Spinning Nuclear Magnetic Resonance Research Articles

Ubiquitous Order-Disorder Transition in the Mn Antisite Sublattice of the (MnBi2Te4)(Bi2Te3)n Magnetic Topological Insulators.

Magnetic topological insulators (TIs) herald a wealth of applications in spin-based technologies, relying on the novel quantum phenomena provided by their topological properties. Particularly promising is the (MnBi2Te4)(Bi2Te3)n layered family of established intrinsic magnetic TIs that can flexibly realize various magnetic orders and topological states. High tunability of this material platform is enabled by manganese-pnictogen intermixing, whose amounts and distribution patterns are controlled by synthetic conditions. Here, nuclear magnetic resonance and muon spin spectroscopy, sensitive local probe techniques, are employed to scrutinize the impact of the intermixing on the magnetic properties of (MnBi2Te4)(Bi2Te3)nand MnSb2Te4. The measurements not only confirm the opposite alignment between the Mn magnetic moments on native sites and antisites in the ground state of MnSb2Te4, but for the first time directly show the same alignment in (MnBi2Te4)(Bi2Te3)n with n = 0, 1 and 2. Moreover, for all compounds, the static magnetic moment of the Mn antisite sublattice is found to disappear well below the intrinsic magnetic transition temperature, leaving a homogeneous magnetic structure undisturbed by the intermixing. The findings provide a microscopic understanding of the crucial role played by Mn-Bi intermixing in (MnBi2Te4)(Bi2Te3)n and offer pathways to optimizing the magnetic gap in its surfacestates.

Dynamic Nuclear Polarization Enhanced Multiple-Quantum Spin Counting of Molecular Assemblies in Vitrified Solutions.

Crystallization pathways are essential to various industrial, geological, and biological processes. In nonclassical nucleation theory, prenucleation clusters (PNCs) form, aggregate, and crystallize to produce higher order assemblies. Microscopy and X-ray techniques have limited utility for PNC analysis due to the small size (0.5-3 nm) and time stability constraints. We present a new approach for analyzing PNC formation based on 31P nuclear magnetic resonance (NMR) spin counting of vitrified molecular assemblies. The use of glassing agents ensures that vitrification generates amorphous aqueous samples and offers conditions for performing dynamic nuclear polarization (DNP)-amplified NMR spectroscopy. We demonstrate that molecular adenosine triphosphate along with crystalline, amorphous, and clustered calcium phosphate materials formed via a nonclassical growth pathway can be differentiated from one another by the number of dipolar coupled 31P spins. We also present an innovative approach for examining spin counting data, demonstrating that a knowledge-based fitting of integer multiples of cosine wave functions, instead of the traditional Fourier transform, provides a more physically meaningful retrieval of the existing frequencies. This is the first report of multiquantum spin counting of assemblies formed in solution as captured under vitrified DNP conditions, which can be useful for future analysis of PNCs and other aqueous molecular clusters.

Biological and equilibrium studies of Co(II), Cu(II), Zn(II), and Cd(II) complexes of 1‐formyl‐3‐semicarbazide: Docking studies

1‐Formyl‐3‐semicarbazide (FSC, HL) and its metal complexes with Co(II), Cu(II), Zn(II), and Cd(II) ions have been synthesized and characterized by elemental analysis, liquid chromatography‐mass spectrometry (LC–MS), infrared (IR), electronic, nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy, thermogravimetric analysis (TGA), magnetic susceptibility, and conductivity measurements. The chelates are non‐electrolytic in nature with distorted octahedral geometry. The kinetic and thermodynamic properties were calculated using the Coats–Redfern relation results in positive enthalpy change values and negative entropy change values. The equilibrium studies of FSC with Co(II), Zn(II), and Cd(II) ion have been carried out by potentiometric pH titrations in 70% v/v DMF‐water medium at 303 K and 0.1 M (KNO3) ionic strength. The study revealed that FSC is monobasic acid with pKa value of 8.84. The stability constants suggested the formation of 1:1 Co(II)‐FSC complex, and Zn(II)‐FSC and Cd(II)‐FSC systems revealed the formation of both 1:1 and 1:2 complexes in the solution. DNA binding studies for the metal chelates have been carried out using electronic absorption spectra, fluorescence emission spectra, and viscosity measurements revealing groove binding for Co(II), and Zn(II) complexes, and intercalation mode of binding for Cu(II)‐FSC complex with CT‐DNA. The Kb values from absorption studies are Co(II)‐FSC = 0.9990 × 102, Cu(II)‐FSC = 2.433 × 104, and Zn(II)‐FSC = 8.277 × 102 M−1, and the KSV values from the competitive fluorescence emission studies are Co(II)‐FSC = 0.19212 and Cu(II)‐FSC = 0.11482 M−1. Molecular docking carried out for both ligand and its Co(II) and Zn(II) complexes also revealed groove mode of binding, and Cu(II) complex showed intercalative mode of binding. The inhibition constants for HL, Co(II), Cu(II), and Zn(II) are 1460, 0.478, 0.122, and 0.194 μM, respectively. The antimicrobial activity has been studied using agar disk diffusion method against Escherichia coli and Bacillus subtilis. FSC has been found to be more active against gram +ve and gram –ve bacteria than its metal chelates.

Topological characterizations on hexagonal and rectangular tessellations of antikekulenes and its computed spectral, nuclear magnetic resonance and electron spin resonance characterizations

AbstractTessellations of antikekulenes are of interest from the standpoints of antiaromaticity, ring currents, unusual ‐electron characteristics, magnetism and their highly reactive nature. Although precursors of antikekulenes have been synthesized, up to now synthesis of antikekulenes has been proven to be formidably difficult. Yet they are predicted to have intriguing properties and their antiaromatic nature together with a combination of four and six‐membered rings makes them intriguing candidates for theoretical indices. In the present study, we have computed the topological indices of antikekulene by employing graph‐theoretical cut methods that simplify the parent tessellations of antikekulenes into simpler graphs. We have derived exact mathematical expressions of several topological descriptors for hexagonal and rectangular antikekulene structures. Furthermore we have obtained the graph‐spectral properties, algebraic structure counts, resonance stabilization and delocalization energies as well as nuclear magnetic resonance and electron spin resonance spectroscopic patterns of the two tessellations of antikekulenes.

On the performance of HRPA(D) for NMR spin–spin coupling constants: Smaller molecules, aromatic and fluoroaromatic compounds

In this study, the performance of the doubles-corrected higher random-phase approximation [HRPA(D)] has been investigated in calculations of nuclear magnetic resonance spin–spin coupling constants (SSCCs) for 58 molecules with the experimental values used as the reference values. HRPA(D) is an approximation to the second-order polarization propagator approximation (SOPPA) and is, therefore, computationally less expensive than SOPPA. HRPA(D) performs comparable and sometimes even better than SOPPA, and therefore, when calculating SSCCs, it should be considered as an alternative to SOPPA. Furthermore, it was investigated whether a coupled-cluster singles, doubles and perturbative triples [CCSD(T)] or Møller-Plesset second order (MP2) geometry optimization was optimal for a SOPPA and a HRPA(D) SSCC calculation for eight smaller molecules. CCSD(T) is the optimal geometry optimization for the SOPPA calculation, and MP2 was optimal for HRPA(D) SSCC calculations.

Quantum sensors in diamonds for magnetic resonance spectroscopy: Current applications and future prospects

Nuclear magnetic resonance (NMR) and electron spin resonance (ESR) methods are indispensable techniques that utilize the spin of particles to probe matter, with applications in various disciplines, including fundamental physics, chemistry, biology, and medicine. Despite their versatility, the technique's sensitivity, particularly for NMR, is intrinsically low, which typically limits the detection of magnetic resonance (MR) signals to macroscopic sample volumes. In recent years, atom-sized magnetic field quantum sensors based on nitrogen-vacancy (NV) centers in diamond paved the way to detect MR signals at the micro- and nanoscale, even down to a single spin. In this perspective, we offer an overview of the most promising directions in which this evolving technology is developing. Significant advancements are anticipated in the life sciences, including applications in single molecule and cell studies, lab-on-a-chip analytics, and the detection of radicals or ions. Similarly, NV-MR is expected to have a substantial impact on various areas in the materials research, such as surface science, catalysis, 2D materials, thin films, materials under extreme conditions, and quantum technologies.

Structural Characterization of Food Allergens by Nuclear Magnetic Resonance Spectroscopy.

As allergies, especially those triggered by food, are becoming more and more prevalent, it is of increasing importance to fully understand the structures and dynamic behaviors of allergenic proteins along with their interactions with potential natural ligands. Therefore, we have established a solid routine to achieve structural characterization of food allergens, especially for birch pollen-related cross-reactive proteins from the class 10 of pathogenesis-related proteins (PR-10), by nuclear magnetic resonance (NMR) spectroscopy. Following expression of the desired allergen in Escherichia coli in isotope-labeled minimal media, the three-dimensional solution structures of these proteins can be determined, and insight into ligand binding mechanics and structural dynamic properties are accessible through NMR spin relaxation experiments.

Structural integrity and healing efficiency study of micro-capsule based composite materials via 1H NMR relaxometry

In this work we present a novel approach utilizing nuclear magnetic resonance (NMR) relaxometry to assess the structural stability of microcapsules employed as self-healing agents in advanced aerospace composites both in ambient and harsh environmental conditions. We successfully correlate the amount of the encapsulated self-healing agent with the signal intensity and confirm non-destructively the quantity of the encapsulated self-healing agent mass for the first time in the literature using 1H NMR spin–spin relaxation techniques on urea–formaldehyde (UF) microcapsules of different diameters containing an epoxy healing agent. The amount of self-healing agent is shown to increase by reducing the capsule diameter; however, the reduced shell mass renders the capsules more fragile and prone to failure. Most notably, via NMR experiments conducted during thermal cycling simulating flight conditions, we demonstrate that the microcapsule integrity under thermal fatigue varies according to their size. Especially we experimentally verify that the microcapsules with the most sensitive shells are the 147 nm and 133 nm diameter microcapsules, which are the most commonly used in self-healing systems. Finally, we were able to retrieve the same results using a portable NMR spectrometer developed in-house for in situ microcapsule testing, thus demonstrating the potential of NMR relaxometry as a powerful non-destructive evaluation tool for the microcapsule production line.

Intracellular environment can change protein conformational dynamics in cells through weak interactions.

Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.

Nuclear Magnetic Resonance Relaxation Pathways in Electrolytes for Energy Storage.

Nuclear Magnetic Resonance (NMR) spin relaxation times have been an instrumental tool in deciphering the local environment of ionic species, the various interactions they engender and the effect of these interactions on their dynamics in conducting media. Of particular importance has been their application in studying the wide range of electrolytes for energy storage, on which this review is based. Here we highlight some of the research carried out on electrolytes in recent years using NMR relaxometry techniques. Specifically, we highlight studies on liquid electrolytes, such as ionic liquids and organic solvents; on semi-solid-state electrolytes, such as ionogels and polymer gels; and on solid electrolytes such as glasses, glass ceramics and polymers. Although this review focuses on a small selection of materials, we believe they demonstrate the breadth of application and the invaluable nature of NMR relaxometry.

New homo‐bimetallic complexes of dihydrazone‐oxime ligand incorporating isatinic moiety: Preparation, characterization, theoretical, microbicidal, and anticancer investigation

A new series of dihydrazone‐oxime ligand's homo‐bimetallic complexes of formulas [M2LCl5(H2O)3].nH2O (M=Fe3+, n=0; Ru3+, n=2), [M2L((O)CH3COO)3(H2O)5].nH2O (M=Co2+, Mn2+, Zn2+ or UO22+, n=4, 6, or 1) and [Cu2L(NO3)3(H2O)3] is designated from the reaction of 3‐((3‐(hydroxyimino)butan‐2‐ylidene)hydrazono)indolin‐2‐one (HL,1) with the salts of Fe3+, Ru3+, Co2+, Cu2+, Mn2+, Zn2+, and UO22+. The newly prepared compounds' structure was elucidated based on traditional techniques such as molar conductance, magnetic measurements, elemental, thermogravimetric (TGA) analyses, and mass spectrometry, as well as spectroscopic tools such as electronic absorption, infrared, nuclear magnetic resonance, mass, and electron spin resonance spectra. The values of complexes molar conductance in DMSO indicated that they were non‐electrolytes. The elemental analysis, in conjunction with other data obtained, confirmed that the ligand performed as a uni‐negative tetradentate chelator that bound two metal cations via the indoline carbonyl; deprotonated oximatic and azomethine groups adopt distorted octahedral or square pyramidal geometries. The chemical formula of these complexes was corroborated by TG analysis, which verified that the homo‐bimetallic complexes were degraded in three or four decaying steps in temperature range 50–596°C ended with the formation of metallic oxide. The prepared compounds' structural characterization was verified by DFT calculations utilizing DFT‐B3LYP technique with a basis set (6–311++G[d,p]). Theoretical calculations' results demonstrated that the homo‐bimetallic complexes' reactivity is higher than un‐complexed ligand's reactivity. The anticancer activity was determined versus three cell lines, namely, SKOV3, PC‐3, and HeLa cell lines. The assignment data revealed that the Zn2+ complex has a stronger inhibitory effect against the three cell lines. Additionally, the synthesized substances' in vitro microbicidal activity was performed versus a variety of bacterial and fungal species.

Unexpected Structural Effects on the Onset of Thermal Reactions of Aromatic Hydrocarbons

This work aims to study the reactivity of a broad range of aromatic hydrocarbons to better understand the reactivities of more complex hydrocarbon mixtures. A set of closed-system pyrolysis experiments were conducted on a diverse range of ∼30 polycyclic aromatic hydrocarbons (PAHs) at the thermal onset reaction temperature of 400 °C to understand structural effects on reactivities and shed light on the early events of thermal reaction mechanisms. Thermal transformations, including methyl transfer (alkylation/dealkylation), rearrangement, condensation, molecular growth, and other chemical transformations, are often indicated by dark carbon materials composed of complex mixtures. Thermal transformation was confirmed by phenomenological changes (color and solubility) and chemical analysis using nuclear magnetic resonance, thermogravimetric analysis, gas chromatography, and electron spin resonance. Unsubstituted PAHs (e.g., phenanthrene, anthracene, pyrene, chrysene, etc.) were unaffected by heating at this temperature, with the exception of tetracene and pentacene which readily transformed into dark and insoluble materials. The reactivity of these unsubstituted PAHs is consistent with aromaticity predicted by the Clar theory. On the contrary, most alkyl-substituted PAHs can be transformed into carbon materials at 400 °C; however, alkyl-substituted phenanthrenes (2,7-dimethyl, 2-ethyl, or 7-ethyl) and benzenes (xylenes and pentamethylbenzene) were unreactive. CH2-containing PAH molecules were unreactive if in a five-membered ring (e.g., fluorene and benzofluorene) but became reactive if in a six-membered ring (9,10-dihydroanthracene), likely as a result of aromatization of the latter. The reactivity of the aryl–aryl linkage depends upon the aromatic moieties to which it is connected. While it is unreactive when connecting phenyl groups, such as in p-terphenyl, it is reactive when connecting pyrenes, such as in 1,1′-bispyrene. These results were unexpected and challenge the conventional thinking about hydrocarbon reactivities. Explanations and possible hypotheses are proposed, but more questions remain unanswered to understand the structural effects on reactivities. These findings are conducive to the sustainable use of aromatic hydrocarbons for higher value carbon materials and relevant to numerous pyrolysis studies on oil shale kerogens, biomass, and waste plastics.

Cation and anion ordering in synthetic lepidolites and lithian muscovites: influence of the OH ∕ F and Li ∕ Al ratios on the mica formation studied by NMR (nuclear magnetic resonance) spectroscopy and X-ray diffraction

Abstract. A large number of lepidolites K(LixAl3−x)[Si2xAl4−2xO10](OH)yF2−y and Li-muscovites K(LixAl2-x/3□1-2x/3)[Si3AlO10](OH)yF2−y were synthesised by a gelling method in combination with hydrothermal syntheses at a pressure of 2 kbar and a temperature of 873 K. The nominal composition ranged between 0.0≤x≤2.0 and 0.0≤y≤2.0, i.e. from polylithionite K[Li2.0Al][Si4.0O10](OH)yF2−y over trilithionite K[Li1.5Al1.5][AlSi3.0O10](OH)yF2−y to muscovite K[Al2.0□][AlSi3.0O10](OH)yF2−y. 1H, 19F, 29Si and 27Al magic-angle spinning nuclear magnetic resonance (MAS NMR) and 27Al multiple-quantum magic-angle spinning (MQMAS) NMR spectroscopy has been performed to investigate the order and/or disorder state of Si and Al in the tetrahedral layers and of Li, Al, OH and F in the octahedral layer. The synthetic mica crystals are very small, ranging from 0.1 to 5 µm. With increasing Al content, the crystal sizes decrease. Rietveld structure analyses on 12 samples showed that nearly all samples consist of two mica polytypes (1M and 2M1) of varying proportions. In the case of lepidolites, the 1M / 2M1 ratio depends on the Li/Al ratio of the reaction mixture. The refinement of the occupancy factors of octahedral sites shows that lepidolites (1.5≤x≤2.0) represent a solid solution series with polylithionite and trilithionite as the endmembers. In the case of the Li-muscovites (0.0≤x≤1.5), the 1M / 2M1 ratio depends on the number of impurity phases like eucryptite or sanidine depleting the reaction mixture of Li or Al. There is no solid solution between trilithionite and muscovite; instead, the Li-muscovite crystals consist of domains differing in the relative proportions of muscovite and trilithionite. The overall composition of the synthesised micas which consist of two polytypes can be characterised by 29Si, 1H and 19F MAS NMR spectroscopy. The Si/Al ratio in the tetrahedral layers and thus the content of [4]Al were calculated by analysing the signal intensities of the 29Si MAS NMR experiments. The Li content xest was calculated from the measured tetrahedral Si/Al ratio of the 29Si MAS NMR signals. The calculated Li contents xest of samples between polylithionite and trilithionite agree with the expected values. The F-rich samples show slightly increased values and the OH samples lower values. Lepidolites with only F (x = 1.5 to 2.0, y = 0.0), but not lepidolites with only OH (x = 1.5 to 2.0 and y = 2.0), were observed after synthesis. With decreasing Li content, x≤1.2, Li-muscovites containing mostly hydroxyl (y>1.0) are formed. It was possible to synthesise fluorine containing micas with a Li content as low as 0.3 and y = 0.2 to 1.8. The 19F and 1H MAS NMR experiments reveal that F and OH are not distributed statistically but local structural preferences exist. F is attracted by Li-rich and OH by Al-rich environments. The quadrupolar coupling constant which represents the anisotropy of the Al coordination is low for polylithionite with CQ=1.5 MHz and increases to CQ=3.8 MHz for trilithionite. For tetrahedral Al a smaller increase of CQ from 1.7 to 2.8 MHz is observed. Advancing from trilithionite to muscovite both quadrupolar coupling constants decrease to 2.5 MHz for octahedral and 1.5 MHz for tetrahedral Al. In polylithionite there is the most isotropic environment for octahedral Al; there are only Li2Al sites coordinated by F in the octahedral sheets and O from the tetrahedral sheets which are regular, containing only Si. The distortion and anisotropy for Al in tetrahedral as well as octahedral sheets increases with rising Al content. The most anisotropic environment can be found in trilithionite, especially for octahedral Al.

Vortex-bound solitons in topological superfluid 3He

The different superfluid phases of 3He are described by p-wave order parameters that include anisotropy axes both in the orbital and spin spaces. The anisotropy axes characterize the broken symmetries in these macroscopically coherent quantum many-body systems. The systems’ free energy has several degenerate minima for certain orientations of the anisotropy axes. As a result, spatial variation of the order parameter between two such regions, settled in different energy minima, forms a topological soliton. Such solitons can terminate in the bulk liquid, where the termination line forms a vortex with trapped circulation of mass and spin superfluid currents. Here we discuss possible soliton-vortex structures based on the symmetry and topology arguments and focus on the three structures observed in experiments: solitons bounded by spin-mass vortices in the B phase, solitons bounded by half-quantum vortices (HQVs) in the polar and polar-distorted A phases, and the composite defect formed by a half-quantum vortex, soliton and the Kibble-Lazarides-Shafi wall in the polar-distorted B phase. The observations are based on nuclear magnetic resonance (NMR) techniques and are of three types: first, solitons can form a potential well for trapped spin waves, observed as an extra peak in the NMR spectrum at shifted frequency; second, they can increase the relaxation rate of the NMR spin precession; lastly, the soliton can present the boundary conditions for the anisotropy axes in bulk, modifying the bulk NMR signal. Owing to solitons’ prominent NMR signatures and the ability to manipulate their structure with external magnetic field, solitons have become an important tool for probing and controlling the structure and dynamics of superfluid 3He, in particular HQVs with core-bound Majorana modes.

Quantitative Susceptibility Mapping as a Biomarker to Assess Middle Cerebral Artery Thrombus Composition in Acute Ischemic Stroke

Objective: To compare the quantitative susceptibility mapping (QSM) susceptibility values and pathology composition with different types of thrombi in the middle cerebral artery (MCA), and assess the value of susceptibility weight imaging in thrombus component diagnosis in stroke. Materials and methods: This study included 15 patients (73.47 ± 10.7 years; 6 males and 9 females) who underwent magnetic resonance imaging before mechanical thrombectomy due to acute middle cerebral artery occlusion between January 2017 and December 2019. All patients had the susceptibility vessel sign (SVS) on SWI (susceptibility weighted imaging), and the thrombus susceptibility was measured by signal processing in nuclear magnetic resonance SPIN software. The retrieved thrombi underwent histopathologic analysis, and the correlation between thrombus susceptibility and the pathologic composition was analyzed by two independent Kolmogorov–Smirnov tests. The location and length of thrombi were evaluated on both SWI and DSA, and the correlation was explored using two independent samples Wilcoxon rank test. The correlations between susceptibility and the infarct core volumes (ADC < 620 mm2/s volume map), hypoperfusion volumes (Tmax > 6 s volume map), 90-day modified Rankin scale (mRS), and the National Institutes of Health Stroke Scale (NIHSS) at admission were analyzed by Spearman’s correlation analysis. Results: Among the 15 retrieved thrombi, the mean thrombus susceptibility of RBC-dominant and fibrin-dominant thrombi were 209.88 ± 11.32 and 155.70 ± 28.20 (ppb), respectively (p = 0.037). The average distance of the proximal end of the thrombi to the midline was 24.67 ± 8.43 mm and 24.62 ± 8.44 mm, as measured by SWI and DSA (digital subtraction angiography), respectively (p < 0.001). The correlation between thrombus susceptibility was weakly negatively correlated with ADC < 620 mm2/s volume map (r = 0.356, p = 0.193) and poorly correlated with Tmax > 6 s volume map (r = 0.252, p = 0.365), 90-day mRS (r = 0.182, p = 0.517), and NIHSS at admission (r = 0.262, p = 0.345). Conclusions: The measurements of the Quantitative susceptibility value of thrombi may help predict the composition of thrombi in patients with acute middle cerebral artery occlusion. QSM provides a more accurate method to evaluate the thrombi.

Measuring of water transport selectively along the plant root plasmodesmata using gradient nuclear magnetic resonance with paramagnetic doping

In this study, we measured translational water diffusion selectively along symplast pathway through plasmodesmata in maize roots, and the effective plasmodesmata permeability coefficient (P) was determined using a nuclear magnetic resonance (NMR) spin echo method. Measuring of water transport selectively along the plant root plasmodesmata was achieved with paramagnetic complexes (PCs) of high relaxation efficiency. PCs penetrate into the intercellular space of root tissue, but not into cells, and accelerate the magnetic relaxation processes of intercellular water, thereby excluding the contribution of intercellular water to the registered NMR diffusion echo attenuation. In result, NMR control of translational diffusion can be applied to the signal of the water moving along the symplast pathway through plasmodesmata, where the PCs do not penetrate. Diethylenetriaminepentaacetic acid (GdDTPA), Mn2+-trans-1,2-diaminocyclohexane-N,N,N′,N′-tetraacetic acid (MnDCTA), and GdCl3 were used as PCs. An increase in the PCs concentration led to a side effect in the form of a varying decrease in diffusive water transport in the roots. The P was determined by extrapolating the concentration dependence to zero concentration of PCs. Among the PCs studied, MnDCTA had the least side effects on the water transport when the concentration dependence was linear. When MnDCTA was used, the P accounted for 30–35% of the total cell water permeability (by transmembrane and symplast pathways). The rate of water flow along the plasmodesmata in the approximation of the piston mode of flow along the linear cell chain was estimated to range from 4.5 × 10−7 to 8.8 × 10−7 m/s.

Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations.

Nuclear magnetic resonance (NMR) spin relaxation is the most informative approach to experimentally probe the internal dynamics of proteins on the picosecond to nanosecond time scale. At the same time, molecular dynamics (MD) simulations of biological macromolecules are steadily improving through better physical models, enhanced sampling methods, and increased computational power, and they provide exquisite information about flexibility and its role in protein stability and molecular interactions. Many examples have shown that MD is now adept in probing protein backbone motion, but improvements are still required toward a quantitative description of the dynamics of side chains, for example, probed by the dynamics of methyl groups. Thus far, the comparison of computation with experiment for side chain dynamics has primarily focused on the relaxation of 13C and 2H nuclei induced by autocorrelated variation of spin interactions. However, the cross-correlation of 13C-1H dipolar interactions in methyl groups offers an attractive alternative. Here, we establish a computational framework to extract cross-correlation relaxation parameters of methyl groups in proteins from all-atom MD simulations. To demonstrate the utility of the approach, cross-correlation relaxation rates of ubiquitin are computed from MD simulations performed with the AMBER99SB*-ILDN and CHARMM36 force fields. Simulation results were found to agree well with those obtained by experiment. Moreover, the data obtained with the two force fields are highly consistent.

Zoo of silicon-based quantum bits

Zoo of silicon-based quantum bits

Natamycin sequesters ergosterol and interferes with substrate transport by the lysine transporter Lyp1 from yeast

Natamycin is a polyene macrolide, widely employed to treat fungal keratitis and other yeast infections as well as to protect food products against fungal molds. In contrast to other polyene macrolides, such as nystatin or amphotericin B, natamycin does not form pores in yeast membranes, and its mode of action is not well understood. Here, we have employed a variety of spectroscopic methods, computational modeling, and membrane reconstitution to study the molecular interactions of natamycin underlying its antifungal activity. We find that natamycin forms aggregates in an aqueous solution with strongly altered optical properties compared to monomeric natamycin. Interaction of natamycin with model membranes results in a concentration-dependent fluorescence increase which is more pronounced for ergosterol- compared to cholesterol-containing membranes up to 20 mol% sterol. Evidence for formation of specific ergosterol-natamycin complexes in the bilayer is provided. Using nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy, we find that natamycin sequesters sterols, thereby interfering with their well-known ability to order acyl chains in lipid bilayers. This effect is more pronounced for membranes containing the sterol of fungi, ergosterol, compared to those containing mammalian cholesterol. Natamycin interferes with ergosterol-dependent transport of lysine by the yeast transporter Lyp1, which we propose to be due to the sequestering of ergosterol, a mechanism that also affects other plasma membrane proteins. Our results provide a mechanistic explanation for the selective antifungal activity of natamycin, which can set the stage for rational design of novel polyenes in the future.

A local hybrid exchange functional approximation from first principles.

Local hybrid functionals are a more flexible class of density functional approximations, allowing for a position-dependent admixture of exact exchange. This additional flexibility, however, comes with a more involved mathematical form and a more complicated design. A common denominator for previously constructed local hybrid functionals is the usage of thermochemical benchmark data to construct these functionals. Herein, we design a local hybrid functional without relying on benchmark data. Instead, we construct it in a more ab initio manner, following the principles of modern meta-generalized gradient approximations and considering theoretical constraints. To achieve this, we make use of the density matrix expansion and a local mixing function based on an approximate correlation length. The accuracy of the developed density functional approximation is assessed for thermochemistry, excitation energies, polarizabilities, magnetizabilities, nuclear magnetic resonance (NMR) spin-spin coupling constants, NMR shieldings, and shifts, as well as EPR g-tensors and hyperfine coupling constants. Here, the new exchange functional shows a robust performance and is especially well suited for atomization energies, barrier heights, excitation energies, NMR coupling constants, and EPR properties, whereas it loses some ground for the NMR shifts. Therefore, the designed functional is a major step forward for functionals that have been designed from first principles.