Fluxional Research Articles

Dynamic nuclear polarization solid-state NMR spectroscopy as a tool to rapidly determine degree of modification in dialcohol cellulose

AbstractDialcohol cellulose can be prepared by periodate-mediated oxidation of cellulose followed by reduction with borohydride. The two-step reaction creates a modified cellulose polymer which is ring-opened between the C2 and C3 carbons in the glucose unit. This material has attracted both scientific and commercial interest, due to its potential role in the transition towards a fossil-fuel-free society. In order to become a reliable component in the materials of tomorrow, chemical properties such as degree of modification must be accurately quantified. In this work we describe how solid-state NMR spectroscopy, enhanced by dynamic nuclear polarization (DNP), can be used for this purpose. Our results illustrate that it is possible to obtain high sensitivity enhancements in dialcohol cellulose with the DNP enhanced solid-state NMR technique. Enhancements above a factor of fifty, on a 400 MHz/263 GHz DNP system in the presence of 12 mM AMUPol radical were achieved. This allows us to quantify the degree of modification in dialcohol cellulose samples in time spans as short as 20 min using DNP enhanced multiple-contact cross polarization experiments. We also exemplify how DNP enhanced, 13C-13C dipolar recoupling experiments can be used for the same purpose and for studying chemical shift correlations in dialcohol cellulose. Graphical abstract

Thawed Gaussian Wavepacket Dynamics with Δ-Machine-Learned Potentials.

A method for performing variable-width (thawed) Gaussian wavepacket (GWP) variational dynamics on machine-learned potentials is presented. Instead of fitting the potential energy surface (PES), the anharmonic correction to the global harmonic approximation (GHA) is fitted using kernel ridge regression─this is a Δ-machine learning approach. The training set consists of energy differences between ab initio electronic energies and values given by the GHA. The learned potential is subsequently used to propagate a single thawed GWP by using the time-dependent variational principle to compute the autocorrelation function, which provides direct access to vibronic spectra via its Fourier transform. We applied the developed method to simulate the photoelectron spectrum of ammonia and found excellent agreement between theoretical and experimental spectra. We show that fitting the anharmonic corrections requires a smaller training set as compared to fitting total electronic energies. We also demonstrate that our approach allows to reduce the dimensionality of the nuclear space used to scan the PES when constructing the training set. Thus, only the degrees of freedom associated with large-amplitude motions need to be treated with Δ-machine learning, which paves a way for reliable simulations of vibronic spectra of large floppy molecules.

Accurate Geometries of Large Molecules at DFT Cost by Semiexperimental and Coupled Cluster Templating Fragments.

Accurate geometries of small semirigid molecules in the gas phase are available thanks to high-resolution spectroscopy and accurate quantum chemical approaches. These results can be employed for validating cheaper low-level quantum chemical models or correcting the corresponding structures of large molecules. On these grounds, in this work, a large panel of semiexperimental equilibrium structures already available in the literature is used to confirm the average error (1 mÅ for bond lengths and 2 mrad for valence angles) of a version of the Pisa composite schemes (PCS2), which is applicable to molecules containing up to about 20 atoms. Then, the geometries of 30 additional medium-sized systems were optimized at the PCS2 level to cover a more balanced chemical space containing moieties poorly represented in SE compilations. The final database is available on a public domain Web site (https://www.skies-village.it/databases/) and can be employed for correcting structures of larger molecules obtained by hybrid or double-hybrid density functionals in the framework of the templating molecule approach. Several examples show that corrections based on the structures of building blocks taken from this database reduce the error of the B3LYP geometrical parameters of large molecules by nearly an order of magnitude without increasing the computational cost. Furthermore, the results of different density functional theory (DFT) or wave function (e.g., MP2) models can be improved in the same way by simply computing both the whole molecule and suitable building blocks at the chosen level. Then, whenever reference structures of some building blocks containing up to about 20 atoms are not available, they can be purposely optimized at the PCS2 level by employing reasonable computer resources. Therefore, a new DFT-cost tool is now available for the accurate characterization of large molecules by experiment-oriented scientists.

Slow Conformational Exchange between Partially Folded and Near-Native States of Ubiquitin: Evidence for a Multistate Folding Model.

The mechanism by which small proteins fold, i.e., via intermediates or via a two-state mechanism, is a subject of intense investigation. Intermediate states in the folding pathways of these proteins are sparsely populated due to transient lifetimes under normal conditions rendering them transparent to a majority of the biophysical methods employed for structural, thermodynamic, and kinetic characterization, which attributes are essential for understanding the cooperative folding/unfolding of such proteins. Dynamic NMR spectroscopy has enabled the characterization of folding intermediates of ubiquitin that exist in equilibrium under conditions of low pH and denaturants. At low pH, an unlocked state defined as N' is in fast exchange with an invisible state, U″, as observed by CEST NMR. Addition of urea to ubiquitin at pH 2 creates two new states F' and U', which are in slow exchange (kF'→U' = 0.14 and kU'→F' = 0.28 s-1) as indicated by longitudinal ZZ-magnetization exchange spectroscopy. High-resolution solution NMR structures of F' show it to be in an "unlocked" conformation with measurable changes in rotational diffusion, translational diffusion, and rotational correlational times. U' is characterized by the presence of just the highly conserved N-terminal β1-β2 hairpin. The folding of ubiquitin is cooperative and is nucleated by the formation of an N-terminal β-hairpin followed by significant hydrophobic collapse of the protein core resulting in the formation of bulk of the secondary structural elements stabilized by extensive tertiary contacts. U' and F' may thus be described as early and late folding intermediates in the ubiquitin folding pathway.

Topological Heterogeneity of Protein Kinase C Modulators in Human T-Cells Resolved with In-Cell Dynamic Nuclear Polarization NMR Spectroscopy.

Phorbol ester analogs are a promising class of anticancer therapeutics and HIV latency reversing agents that interact with cellular membranes to recruit and activate protein kinase C (PKC) isoforms. However, it is unclear how these esters interact with membranes and how this might correlate with the biological activity of different phorbol ester analogs. Here, we have employed dynamic nuclear polarization (DNP) NMR to characterize phorbol esters in a native cellular context. The enhanced NMR sensitivity afforded by DNP and cryogenic operation reveals topological heterogeneity of 13C-21,22-phorbol-myristate-acetate (PMA) within T cells utilizing 13C-13C correlation and double quantum filtered NMR spectroscopy. We demonstrate the detection of therapeutically relevant amounts of PMA in T cells down to an upper limit of ∼60.0 pmol per million cells and identify PMA to be primarily localized in cellular membranes. Furthermore, we observe distinct 13C-21,22-PMA chemical shifts under DNP conditions in cells compared to model membrane samples and homogenized cell membranes, that cannot be accounted for by differences in conformation. We provide evidence for distinct membrane topologies of 13C-21,22-PMA in cell membranes that are consistent with shallow binding modes. This is the first of its kind in-cell DNP characterization of small molecules dissolved in the membranes of living cells, establishing in-cell DNP-NMR as an important method for the characterization of drug-membrane interactions within the context of the complex heterogeneous environment of intact cellular membranes. This work sets the stage for the identification of the in-cell structural interactions that govern the biological activity of phorbol esters.

Investigation of biomolecular dynamics by sensitivity-enhanced 1H–2H CPMAS NMR using matrix-free dynamic nuclear polarization

Molecular dynamics of functional groups contain valuable information about structural properties and functional activities in biomolecules. NMR spectroscopy is a sensitive tool for the investigation of molecular dynamics over a wide range of timescales and thus may deepen the understanding of the biomolecules of interest. Here, we present an approach to use DNP-enhanced 2H NMR to study dynamics of selectively deuterated methyl groups in insoluble proteins such as amyloid beta (Aβ) fibrils. We adopted and optimized the matrix-free DNP approach by varying the amount of added polarizing agent as well as the rehydration level of model proteins. We show that the DNP enhancement obtained in 1H–2H cross-polarization (CP) MAS spectra may increase the sensitivity for selectively deuterated Aβ fibril samples by more than one order of magnitude, accelerating the collection of spin-lattice relaxation data in the DNP-accessible temperature range between 100 and 150 K by up to 400-fold. However, below the coalescence temperature, which describes the transition from the fast to the slow exchange regime, the experimentally obtained relaxation time constants suffer from a paramagnetic relaxation enhancement effect due to the presence of the polarizing agent. This seems to be a general effect for biomolecules as it is also confirmed for two other protein model systems. Our demonstration opens the possibility to extend the scope of 2H NMR for dynamics measurements to effective concentrations and/or temperatures below what is currently accessible; however, the observed interplay between paramagnetic relaxation and molecular dynamics also emphasizes the necessity for a better understanding of relaxation effects in DNP-enhanced NMR.

Comparison of curvilinear coordinates within vibrational structure calculations based on automatically generated potential energy surfaces.

For floppy molecules showing internal rotations and/or large amplitude motions, curvilinear internal coordinates are known to be superior to rectilinear normal coordinates within vibrational structure calculations. Due to the myriad definitions of internal coordinates, automated and efficient potential energy surface generators necessitate a high degree of flexibility, supporting the properties arising from these coordinates. Within this work, an approach to deal with these challenges is presented, including key elements, such as the selection of appropriate fit functions, the exploitation of symmetry, the positioning of grid points, or elongation limits for different coordinates. These elements are tested for five definitions of curvilinear coordinates, with three of them being generated in an automated manner. Calculations for semi-rigid molecules, namely H2O, H2CO, CH2F2, and H2CNH, demonstrate the general functionality of the implemented algorithms. Additional calculations for the HOPO molecule highlight the benefits of these curvilinear coordinates for systems with large amplitude motions. This new implementation allowed us to compare the performance of these different coordinate systems with respect to the convergence of the underlying expansion of the potential energy surface and subsequent vibrational configuration interaction calculations.

Accurate Quantum Monte Carlo Forces for Machine-Learned Force Fields: Ethanol as a Benchmark.

Quantum Monte Carlo (QMC) is a powerful method to calculate accurate energies and forces for molecular systems. In this work, we demonstrate how we can obtain accurate QMC forces for the fluxional ethanol molecule at room temperature by using either multideterminant Jastrow-Slater wave functions in variational Monte Carlo or just a single determinant in diffusion Monte Carlo. The excellent performance of our protocols is assessed against high-level coupled cluster calculations on a diverse set of representative configurations of the system. Finally, we train machine-learning force fields on the QMC forces and compare them to models trained on coupled cluster reference data, showing that a force field based on the diffusion Monte Carlo forces with a single determinant can faithfully reproduce coupled cluster power spectra in molecular dynamics simulations.

5-Aza-adenine Derivatives for Crop-Protection: Multicomponent Synthesis, Experimental and Theoretical Structural Analysis.

A microwave-assisted synthesis of 7-amino-1,2,4-triazolo[1,5-a][1,3,5]triazine-2-propanamides was developed using a three-component, catalyst-free reaction of cyanamide and trimethyl orthoformate with 3-(5-amino-1H-1,2,4-triazol-3-yl)propanamides (3). The reaction tolerated structurally diverse substrates and proceeded chemo- and regio-selectively, affording the target compounds in high purity in 5-10 minutes. The convenient chromatography-free isolation and purification of the products add practicality to this method. The structural features of the prepared compounds were investigated using dynamic NMR spectroscopy, X-ray crystallography and computational chemistry calculations. X-ray crystallography performed on a representative compound, 3-(7-amino-1,2,4-triazolo[1,5-a][1,3,5]triazin-2-yl)-N-(4-benzyl)propanamide (4 l), showed the overall molecular conformation to adopt the shape of the letter C. Notable localisation of π-electron density is found within the 1,2,4-triazolo[1,5-a][1,3,5]triazine system; a relatively short C-NH2 bond is consistent with restricted rotation about this bond. This study also presents a detailed analysis of the molecular interactions in 4 l using DFT and QTAIM methods with a focus on the hydrogen-bonding and π-stacking interactions that influence the molecular packing of 4 l. The findings reveal the significant roles of N-H⋅O, N-H⋅N and C-H⋅N interactions, along with electrostatically enhanced π⋅π contacts. A broad screening for insecticidal, fungicidal and herbicidal properties identified several compounds with potent herbicidal activity against Matricaria inodora.

VSCF/VCI theory based on the Podolsky Hamiltonian.

While the vibrational spectra of semi-rigid molecules can be computed on approaches relying on the Watson Hamiltonian, floppy molecules or molecular clusters are better described by Hamiltonians, which are capable of dealing with any curvilinear coordinates. It is the kinetic energy operator (KEO) of these Hamiltonians, which render the correlated calculations relying on them rather costly. Novel implementation of vibrational self-consistent field theory and vibrational configuration interaction theory on the basis of the Podolsky Hamiltonian are reported, in which the inverse of the metric tensor, i.e., the G matrix, is represented by an n-mode expansion expressed in terms of polynomials. An analysis of the importance of the individual terms of the KEO with respect to the truncation orders of the n-mode expansion is provided. Benchmark calculations have been performed for the cis-HOPO and methanimine, H2CNH, molecules and are compared to experimental data and to calculations based on the Watson Hamiltonian and the internal coordinate path Hamiltonian.

The Far-Infrared Spectrum of Methoxymethanol (CH3-O-CH2OH): A Theoretical Study.

Methoxymethanol (CH3OCH2OH), an oxygenated volatile organic compound of low stability detected in the interstellar medium, represents an example of nonrigid organic molecules showing various interacting and inseparable large-amplitude motions. The species discloses a relevant coupling among torsional modes, strong enough to prevent complete assignments using effective Hamiltonians of reduced dimensionality. Theoretical models for rotational spectroscopy can improve if they treat three vibrational coordinates together. In this paper, the nonrigid properties and the far-infrared region are analyzed using highly correlated ab initio methods and a three-dimensional vibrational model. The molecule displays two gauche-gauche (CGcg and CGcg') and one trans-gauche (Tcg) conformers, whose relative energies are very small (CGcg/CGcg'/Tcg = 0.0:641.5:792.7 cm-1). The minima are separated by relatively low barriers (1200-1500 cm-1), and the corresponding methyl torsional barriers V 3 are estimated to be 595.7, 829.0, and 683.7 cm-1, respectively. The ground vibrational state rotational constants of the most stable geometry have been computed to be A 0 = 17233.99 MHz, B 0 = 5572.58 MHz, and C 0 = 4815.55 MHz, at ΔA 0 = -3.96 MHz, ΔB 0 = 4.76 MHz, and ΔC 0 = 2.51 MHz from previous experimental data. Low-energy levels and their tunneling splittings are determined variationally up to 700 cm-1. The A/E splitting of the ground vibrational state was computed to be 0.003 cm-1, as was expected given the methyl torsional barrier (∼600 cm-1). The fundamental levels (100), (010), and (001) are predicted at 132.133 and 132.086 cm-1 (methyl torsion), 186.507 and 186.467 cm-1 (O-CH3 torsion), and 371.925 and 371.950 cm-1 (OH torsion), respectively.

Porous Organic Polymers for Efficient and Selective SO2 Capture from CO2‐rich Flue Gas

AbstractThe quest for effective technologies to reduce SO2 pollution is crucial due to its adverse effects on the environment and human health. Markedly, removing a ppm level of SO2 from CO2‐containing waste gas is a persistent challenge, and current technologies suffer from low SO2/CO2 selectivity and energy‐intensive regeneration processes. Here using the molecular building blocks approach and theoretical calculation, we constructed two porous organic polymers (POPs) encompassing pocket‐like structures with exposed imidazole groups, promoting preferential interactions with SO2 from CO2‐containing streams. Markedly, the evaluated POPs offer outstanding SO2/CO2 selectivity, high SO2 capacity, and an easy regeneration process, making it one of the best materials for SO2 capture. To gain better structural insights into the notable SO2 selectivity of the POPs, we used dynamic nuclear polarization NMR spectroscopy (DNP) and molecular modelling to probe the interactions between SO2 and POP adsorbents. The newly developed materials are poised to offer an energy‐efficient and environment‐friendly SO2 separation process while we are obliged to use fossil fuels for our energy needs.

Porous Organic Polymers for Efficient and Selective SO2 Capture from CO2-rich Flue Gas.

The quest for effective technologies to reduce SO2 pollution is crucial due to its adverse effects on the environment and human health. Markedly, removing a ppm level of SO2 from CO2-containing waste gas is a persistent challenge, and current technologies suffer from low SO2/CO2 selectivity and energy-intensive regeneration processes. Here using the molecular building blocks approach and theoretical calculation, we constructed two porous organic polymers (POPs) encompassing pocket-like structures with exposed imidazole groups, promoting preferential interactions with SO2 from CO2-containing streams. Markedly, the evaluated POPs offer outstanding SO2/CO2 selectivity, high SO2 capacity, and an easy regeneration process, making it one of the best materials for SO2 capture. To gain better structural insights into the notable SO2 selectivity of the POPs, we used dynamic nuclear polarization NMR spectroscopy (DNP) and molecular modelling to probe the interactions between SO2 and POP adsorbents. The newly developed materials are poised to offer an energy-efficient and environment-friendly SO2 separation process while we are obliged to use fossil fuels for our energy needs.

Formation of Stable Radicals by Mechanochemistry and Their Application for Magic Angle Spinning Dynamic Nuclear Polarization Solid-State NMR Spectroscopy.

High-field magic angle spinning (MAS) dynamic nuclear polarization (DNP) is becoming a common technique for improving the sensitivity of solid-state nuclear magnetic resonance (SSNMR) by the hyperpolarization of nuclear spins. Recently, we have shown that gamma irradiation is capable of creating long-lived free radicals that are amenable to MAS DNP in quartz and a variety of organic solids. Here, we demonstrate that ball milling is able to generate millimolar concentrations of stable radical species in diverse materials such as polystyrene, cellulose, borosilicate glass, and fused quartz. High-field electron paramagnetic resonance (EPR) was used to obtain further insight into the nature of the radicals formed in ball milled quartz and borosilicate glass. We further show that radicals generated in quartz by ball milling can be used for solid-effect DNP. We obtained 29Si DNP enhancements of approximately 114 and 33 at 110 K and room temperature, respectively, from a sample of ball milled quartz.

Study of the Reversible Hawthorne Rearrangement between Isomeric Forms of the Octadecahydroeicosaborate Anion Using Dynamic 11B NMR Spectroscopy

Study of the Reversible Hawthorne Rearrangement between Isomeric Forms of the Octadecahydroeicosaborate Anion Using Dynamic 11B NMR Spectroscopy

Structural and morphological evolution of biogenic hydroxyapatite: Effects of heating and cooling treatment

Despite extensive research, many aspects of biogenic hydroxyapatite (BHA) structural changes during heating remain unresolved. This work aims to understand how heating and cooling affect the growth of BHA crystallites obtained from porcine bone through an in-situ study. Wavelength-dispersive X-ray fluorescence of BHA has revealed the presence of trace elements such as Si, Al, Fe, Mg, and K. These elements serve as substitutional defects within the BHA structure. Vibrational analysis using infrared spectroscopy helped to verify the removal of the organic phase by combustion. In situ high-temperature X-ray diffraction and Rietveld refinement were used to analyze the changes in BHA crystallite size, lattice parameters, and microstrain. High-resolution micrographics confirmed the simulation of crystal habit using family planes (002), (111), (100), and (110) and validated the removal of organic material. Remarkably, the crystallite size increased dramatically after organic debris removal and coalescence events, while it remained constant before coalescence temperature.

Forensic implications of novel synthesis of cathinone derivatives by Neber and modified Neber rearrangements

Cathinone and its synthetic analogues are known compounds of clandestine interest. Investigation into novel pathways for synthesising cathinone derivatives has potential for forensic analysis and tracking. The known Neber rearrangement of commercially available phenylpropanones that were evaluated yielded amides described herein and was not viable for clandestine synthesis of cathinone derivatives. Whereas the known modified Neber rearrangement of phenylpropanones that were evaluated via stable aziridine salts and subsequent treatment with acid, gave cathinone derivatives described herein in poor to low yields (2–17%). Assessment of the reagents, equipment, and procedures required for the modified Neber rearrangement was considered as only viable for more advanced clandestine operations. An improved understanding of the potential by-product formation from the modified Neber rearrangement was determined by density functional theory (DFT) of hydrazone to azirine to aziridine intermediates and attempted dynamic NMR spectroscopy of a hydrazone described herein. The substantially lower energy of the azirine step compared to the starting hydrazonium salt step of the reaction mechanism implied that the azirine structure was a short-lived intermediate, and unable to be experimentally determined. New mass-spectral fragmentation data of compounds described herein was reported, where differentiation was observed for some individual compounds at the GC-EIMS fragmentation pattern level. From this study, individual mass-spectrometry fragmentation of key compounds evaluated from the modified Neber rearrangement of commercially available phenylpropanones indicates potential for forensic profiling analysis applications.

Determination of the Conjugacy Classes and Character Table of the Full Non-Rigid Group of Hexachlorocyclopropane Chemical Compound Via Wreath Product of Pair of Permutation Groups

The use of full non-rigid (f.NRG) molecules group theory to study the internal dynamics of molecular structures of chemical compounds is trending in the research space. In this paper, we use computational method to compute the group elements and group table of the Hexachlorocyclopropane molecular (algebraic) structure and thereafter determine the order and conjugacy classes of the group and finally the corresponding symmetry for each permutation group. We considered the point group of the compound which turns out to be isomorphic to the Wreath Products C3wrC2, where Cn denotes a cyclic group of order n. We found that the group has order 18 and 9 conjugacy classes. Investigating the solubility of the components of Hexachlorocyclopropane chemical compound can be considered for further study.

Synthesis of Organosilicon‐Based Thioether Ligand Class Showing Defined S‐Stereogenic Coordination in Crystalline Palladium(II) Complexes

AbstractA synthesis route to aromatic organosilicon‐based thioether ligands could be established and utilised for three congeners 2. These ligands were suitable for complexation with palladium(II) chloride forming three new complexes 3. The single crystal X‐ray diffraction and temperature‐dependent 1H and 13C‐NMR analysis of 3 are presented. The elucidated solid‐state structures suggested that one pair of diastereomers is favoured in crystalline phase and is controllable by the aromatic substituent. However, at room temperature in solution, the conformation at the sulphur atoms can fluctuate with a coalescence temperature for 1H‐NMR around 24 °C. At −31 °C, two signal sets could be observed since the inversion is slower than the 1H‐NMR timescale at lower temperatures.

High-level ab initio evidence of bipyramidal Cu5 clusters as fluxional Jahn-Teller molecules.

The front cover artwork is provided by María Pilar de Lara-Castells, Head of the AbinitFot Group at IFF-CSIC (Madrid), Coordinator of the National Project "COSYES", and Chair of the COST Action CA21101 "COSY", and Alexander O. Mitrushchenkov from the Université Paris-Est. The image shows the connection between the Jahn-Teller effect featured by bypiramidal Cu5 clusters and the property of fluxionality. Cover design by Katarzyna Krupka. Read the full text of the Research Article at 10.1002/cphc.202300317.