Quantum-mechanical simulations for in vivo MR spectroscopy: Principles and possibilities demonstrated with the program NMRScopeB.

Current possibilities and limitations of the simulation of in vivo magnetic resonance spectroscopic signals are demonstrated from the point of view of a simulation software user as well as its programmer. A brief review of the quantum-mechanical background addresses the specific needs of simulation implementation and in vivo MR spectroscopy in general. Practical application examples demonstrate how flexible simulation software, such as NMRScopeB, can be utilized not only for the preparation of metabolite basis signals for quantification of metabolite concentrations, but also in pulse sequence development, assessment of artifacts and analyzing mechanism leading to unexpected signal phenomena.

Renormalization of myoglobin-ligand binding energetics by quantum many-body effects.

We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory. This combination of methods explicitly accounts for dynamical and multireference quantum physics, such as valence and spin fluctuations, of the 3d electrons, while treating a significant proportion of the protein (more than 1,000 atoms) with DFT. The computed electronic structure of the myoglobin complexes and the nature of the Fe-O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long-standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of the many-body effects induced by the Hund's coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin.

Ecological spectroscopic methodologies for quantifying co-administered drugs in human plasma by photochemical quantum mechanical simulation.

Urinary tract infections (UTIs) constitute the second most prevalent bacterial infections in the elderly demographic. The treatment landscape involves various antibiotics targeting the causative organisms; nevertheless, the emergence of resistance significantly impacts therapeutic effectiveness. Presently, a fixed-dose pharmaceutical combination is advocated to optimize patient outcomes by mitigating the risks of bacterial resistance and associated side effects. Ofloxacin (OFL) and cefpodoxime proxetil (CPD) combinations, co-administered with flavoxate hydrochloride (FLV), have demonstrated efficacy in UTI cases, offering relief from concomitant symptoms. In the pharmaceutical market, fixed-dose combinations have gained prominence, driven by advantages such as enhanced patient medication adherence and compliance. In the realm of analytical chemistry, the integration of green practices in the initial phases of method development is exemplified by the Greenness by Design (GbD) strategy. While univariate spectroscopic methods are conventionally considered suboptimal compared to chemometric techniques for resolving intricate mixtures, GbD approach, when applied to UV spectroscopy, enable univariate methods to attain comparable or superior outcomes. GbD adopts a systematic approach to optimize experimental conditions, minimizing environmental impact and maximizing analytical performance. Critical to GbD applications in UV spectroscopy is solvent selection, influencing spectral resolution and measurement sensitivity. GbD employs a combination of in-vitro and in-silico experiments to evaluate solute-solvent interactions with underlying photochemical quantum phenomena affecting the resulting spectral morphology, identifying an optimal compromise solvent with high resolution and minimal ecological impact. Consequently, it facilitates the efficient resolution of spectral overlapping and determination of complex mixtures in UV spectroscopy using univariate methods. Comparative analysis with chemometric techniques, acknowledged as potent spectral resolving methods, demonstrated that GbD-based univariate methods performed equivalently. The methodology was validated according to ICH recommendations, establishing a linear quantitation range (2-30 µg/mL) and a limit of detection (0.355-0.414 µg/mL) for the three drugs in human plasma. The greenness of the developed methodology was affirmed through the AGREE assessment protocol, confirming its environmentally conscious attributes.

Computation in biological systems as a quantum mechanical simulation.

Our initial premise is that computation as we know it is formally derived from our bodies' internal processing, via our neural processors. Going backwards in time, our bodies' internal processing is in turn derived from wider Nature's own style of processing, which in turn is a rendition of the Universe's processing following the Big Bang. Computation is described as consisting of two intimately connected parts: comparative processing and conclusive processing. Our examination of post-Big Bang processing, biological processing, neural processing and human thinking supports our initial premise and the conclusion that computation is the motor for evolutionary emergence across the entire timescale of the Universe.

Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides.

We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C6H12O2S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (AuTS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of AuTS/linker/tau//Ga2O3/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation demonstrated a wider energy bandgap of the CT peptide, as compared to the TT peptide, which causes a reduction in its electron tunneling current. Our findings also revealed the critical role of phosphorylation in altering the charge transport characteristics of short peptides; more specifically, we found that the presence of phosphate groups can reduce the energy band gap in tau peptides and alter their electrical properties. Our results suggest that conformational and phosphorylation of short peptides (e.g., tau) can significantly change their charge transport characteristics and energy levels.

Role of electron spin dynamics and coupling network in designing dynamic nuclear polarization.

Dynamic nuclear polarization (DNP) has emerged as a powerful sensitivity booster of nuclear magnetic resonance (NMR) spectroscopy for the characterization of biological solids, catalysts and other functional materials, but is yet to reach its full potential. DNP transfers the high polarization of electron spins to nuclear spins using microwave irradiation as a perturbation. A major focus in DNP research is to improve its efficiency at conditions germane to solid-state NMR, at high magnetic fields and fast magic-angle spinning. In this review, we highlight three key strategies towards designing DNP experiments: time-domain "smart" microwave manipulation to optimize and/or modulate electron spin polarization, EPR detection under operational DNP conditions to decipher the underlying electron spin dynamics, and quantum mechanical simulations of coupled electron spins to gain microscopic insights into the DNP mechanism. These strategies are aimed at understanding and modeling the properties of the electron spin dynamics and coupling network. The outcome of these strategies is expected to be key to developing next-generation polarizing agents and DNP methods.

Unraveling the Ion Adsorption Kinetics in Microporous Carbon Electrodes: A Multiscale Quantum-Continuum Simulation and Experimental Approach.

Understanding sorption in porous carbon electrodes is crucial to many environmental and energy technologies, such as capacitive deionization (CDI), supercapacitor energy storage, and activated carbon filters. In each of these examples, a practical model that can describe ion electrosorption kinetics is highly desirable for accelerating material design. Here, we proposed a multiscale model to study the ion electrosorption kinetics in porous carbon electrodes by combining quantum mechanical simulations with continuum approaches. Our model integrates the Butler-Volmer (BV) equation for sorption kinetics and a continuously stirred tank reactor (CSTR) formulation with atomistic calculations of ion hydration and ion-pore interactions based on density functional theory (DFT). We validated our model experimentally by using ion mixtures in a flow-through electrode CDI device and developed an in-line UV absorption system to provide unprecedented resolution of individual ions in the separation process. We showed that the multiscale model captures unexpected experimental phenomena that cannot be explained by the traditional ion electrosorption theory. The proposed multiscale framework provides a viable approach for modeling separation processes in systems where pore sizes and ion hydration effects strongly influence the sorption kinetics, which can be leveraged to explore possible strategies for improving carbon-based and, more broadly, pore-based technologies.

The superexchange mechanism in crystalline compounds. The case of KMF3(M = Mn, Fe, Co, Ni) perovskites.

The ferromagnetic and antiferromagnetic wavefunctions of four KMF3(M = Mn, Fe, Co and Ni) perovskites have been obtained quantum-mechanically with the CRYSTAL code, by using the Hartree-Fock (HF) Hamiltonian and three flavours of DFT (PBE, B3LYP and PBE0) and anall-electronGaussian type basis set. In the Fe and Co cases, with d6and d7occupation, the Jahn-Teller distortion of the cubic cell is as large as 0.12 Å. Various features of the superexchange interaction energies (SIE), namely additivity, dependence on the M-M distance, on theMFM̂angle, and on the adopted functional, are explored. The contribution to SIE by the Coulomb, exchange and kinetic energy terms is analyzed. It is shown that, when using density functionals, SIE clearly correlates with the amount of exact (Hartree-Fock) exchange in the functional. The effect of SIE on the equilibrium geometry and volume of the unit cell is discussed, and it is shown that the key quantity is the spin polarization of the (closed shell) F ions along the M-F-M path. The effect of thismagneticpressureis evaluated quantitatively for the first time. The superexchange coupling constantJ, evaluated at the HF level and through the Ising model, underestimates the experimental values by about 60%-70%. The more sophisticated Yamaguchi model (that takes into account the contamination of the FM and AFM spin states) does not reduce the discrepancy. The B3LYP hybrid functional overestimates the experiments. These last are bracketed by HF and PBE0. For PBE, the overestimation is huge. Finally, Mulliken population data, charge and spin density maps and density of states are used to illustrate the electronic structure.