On the importance of nuclear quantum motions in near edge x-ray absorption fine structure spectroscopy of molecules

Routine Molecular Dynamics Simulations Including Nuclear Quantum Effects: From Force Fields to Machine Learning Potentials

We report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP, exploits two simulation strategies: the Ring-Polymer Molecular Dynamics (RPMD) that provides exact structural properties at the cost of a MD simulation in an extended space of multiple replicas and the adaptive Quantum Thermal Bath (adQTB) that imposes the quantum distribution of energy on a classical system via a generalized Langevin thermostat and provides computationally affordable and accurate (though approximate) NQEs. We discuss some implementation details, efficient numerical schemes, and parallelization strategies and quickly review the GPU acceleration of our code. Our implementation allows an efficient inclusion of NQEs in MD simulations for very large systems, as demonstrated by scaling tests on water boxes with more than 200,000 atoms (simulated using the AMOEBA polarizable force field). We test the compatibility of the approach with Tinker-HP's recently introduced Deep-HP machine learning potentials module by computing water properties using the DeePMD potential with adQTB thermostatting. Finally, we show that the platform is also compatible with the alchemical free energy estimation capabilities of Tinker-HP and fast enough to perform simulations. Therefore, we study how NQEs affect the hydration free energy of small molecules solvated with the recently developed Q-AMOEBA water force field. Overall, the Quantum-HP platform allows users to perform routine quantum MD simulations of large condensed-phase systems and will help to shed new light on the quantum nature of important interactions in biological matter.

Temperature dependence of X-ray absorption and nuclear magnetic resonance spectra: probing quantum vibrations of light elements in oxides

Probing the quantum thermal fluctuations of nuclei in light-element oxides using XANES and NMR spectroscopies.

Quasiparticle Lifetime Broadening in Resonant X-ray Scattering of NH4NO3

It has been previously shown that two effects cause dramatic changes in the x-ray absorption and emission spectra from the N K edge of the insulating crystal ammonium nitrate. First, vibrational disorder causes major changes in the absorption spectrum, originating not only from the thermal population of phonons, but, significantly, from zero-point motion as well. Second, the anomalously large broadening (~ 4 eV) of the emission originating from nitrate σ states is due to unusually short lifetimes of quasiparticles in an otherwise extremely narrow band. In this work we investigate the coupling of these effects to core and valence excitons that are created as the initial x-ray excitation energy is progressively reduced toward the N edge. Using a GW/Bethe-Salpeter approach, we show the extent to which this anomalous broadening is captured by the GW approximation. The data and calculations demonstrate the importance that the complex self-energies (finite lifetimes) of valence bands have on the interpretation of emission spectra. We produce a scheme to explain why extreme lifetimes should appear in σ states of other similar compounds.

X-ray and Electron Spectroscopy of Water

Here we present an overview of recent developments of X-ray and electron spectroscopy to probe water at different temperatures. Photon-induced ionization followed by detection of electrons from either the O 1s level or the valence band is the basis of photoelectron spectroscopy. Excitation between the O 1s and the unoccupied states or occupied states is utilized in X-ray absorption and X-ray emission spectroscopies. These techniques probe the electronic structure of the liquid phase and show sensitivity to the local hydrogen-bonding structure. Both experimental aspects related to the measurements and theoretical simulations to assist in the interpretation are discussed in detail. Different model systems are presented such as the different bulk phases of ice and various adsorbed monolayer structures on metal surfaces.

Unified theory of electron-phonon renormalization and phonon-assisted optical absorption

We present a theory of electronic excitation energies and optical absorption spectra which incorporates energy-level renormalization and phonon-assisted optical absorption within a unified framework. Using time-independent perturbation theory we show how the standard approaches for studying vibronic effects in molecules and those for addressing electron-phonon interactions in solids correspond to slightly different choices for the non-interacting Hamiltonian. Our present approach naturally leads to the Allen-Heine theory of temperature-dependent energy levels, the Franck-Condon principle, the Herzberg-Teller effect and to phonon-assisted optical absorption in indirect band gap materials. In addition, our theory predicts sub-gap phonon-assisted optical absorption in direct gap materials, as well as an exponential edge which we tentatively assign to the Urbach tail. We also consider a semiclassical approach to the calculation of optical absorption spectra which simultaneously captures energy-level renormalization and phonon-assisted transitions and is especially suited to first-principles electronic structure calculations. We demonstrate this approach by calculating the phonon-assisted optical absorption spectrum of bulk silicon.

X-Ray absorption spectroscopy of LiBF4 in propylene carbonate: a model lithium ion battery electrolyte

X-ray absorption spectra, interpreted using first-principles electronic structure calculations, provide insight into the solvation of the lithium ion in propylene carbonate.

Quantum simulation of thermally-driven phase transition and oxygen K-edge x-ray absorption of high-pressure ice

The structure and phase transition of high-pressure ice are of long-standing interest and challenge, and there is still a huge gap between theoretical and experimental understanding. The quantum nature of protons such as delocalization, quantum tunneling and zero-point motion is crucial to the comprehension of the properties of high-pressure ice. Here we investigated the temperature-induced phase transition and oxygen K-edge x-ray absorption spectra of ice VII, VIII and X using ab initio path-integral molecular dynamics simulations. The tremendous difference between experiments and the previous theoretical predictions is closed for the phase diagram of ice below 300 K at pressures up to 110 GPa. Proton tunneling assists the proton-ordered ice VIII to transform into proton-disordered ice VII where only thermal activated proton-transfer cannot occur. The oxygen K edge with its shift is sensitive to the order-disorder transition, and therefore can be applied to diagnose the dynamics of ice structures.

Importance of electronic relaxation for inter-coulombic decay in aqueous systems

Inspired by recent photoelectron spectroscopy experiments on hydroxide solutions, we have examined the conditions necessary for enhanced (and, in the case of solutions, detectable) inter-Coulombic decay (ICD)--Auger emission from an atomic site other than that originally excited. We present general guidelines, based on energetic and spatial overlap of molecular orbitals, for this enhancement of inter-Coulombic decay-based energy transfer in solutions. These guidelines indicate that this decay process should be exhibited by broad classes of biomolecules and suggest a design criterion for targeted radiooncology protocols. Our findings show that photoelectron spectroscopy cannot resolve the current hydroxide coordination controversy.

Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

Nitrogen K-edge spectra of aqueous triglycine were measured using liquid microjets, and the effects of Hofmeister-active salts on the spectra were observed. Spectra simulated using density functional theory, sampled from room temperature classical molecular dynamics trajectories, capture all major features in the measured spectra. The spectrum of triglycine in water is quite similar to that in the presence of chaotropic sodium bromide (and other halides), which raises the solubility of proteins. However, a new feature is found when kosmotropic Na(2)SO(3), which lowers solubility, is present; this feature results from excitations of the nitrogen atom in the terminal amino group of triglycine. Both direct interactions between this salt and the protonated amino terminus, as well as corresponding changes in the conformational dynamics of the system, contribute to this new feature. These molecular measurements support a different mechanism for the Hofmeister effect than has previously been suggested based on thermodynamic measurements. It is also shown that near edge X-ray absorption fine structure (NEXAFS) is sensitive to strong direct interaction between certain salts and charged peptides. However, by investigating the sensitivity of NEXAFS to the extreme structural differences between model beta-sheets and alpha-helices, we conclude that this technique is relatively insensitive to secondary structure of peptides and proteins.

Monopeptide versus monopeptoid: insights on structure and hydration of aqueous alanine and sarcosine via X-ray absorption spectroscopy

Despite the obvious significance, the aqueous interactions of peptides remain incompletely understood. Their synthetic analogues called peptoids (poly-N-substituted glycines) have recently emerged as a promising biomimetic material, particularly due to their robust secondary structure and resistance to denaturation. We describe comparative near-edge X-ray absorption fine structure spectroscopy studies of aqueous sarcosine, the simplest peptoid, and alanine, its peptide isomer, interpreted by density functional theory calculations. The sarcosine nitrogen K-edge spectrum is blue shifted with respect to that of alanine, in agreement with our calculations; we conclude that this shift results primarily from the methyl group substitution on the nitrogen of sarcosine. Our calculations indicate that the nitrogen K-edge spectrum of alanine differs significantly between dehydrated and hydrated scenarios, while that of the sarcosine zwitterion is less affected by hydration. In contrast, the computed sarcosine spectrum is greatly impacted by conformational variations, while the alanine spectrum is not. This relates to a predicted solvent dependence for alanine, as compared to sarcosine. Additionally, we show the theoretical nitrogen K-edge spectra to be sensitive to the degree of hydration, indicating that experimental X-ray spectroscopy may be able to distinguish between bulk and partial hydration, such as found in confined environments near proteins and in reverse micelles.