glucose, C/MoS₂ consists of one- or three-layered MoS₂ and carbon spheres with a diameter less than 1 nm to give a large Brunauer-Emmett-Teller surface area (3-20 times larger than the individual materials). The surface characterizations reveal that both MoS₂ and carbon spheres of C/MoS₂ have a negative charge on the surface, suggesting that the previously reported explanation, in which the adsorption of MoS₂ and/or molybdate ions on carbon spheres inhibits the growth and aggregation of MoS₂, is not correct. Based on Fourier transform infrared and ¹H NMR spectra, it is demonstrated that glucose acts as the hydrogen bond donor toward polyoxomolybdate species such as Mo₈O₂₆^4-, Mo₇O₂₄^6-, and MoO₄^2- in the range of pH = 2-12. The intermolecular hydrogen bond not only inhibits the growth of both the (002) plane of MoS₂ and carbon spheres, but also enables the formation of C-O-Mo bonds in the in situ generated C/MoS₂. Compared with bare MoS₂, C/MoS₂ not only show a lower over-potential by 60 mV for the electrocatalytic evolution of hydrogen, but also has a larger mass specific capacitance by three times, due to the larger surface area and the interfacial interaction through the C-O-Mo bonds.

Computational studies, NMR, Raman and infrared spectral analysis of centrosymmetric (2Z,4Z)-Hexa-2,4-dienedinitrile

The Raman (50–3500[Formula: see text]cm[Formula: see text]) and infrared (200–3500[Formula: see text]cm[Formula: see text]) spectra of (2Z,4Z)-Hexa-2,4-dienedinitrile (C6H4N2; cis,cis-HDDN) have been recorded. Initially, three conformers were proposed based on following point groups: C2h, C2v and [Formula: see text] (gauche). For comparison purposes, M05-2X, M06-2X method were used in addition to B3LYP, MP2[Formula: see text]full and MP4[Formula: see text]full quantum mechanical calculations employing 6-31G(d) and 6-311+G(d,p) basis sets using Gaussian 09 program. Aided by potential energy surface scan, the C2h conformer is verified as a global minimum and the gauche ([Formula: see text]) being a local minimum with an energy barrier of 2.82[Formula: see text]kcal/mol. The energy difference ranged from 4.87 to 13.70[Formula: see text]kcal/mol favors the C2h conformer in good agreement with Raman and infrared spectral analysis. These results were also supported by the observed [Formula: see text] value (H9-H[Formula: see text]) at 10.8[Formula: see text]Hz which is consistent to 10.19[Formula: see text]Hz estimated for centrosymmetric conformer (C2h) rather than 4.81[Formula: see text]Hz predicted for gauche ([Formula: see text]). Complete vibrational assignments are proposed herein based on normal coordinate analysis (NCA) and potential energy distributions (PEDs) combined with theoretical vibrational frequencies and force constants in internal coordinates. It is crucial that NCA using VEDA 4 program with mixing shows large deviations from ours due to neglecting symmetry elements while mixing molecular vibrational motions. The results of these spectroscopic and theoretical studies are reported herein and compared with similar molecules whenever appropriate.

Intramolecular O-H⋯O and C-H⋯O hydrogen bond cooperativity in D-glucopyranose and D-galactopyranose-A DFT/GIAO, QTAIM/IQA, and NCI approach

Density functional theory calculations are used to compute proton nuclear magnetic resonance (NMR) chemical shifts, interatomic distances, atom-atom interaction energies, and atomic charges for partial structures and conformers of α-D-glucopyranose, β-D-glucopyranose, and α-D-galactopyranose built up by introducing OH groups into 2-methyltetrahydropyran stepwisely. For the counterclockwise conformers, the most marked effects on the NMR shift and the charge on the OH1 proton are produced by OH2, those of OH3 and OH4 being somewhat smaller. This argues for a diminishing cooperative effect. The effect of OH6 depends on the configuration of the hydroxymethyl group and the position, axial or equatorial, of OH4, which controls hydrogen bonding in the 1,3-diol motif. Variations in the interaction energies reveal that a "new" hydrogen bond is sometimes formed at the expense of a preexisting one, probably due to geometrical constraints. Whereas previous work showed that complexing a conformer with pyridine affects only the nearest neighbour, successive OH groups increase the interaction energy of the N⋯H1 hydrogen bond and reduce its length. Analogous results are obtained for the clockwise conformers. The interaction energies for C-H⋯OH hydrogen bonding between axial CH protons and OH groups in certain conformers are much smaller than for O-H⋯OH bonds but they are largely covalent, whereas those of the latter are predominantly coulombic. These interactions are modified by complexation with pyridine in the same way as O-H⋯OH interactions: the computed NMR shifts of the CH protons increase, the atom-atom distances are shorter, and interaction energies are enhanced.

Characterization of cellulase from Aspergillus tubingensis NKBP-55 for generation of fermentable sugars from agricultural residues

The aim of this work was to characterize cellulase from Aspergillus tubingensis NKBP-55 for generation of fermentable sugars from agricultural residues. The strain produced high titres of cellulase (750 U/gds) on copra meal in solid state fermentation (SSF). The enzyme preparation also showed hemicellulolytic activities (U/gds) viz. endo-mannanase (1023), endo-xylanase (167), β-glucosidase (72) and α-galactosidase (54). Zymography revealed presence of six cellulases, six mannanases and one β-glucosidase. It effectively degraded sugarcane bagasse (SCB) and rice straw (RS) releasing xylose, glucose and cellobiose. One cellulase (Cat 1, Mr ∼65 kDa) was purified and characterized. It retained more than 50% activity at 70 °C after 150 mins and its activity was enhanced in the presence of Mn²⁺ ions (130%) and β-mercaptoethanol (140%). FTIR and ¹³C CP/MAS NMR analysis of the enzyme treated SCB and RS revealed degradation of cellulose and hemicellulose, while ¹H and ¹³C liquid state NMR experiments confirmed release of glucose.

On the importance of intramolecular hydrogen bond cooperativity in d-glucose - an NMR and QTAIM approach

The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge-including atomic orbital calculations on the known conformers of the α and β anomers of d-glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom-atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules. Association of OH1 in the counterclockwise conformers with a strong acceptor, pyridine, is accompanied by cooperative participation from OH2, but there is no significant change in the bonding of the two following 1,2-diol motifs. The OH6^... O5 (G-g+/cc/t and G+g-/cc/t conformers) or OH6^... O4 (Tg+/cc/t conformer) distance is reduced, and the OH6 proton is slightly deshielded. In the latter case, this shortening and the associated increase in the OH6-O4 interaction energy may be interpreted as a small cooperative effect, but intermolecular interaction energies are practically the same for all three conformers. In most of the pyridine complexes, one ortho proton interacts with the endocyclic oxygen O5. Analogous results are obtained when the clockwise conformer, G-g+/cl/g-, detected for the α anomer, and a hypothetical conformer, Tt/cl/g-, are complexed with pyridine through OH6. Generally, the cooperative effect does not go beyond the first two OH groups of a chain. Copyright © 2017 John Wiley & Sons, Ltd.

The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis

NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites.

Towards theory driven structure elucidation of complex natural products: mandelalides and coibamide A

The effectiveness of computational tools in determining relative configurations of complex molecules is investigated, using natural products mandelalides A–D and coibamide A, towards a generalized recipe for the scientific community at large.

Predicting the spin state of paramagnetic iron complexes by DFT calculation of proton NMR spectra

Many transition-metal complexes easily change their spin state S in response to external perturbations (spin crossover). Determining such states and their dynamics can play a central role in the understanding of useful properties such as molecular magnetism or catalytic behavior, but is often far from straightforward. In this work we demonstrate that, at a moderate computational cost, density functional calculations can predict the correct ground spin state of Fe(ii) and Fe(iii) complexes and can then be used to determine the (1)H NMR spectra of all spin states. Since the spectral features are remarkably different according to the spin state, calculated (1)H NMR resonances can be used to infer the correct spin state, along with supporting the structure elucidation of numerous paramagnetic complexes.

Accumulation of d-glucose from pentoses by metabolically engineered Escherichia coli

Escherichia coli that is unable to metabolize d-glucose (with knockouts in ptsG, manZ, and glk) accumulates a small amount of d-glucose (yield of about 0.01 g/g) during growth on the pentoses d-xylose or l-arabinose as a sole carbon source. Additional knockouts in the zwf and pfkA genes, encoding, respectively, d-glucose-6-phosphate 1-dehydrogenase and 6-phosphofructokinase I (E. coli MEC143), increased accumulation to greater than 1 g/liter d-glucose and 100 mg/liter d-mannose from 5 g/liter d-xylose or l-arabinose. Knockouts of other genes associated with interconversions of d-glucose-phosphates demonstrate that d-glucose is formed primarily by the dephosphorylation of d-glucose-6-phosphate. Under controlled batch conditions with 20 g/liter d-xylose, MEC143 generated 4.4 g/liter d-glucose and 0.6 g/liter d-mannose. The results establish a direct link between pentoses and hexoses and provide a novel strategy to increase carbon backbone length from five to six carbons by directing flux through the pentose phosphate pathway.

Quantum chemical calculations of31P NMR chemical shifts: scopes and limitations

High level of theory is not necessarily needed to obtain rather accurate predictions of³¹P chemical shifts by GIAO method. For example, the PBE1PBE/6-311G(2d,2p)//PBE1PBE/6-31+G(d) combination allowed to obtain good results for variety of middle-size organophosphorus compounds (M= 200–700 Da).