Fluxional Research Articles

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.

A numerical-tensorial "hybrid" nuclear motion Hamiltonian and dipole moment operator for spectra calculation of polyatomic nonrigid molecules.

The analysis and modeling of high-resolution spectra of nonrigid molecules require a specific Hamiltonian and group-theoretical formulation that differs significantly from that of more familiar rigid systems. Within the framework of Hougen-Bunker-Johns (HBJ) theory, this paper is devoted to the construction of a nonrigid Hamiltonian based on a suitable combination of numerical calculations for the nonrigid part in conjunction with the irreducible tensor operator method for the rigid part. For the first time, a variational calculation from abinitio potential energy surfaces is performed using the HBJ kinetic energy operator built from vibrational, large-amplitude motion, and rotational tensor operators expressed in terms of curvilinear and normal coordinates. Group theory for nonrigid molecules plays a central role in the characterization of the overall tunneling splittings and is discussed in the present approach. The construction of the dipole moment operator is also examined. Validation tests consisting of a careful convergence study of the energy levels as well as a comparison of results obtained from independent computer codes are given for the nonrigid molecules CH2, CH3, NH3, and H2O2. This work paves the way for the modeling of high-resolution spectra of larger nonrigid systems.

Conformational landscapes of symmetrically fluorine-substituted benzoic acids II: Calculations and measurements for the rotational spectrum and structure of 3,4,5-trifluorobenzoic acid

Calculations on the structure of 3,4,5-trifluorobenzoic acid were made using the Gaussian 16 program. The potential energy surfaces were scanned along CCCO and OCOH dihedral angles at the B3LYP/6-311G level to analyze its conformational landscape. Two conformations were identified and reoptimized at the B3LYP/aug-cc-pVTZ level. The result indicates that 3,4,5-trifluorobenzoic acid prefers a planar structure in its global minimum conformation. The pure rotational spectra of 3,4,5-trifluorobenzoic acid were measured in the frequency range of 6 – 12.5 GHz using a chirped pulse Fourier transform microwave (CP-FTMW) spectrometer. The spectra of the parent, seven 13C, and one deuterium singly substituted isotopologues were analyzed and fitted to measurement accuracy for a semi-rigid asymmetric top molecule. The rotational constants and centrifugal distortion constants were accurately determined. The rotational constants for the parent isotopologue are A = 1535.31408(32) MHz, B = 650.31751(16) MHz, and C = 456.98499(12) MHz. The effective structure of its ground vibrational state was determined from the spectra of the mono-substituted isotopologues. The agreement between the calculated and experimental spectroscopic constants is excellent.

Hemilability and structural considerations in complexes of platinum(II) comprising bis(diphenylphosphanyl)methane monoxide, monosulfide, and monoselenide.

The structure of a platinum(II) complex containing (R)-(dimethylamino)ethylnapthyl and bis(diphenylphosphanyl)methane monosulfide ligands, namely, {(R)-1-[1-(dimethylamino)ethyl]napthyl-κ2N,C2}[(diphenylphosphanylmethyl)diphenylphosphine sulfide-κ2P,S]platinum(II) hexafluoridoantimonate dichloromethane monosolvate, [Pt(C14H16N)(C25H22P2S)][SbF6]·CH2Cl2, was determined. The structural features are compared with analogous platinum bis(diphenylphosphanyl)methane monoxide [dppm(O)] and bis(diphenylphosphanyl)methane monoselenide [dppm(Se)] complexes in relation to their potential hemilability and stereochemical nonrigidity.

PCS/Bonds and PCS0: Pick your molecule and get its accurate structure and ground state rotational constants at DFT cost.

An unsupervised computational protocol is proposed with the aim of obtaining accurate structures of large molecules in the gas phase at the cost of standard density functional theory (DFT) computations. The whole workflow is fully automated and provides optimized equilibrium geometries and ground state rotational constants to be directly compared with experiments. The results for a panel of molecules of biological or medicinal interest show that the accuracy of the results delivered by the new tool at the cost of a single DFT geometry optimization is close to that delivered by state-of-the-art composite wavefunction methods for small semi-rigid molecules.

High-level Ab InitioEvidence of Bipyramidal Cu5Clusters as FluxionalJahn-Teller Molecules.

Novel highly selective synthesis techniques have enable the production of atomically precise monodisperse metal clusters (AMCs) of subnanometer size. These AMCs exhibit `molecule-like' structures that have distinct physical and chemical properties, significantly different from those of nanoparticles and bulk material. In this work, we study copper pentamer Cu5clusters as model AMCs by applying both density functional theory (DFT) and high-level (wave-function-based) ab initiomethods, including those which are capable of accounting for the multi-state multi-reference character of the wavefunction at the conical intersection between different electronic states and augmenting the electronic basis set till convergence. After assessing the accuracy of a high-level multi-multireference ab initioprotocol for the well-known Cu3case, we apply it to demonstrate that bypiramidal Cu5clusters are distorted Jahn-Teller (JT) molecules. The method is further used to evaluate the accuracy of single-reference approaches, finding that the coupled cluster singles and doubles and perturbative triples CCSD(T) method are very closeto our ab initiopredictions.Finally, we discuss how JT effects and, more generally, conical intersections, are intimately connected to the fluxionality of AMCs, giving them a `floppy' character that ultimately facilitates their interaction with environmental molecules and thus enhances their functioning as catalysts.

Accuracy Meets Feasibility for the Structures and Rotational Constants of the Molecular Bricks of Life: A Joint Venture of DFT and Wave-Function Methods.

A fully unsupervised computational protocol is proposed with the aim of obtaining reliable structural properties for molecular bricks of life in the gas phase. The results of the new composite scheme approach spectroscopic accuracy at a moderate cost without any empirical parameter in addition to those of the underlying electronic structure method. The whole workflow is fully automated and provides optimized geometries and equilibrium rotational constants. Direct comparison with experimental ground state rotational constants can be performed thanks to the effective computation of vibrational corrections in the framework of second-order vibrational perturbation theory. The results for all the nucleic acid bases and several flexible molecules of biological or medicinal interest show that the accuracy of the new tool is close to that delivered by state-of-the-art composite wave function methods for small semirigid molecules.

Exploiting Solid-State Dynamic Nuclear Polarization NMR Spectroscopy to Establish the Spatial Distribution of Polymorphic Phases in a Solid Material

Exploiting Solid-State Dynamic Nuclear Polarization NMR Spectroscopy to Establish the Spatial Distribution of Polymorphic Phases in a Solid Material

Sydnone Methides: Intermediates between Mesoionic Compounds and Mesoionic N‐Heterocyclic Olefins

AbstractSydnone methides represent an almost unknown class of mesoionic compounds which possess exocyclic carbon substituents instead of oxygen (sydnones) or nitrogen (sydnone imines) in the 5‐position of a 1,2,3‐oxadiazolium ring. Unsubstituted 4‐positions give rise to the generation of anionic N‐heterocyclic carbenes by deprotonation. Preparations of new sydnone methides are described here. They can be represented by mesomeric structures with either exocyclic carbanionic groups like −C(CN)2−, −C(CN)(COOMe)−, −C(CN)(CONH2)−, and −C(CN)(SO2Me)−, or with the corresponding exocyclic C=C double bonds as a common feature with mesoionic N‐heterocyclic olefins. An X‐ray single structure analysis revealed a length of 140.7(3) pm of the exocyclic bond in the solid state. From the coalescence temperature (55 °C) determined by a series of 13C NMR experiments (150 MHz) at various temperatures, an energy of rotation of 18.5 Kcal/mol was calculated for this bond. The 13C NMR signals of the anionic N‐heterocyclic carbenes, from which the 2‐mesityl‐substituted anionic NHC proved to be stable up to 10 °C, are highly shifted upfield (δcarbene=157.9 ppm−160.5 ppm). The carbenes can be reacted in situ with elemental selenium and chlorophosphanes to yield sydnone methide selenoethers after methylation and 4‐phosphanylsydnone methides in good to excellent yields, respectively.

A nuclear magnetic resonance-based study of the behavior of the tautomers of triclabendazole in DMSO-d6, in the presence of water

The benzimidazole antihelmintic agent triclabendazole (TCB) exhibits tautomeric polymorphism. It has been claimed that DMSO-d6 solutions prepared from the polymorphs of TCB display different NMR behavior. Therefore, a comprehensive NMR study was undertaken, in order to unveil the causes behind this unusual observation.In a first instance, 1H and 13C spectra of TCB were unequivocally assigned. Then, isothermal and variable temperature 1H NMR experiments were conducted in order to explore the relationship between the spectral changes with system variables: time, temperature and amount of water. Solutions prepared from both polymorphs experienced water-dependent spectral changes related to a tautomerization process at 298 K, and EXSY experiments confirmed the participation of H2O in the NH exchange. The tautomerization constant (KT = 1.14 ± 0.07) was determined from the signals of H4 at 298 K.On the other hand, variable temperature 1H NMR enabled estimation of coalescence temperatures (Tc) for the signals of H4, H6’ and NH, where a water-dependence was found for H4 (Tc = 298→334 K when H2O:TCB = 8:1→16:1). The exchange constants at coalescence (kc = 111.8 s−1 at 303 K, H2O:TCB = 9:1 and kc = 179.7 s−1 at 334 K, H2O:TCB = 16:1) were also determined. Thermodynamic data of the tautomerization, including free energy (ΔG‡ = 15.03 Kcal mol−1 at 300 K), enthalpy (ΔH‡ = 7.75 Kcal mol−1) and entropy (ΔS‡ = –0.0244 Kcal mol−1 K at 300 K) were obtained from the Eyring graph of linewidth-corrected exchange constant values of H4, while the activation energy (Eact = 8.48 Kcal mol−1) was obtained from an Arrhenius plot. A 1H NMR/chemometric approach demonstrated the reversibility of the temperature-driven changes in the range 298–355 K. Finally, a novel mechanism was proposed to account for the observations and dismiss the original claim, taking the presence of water in the system as the agent responsible for the detected variations.

One-step photocatalyzed functionalization of [60]Fullerene: A study on the direct incorporation of amides and lactams to C60

A direct, selective functionalization of C60 with amides and lactams has been developed. This efficient photochemical approach utilizes a diverse variety of radicals deriving from secondary and tertiary carboxy-, sulfonyl-, phosphoramides as well as lactams through a hydrogen atom transfer (HAT) process mediated by tetrabutylammonium decatungstate [(n-Bu4N)4W10O32]. The single addition of these carbon-centered radicals to [60]fullerene proceeded smoothly to produce a novel class of previously unexplored fullerene-based materials. Important structural insight, such as the rotational energy barrier of the amide C(O)–N bond, for these nanostructures is provided and has been experimentally determined by the use of Dynamic NMR spectroscopy. A mechanism for this new reaction has been proposed based mainly on the structure of reaction products and kinetic H/D isotope effect studies.

SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973–1977

This essay traces the history of early molecular dynamics simulations, specifically exploring the development of SHAKE, a constraint-based technique devised in 1976 by Jean-Paul Ryckaert, Giovanni Ciccotti and the late Herman Berendsen at CECAM (Centre Européen de Calcul Atomique et Moléculaire). The work of the three scientists proved to be instrumental in giving impetus to the MD simulation of complex polymer systems and it currently underpins the work of thousands of researchers worldwide who are engaged in computational physics, chemistry and biology. Despite its impact and its role in bringing different scientific fields together, accurate historical studies on the birth of SHAKE are virtually absent. By collecting and elaborating on the accounts of Ryckaert and Ciccotti, this essay aims to fill this gap, while also commenting on the conceptual and computational difficulties faced by its developers.

Crystal structure of the insecticide ethiprole (C13H9Cl2F3N4OS): a case study of whole-mol-ecule configurational disorder.

The crystal structure of ethiprole {systematic name: 5-amino-1-[2,6-di-chloro-4-(tri-fluoro-meth-yl)phen-yl]-4-ethane-sulfinyl-1H-imidazole-3-carbo-nitrile}, C13H9Cl2F3N4OS, a phenyl-pyrazole-based insecticide, is presented. The pyrazole ring carries four substituents: an N-bound 2,6-di-chloro-4-tri-fluoro-methyl-phenyl ring and C-bound amine, ethane-sulfinyl, and cyano groups. The sulfur atom of the ethane-sulfinyl group is trigonal-pyramidal and stereogenic. The structure exhibits whole-mol-ecule configurational disorder due to superposition of enanti-omers. The crystal packing is dominated by strong N-H⋯O and N-H⋯N hydrogen bonds, which form R 4 4(18) and R 2 2(12) ring motifs. Since the ethiprole mol-ecule is quite small, and structure solution and refinement were straightforward, the structure presents a convenient instructional example for modelling whole-body disorder of a non-rigid mol-ecule. To this end, a step-by-step overview of the model-building and refinement process is also given. The structure could form the basis of a useful classroom, practical, or workshop-style example.

Exploiting solid-state dynamic nuclear polarization NMR spectroscopy to establish the spatial distribution of polymorphic phases in a solid material.

Solid-state DNP NMR can enhance the ability to detect minor amounts of solid phases within heterogenous materials. Here we demonstrate that NMR contrast based on the transport of DNP-enhanced polarization can be exploited in the challenging case of early detection of a small amount of a minor polymorphic phase within a major polymorph, and we show that this approach can yield quantitative information on the spatial distribution of the two polymorphs. We focus on the detection of a minor amount (<4%) of polymorph III of m-aminobenzoic acid within a powder sample of polymorph I at natural isotopic abundance. Based on proposed models of the spatial distribution of the two polymorphs, simulations of 1H spin diffusion allow NMR data to be calculated for each model as a function of particle size and the relative amounts of the polymorphs. A comparison between simulated and experimental NMR data allows the model(s) best representing the spatial distribution of the polymorphs in the system to be established.