Project description:Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R(1ρ) relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R(1ρ) RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p ~ 10%) and shortly lived (τ ~ 10 ms) NMR "invisible" state. The utility of CEST and low spin-lock field R(1ρ) RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as ~60 s(-1).
Project description:Spin echo is a fundamental tool for quantum registers and biomedical imaging. It is believed that a strong magnetic field is needed for the spin echo to provide long memory and high resolution, since a degenerate spin cannot be controlled or addressed under a zero magnetic field. While a degenerate spin is never subject to dynamic control, it is still subject to geometric control. Here we show the spin echo of a degenerate spin subsystem, which is geometrically controlled via a mediating state split by the crystal field, in a nitrogen vacancy centre in diamond. The demonstration reveals that the degenerate spin is protected by inherent symmetry breaking called zero-field splitting. The geometric spin echo under zero field provides an ideal way to maintain the coherence without any dynamics, thus opening the way to pseudo-static quantum random access memory and non-invasive biosensors.
Project description:Electron spin resonance (ESR) spectroscopy has broad applications in physics, chemistry, and biology. As a complementary tool, zero-field ESR (ZF-ESR) spectroscopy has been proposed for decades and shown its own benefits for investigating the electron fine and hyperfine interaction. However, the ZF-ESR method has been rarely used due to the low sensitivity and the requirement of much larger samples than conventional ESR. In this work, we present a method for deploying ZF-ESR spectroscopy at the nanoscale by using a highly sensitive quantum sensor, the nitrogen vacancy center in diamond. We also measure the nanoscale ZF-ESR spectrum of a few P1 centers in diamond, and show that the hyperfine coupling constant can be directly extracted from the spectrum. This method opens the door to practical applications of ZF-ESR spectroscopy, such as investigation of the structure and polarity information in spin-modified organic and biological systems.
Project description:The response of the geometric and NMR properties of molecular systems to an external electric field has been studied theoretically in a wide field range. It has been shown that this adduct under field approach can be used to model the geometric and spectral changes experienced by molecular systems in polar media if the system in question has one and only one bond, the polarizability of which significantly exceeds the polarizability of other bonds. If this requirement is met, then it becomes possible to model even extreme cases, for example, proton dissociation in hydrogen halides. This requirement is fulfilled for many complexes with one hydrogen bond. For such complexes, this approach can be used to facilitate a detailed analysis of spectral changes associated with geometric changes in the hydrogen bond. For example, in hydrogen-bonded complexes of isocyanide C≡15N-1H⋯X, 1J(15N1H) depends exclusively on the N-H distance, while δ(15N) is also slightly influenced by the nature of X.
Project description:DL_FFLUX is a force field based on quantum chemical topology that can perform molecular dynamics for flexible molecules endowed with polarizable atomic multipole moments (up to hexadecapole). Using the machine learning method kriging (aka Gaussian process regression), DL_FFLUX has access to atomic properties (energy, charge, dipole moment, etc.) with quantum mechanical accuracy. Newly optimized and parallelized using domain decomposition Message Passing Interface (MPI), DL_FFLUX is now able to deliver this rigorous methodology at scale while still in reasonable time frames. DL_FFLUX is delivered as an add-on to the widely distributed molecular dynamics code DL_POLY 4.08. For the systems studied here (103-105 atoms), DL_FFLUX is shown to add minimal computational cost to the standard DL_POLY package. In fact, the optimization of the electrostatics in DL_FFLUX means that, when high-rank multipole moments are enabled, DL_FFLUX is up to 1.25× faster than standard DL_POLY. The parallel DL_FFLUX preserves the quality of the scaling of MPI implementation in standard DL_POLY. For the first time, it is feasible to use the full capability of DL_FFLUX to study systems that are large enough to be of real-world interest. For example, a fully flexible, high-rank polarized (up to and including quadrupole moments) 1 ns simulation of a system of 10 125 atoms (3375 water molecules) takes 30 h (wall time) on 18 cores.
Project description:Organophosphorus compounds are a wide and diverse class of chemicals playing a crucial role in living organisms. This aspect has been often investigated using nuclear magnetic resonance (NMR), which provides information about molecular structure and function. In this paper, we report the results of theoretical and experimental studies on basic organophosphorus compounds using zero-field NMR, where spin dynamics are investigated in the absence of a magnetic field with the dominant heteronuclear J-coupling. We demonstrate that the zero-field NMR enables distinguishing the chemicals owing to their unique electronic environment even though their spin systems have the same alphabetic designation. Such information can be obtained just in a single measurement, while amplitudes and widths of observed low-field NMR resonances enable the study of processes affecting spin dynamics. An excellent agreement between simulations and measurements of the spectra, particularly in the largest frequency J-couplings range ever reported in zero-field NMR, is demonstrated.
Project description:Nuclear magnetic resonance (NMR) relaxometry is an analytical method that provides information about molecular environments, even for NMR "silent" molecules (spin-0), by analyzing the properties of NMR signals versus the magnitude of the longitudinal field. Conventionally, this technique is performed at fields much higher than Earth's magnetic field, but our work focuses on NMR relaxometry at zero and ultra-low magnetic fields (ZULFs). Operating under such conditions allows us to investigate slow (bio)chemical processes occurring on a timescale from milliseconds to seconds, which coincide with spin evolution. ZULFs also minimize T2 line broadening in heterogeneous samples resulting from magnetic susceptibility. Here, we use ZULF NMR relaxometry to analyze (bio)chemical compounds containing 1H-13C, 1H-15N, and 1H-31P spin pairs. We also detected high-quality ULF NMR spectra of human whole-blood at 0.8 μT, despite a shortening of spin relaxation by blood proteomes (e.g., hemoglobin). Information on proton relaxation times of blood, a potential early biomarker of inflammation, can be acquired in under a minute using inexpensive, portable/small-size NMR spectrometers based on atomic magnetometers.
Project description:In the stationary, aligned samples used in oriented sample (OS) solid-state NMR, (1)H-(1)H homonuclear dipolar couplings are not attenuated as they are in magic angle spinning solid-state NMR; consequently, they are available for participation in dipolar coupling-based spin-exchange processes. Here we describe analytically the pathways of (15)N-(15)N spin-exchange mediated by (1)H-(1)H homonuclear dipolar couplings. The mixed-order proton-relay mechanism can be differentiated from the third spin assisted recoupling mechanism by setting the (1)H to an off-resonance frequency so that it is at the "magic angle" during the spin-exchange interval in the experiment, since the "magic angle" irradiation nearly quenches the former but only slightly attenuates the latter. Experimental spectra from a single crystal of N-acetyl leucine confirm that this proton-relay mechanism plays the dominant role in (15)N-(15)N dilute-spin-exchange in OS solid-state NMR in crystalline samples. Remarkably, the "forbidden" spin-exchange condition under "magic angle" irradiation results in (15)N-(15)N cross-peaks intensities that are comparable to those observed with on-resonance irradiation in applications to proteins. The mechanism of the proton relay in dilute-spin-exchange is crucial for the design of polarization transfer experiments.
Project description:Skyrmions, magnetic textures with topological stability, hold promises for high-density and energy-efficient information storage devices owing to their small size and low driving-current density. Precise creation of a single nanoscale skyrmion is a prerequisite to further understand the skyrmion physics and tailor skyrmion-based applications. Here, we demonstrate the creation of individual skyrmions at zero-field in an exchange-biased magnetic multilayer with exposure to soft X-rays. In particular, a single skyrmion with 100-nm size can be created at the desired position using a focused X-ray spot of sub-50-nm size. This single skyrmion creation is driven by the X-ray-induced modification of the antiferromagnetic order and the corresponding exchange bias. Furthermore, artificial skyrmion lattices with various arrangements can be patterned using X-ray. These results demonstrate the potential of accurate optical control of single skyrmion at sub-100 nm scale. We envision that X-ray could serve as a versatile tool for local manipulation of magnetic orders.
Project description:Exchange bias effect obtained after zero-field cooling from unmagnetized state usually exhibits a shift of hysteresis loop negative to the direction of the initial magnetic field, known as negative zero-field cooled exchange bias. Here, positive zero-field cooled exchange bias is reported in La0.5Sr0.5Mn0.8Co0.2O3 ceramics. In addition, a transition from positive to negative exchange bias has been observed with increasing initial magnetization field and measurement temperature. Based on a simple spin bidomain model with variable interface, two type of interfacial spin configuration formed during the initial magnetization process are proposed to interpret the observed phenomenon.