Revealing the Molecular Origin of Anisotropy around Chloride Ions in Bulk Water

A clear picture of the local solvation structure around halide anions in liquid water remains elusive. This discussion has been stimulated by pioneering simulation results that proposed a "hydrophobic cavity" around anions in the bulk, which is analogous to air at the air-water interface. However, there is also sound experimental and theoretical evidence that halide ions are rather symmetrically solvated in the bulk, leading to a different viewpoint. Using extensive ab initio molecular dynamics simulations of an aqueous Cl- solution, we indeed find an anisotropic arrangement of H-bonded versus interstitial water molecules. The latter are not H-bonded to the anions and thus do not couple much electronically to Cl-. The resulting purely electronic anisotropy of the local solvation environment correlates with that structural anisotropy, which however should not be understood as an empty cavity─as it would be at the air-water interface─but rather contains interstitial water molecules.

The accuracy limit of chemical shift predictions for species in aqueous solution

Interpreting NMR experiments benefits from first-principles predictions of chemical shifts. Reaching the accuracy limit of theory is relevant for unambiguous structural analysis and dissecting theoretical approximations. Since accurate chemical shift measurements are based on using internal reference compounds such as trimethylsilylpropanesulfonate (DSS), a detailed comparison of experimental with theoretical data requires simultaneous consideration of both target and reference species ensembles in the same solvent environment. Here we show that ab initio molecular dynamics simulations to generate liquid-state ensembles of target and reference compounds, including explicitly their short-range solvation environments and combined with quantum-mechanical solvation models, allows for predicting highly accurate 1H (∼0.1-0.5 ppm) and aliphatic 13C (∼1.5 ppm) chemical shifts for aqueous solutions of the model compounds trimethylamine N-oxide (TMAO) and N-methylacetamide (NMA), referenced to DSS without any system-specific adjustments. This encompasses the two peptide bond conformations of NMA identified by NMR. The results are used to derive a general-purpose guideline set for predictive NMR chemical shift calculations of NMA in the liquid state and to identify artifacts of force field models. Accurate predictions are only obtained if a sufficient number of explicit water molecules is included in the quantum-mechanical calculations, disproving a purely electrostatic model of the solvent effect on chemical shifts.

Anisotropic pressure effects on nanoconfined water within narrow graphene slit pores

There is an increasing interest toward disclosing and explaining confinement effects on liquids, such as water or aqueous solutions, in slit pore setups. Particularly puzzling are the changes of physical and chemical properties in the nanoconfinement regime where no bulk-like water phase exists between the two interfacial water layers such that the density profile across the slit pore becomes highly stratified, ultimately leading to bilayer and monolayer water. These changes must be quantified with respect to some meaningful reference state of water, the most natural one being bulk water at the same pressure and temperature conditions. However, bulk water is a homogeneous liquid with isotropic properties, whereas water confined in slit pores is inhomogeneous, implying anisotropic properties as described by the perpendicular and parallel components of the respective tensors. In the case of pressure, the inhomogeneous nature of the setup results in a well-defined difference between the perpendicular and parallel pressure tensor components that is uniquely determined by the interfacial tension being a thermodynamic property. For bilayer water constrained in graphene slit pores that are only about 1 nm wide, we demonstrate that there exists a thermodynamic point where the pressure tensor of the inhomogeneous fluid, nanoconfined water, is effectively isotopic and the pressure is thus scalar as in the homogeneous fluid, bulk water. This specific point of vanishing effective interfacial tension is proposed to serve as a well-defined reference state to compare the properties of nanoconfined liquids to those of the corresponding bulk liquid at the same (isotropic) pressure and temperature conditions. In future work, this idea could be applied to assess confinement effects on chemical reactivity in aqueous solutions as well as to other nanoconfined liquids in other pores such as layered minerals.

Quantum Nuclear Delocalization and its Rovibrational Fingerprints

Quantum mechanics dictates that nuclei must undergo some delocalization. In this work, emergence of quantum nuclear delocalization and its rovibrational fingerprints are discussed for the case of the van der Waals complexHHe 3 + ${{\rm{HHe}}_3^ + }$ . The equilibrium structure ofHHe 3 + ${{\rm{HHe}}_3^ + }$ is planar and T-shaped, one He atom solvating the quasi-linear He-H+ -He core. The dynamical structure ofHHe 3 + ${{\rm{HHe}}_3^ + }$ , in all of its bound states, is fundamentally different. As revealed by spatial distribution functions and nuclear densities, during the vibrations of the molecule the solvating He is not restricted to be in the plane defined by the instantaneously bentHHe 2 + ${{\rm{HHe}}_2^ + }$ chomophore, but freely orbits the central proton, forming a three-dimensional torus around theHHe 2 + ${{\rm{HHe}}_2^ + }$ chromophore. This quantum delocalization is observed for all vibrational states, the type of vibrational excitation being reflected in the topology of the nodal surfaces in the nuclear densities, showing, for example, that intramolecular bending involves excitation along the circumference of the torus.

Elucidating the Self-cleavage Dynamics of Hairpin Ribozyme by Mode-decomposed Infrared Spectroscopy

While catalytic reactions of biomolecular processes play an indispensable role in life, extracting the underlying molecular picture often remains challenging. Based on ab initio simulations of the self-cleavage reaction of hairpin ribozyme, mode-decomposed infrared spectra, and cosine similarity analysis to correlate the product with reactant IR spectra, we demonstrate a strategy to extract molecular details from characteristic spectral changes. Our results are in almost quantitative agreement with the experimental IR band library of nucleic acids and suggest that the spectral range of 800-1200 cm-1 is particularly valuable to monitor self-cleavage. Importantly, the cosine similarities also disclose that IR peaks subject to slight shifts due to self-cleavage might be unrelated, while strongly shifting resonances can correspond to the same structural dynamics. This framework of correlating complex IR spectra at the molecular level along biocatalytic reaction pathways is broadly applicable.

Dissecting the Molecular Origin of g-Tensor Heterogeneity and Strain in Nitroxide Radicals in Water: Electron Paramagnetic Resonance Experiment versus Theory

Nitroxides are common EPR sensors of microenvironmental properties such as polarity, numbers of H-bonds, pH, and so forth. Their solvation in an aqueous environment is facilitated by their high propensity to form H-bonds with the surrounding water molecules. Their g- and A-tensor elements are key parameters to extracting the properties of their microenvironment. In particular, the gxx value of nitroxides is rich in information. It is known to be characterized by discrete values representing nitroxide populations previously assigned to have different H-bonds with the surrounding waters. Additionally, there is a large g-strain, that is, a broadening of g-values associated with it, which is generally correlated with environmental and structural micro-heterogeneities. The g-strain is responsible for the frequency dependence of the apparent line width of the EPR spectra, which becomes evident at high field/frequency. Here, we address the molecular origin of the gxx heterogeneity and of the g-strain of a nitroxide moiety (HMI: 2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water. To treat the solvation effect on the g-strain, we combined a multi-frequency experimental approach with ab initio molecular dynamics simulations for structural sampling and quantum chemical EPR property calculations at the highest realistically affordable level, including an explicitly micro-solvated HMI ensemble and the embedded cluster reference interaction site model. We could clearly identify the distinct populations of the H-bonded nitroxides responsible for the gxx heterogeneity experimentally observed, and we dissected the role of the solvation shell, H-bond formation, and structural deformation of the nitroxide in the creation of the g-strain associated with each nitroxide subensemble. Two contributions to the g-strain were identified in this study. The first contribution depends on the number of hydrogen bonds formed between the nitroxide and the solvent because this has a large and well-understood effect on the gxx-shift. This contribution can only be resolved at high resonance frequencies, where it leads to distinct peaks in the gxx region. The second contribution arises from configurational fluctuations of the nitroxide that necessarily lead to g-shift heterogeneity. These contributions cannot be resolved experimentally as distinct resonances but add to the line broadening. They can be quantitatively analyzed by studying the apparent line width as a function of microwave frequency. Interestingly, both theory and experiment confirm that this contribution is independent of the number of H-bonds. Perhaps even more surprisingly, the theoretical analysis suggests that the configurational fluctuation broadening is not induced by the solvent but is inherently present even in the gas phase. Moreover, the calculations predict that this broadening decreases upon solvation of the nitroxide.

Structural Sampling and Solvation Models for the Simulation of Electronic Spectra: Pyrazine as a Case Study

The impact of sampling methods on spectral broadening in the gas phase and on the convergence of spectra in aqueous solution when using microsolvation, continuum solvation, and hybrid models is studied using pyrazine as a test case. For the sake of comparing classical Maxwell-Boltzmann and Wigner samplings in the gas phase, static and time-resolved X-ray absorption spectra after photoexcitation to the lowest ¹B_2u(ππ*) state, as well as the static UV-vis absorption spectrum, are considered. In addition, the UV-vis absorption spectrum of pyrazine in aqueous solution is also computed in order to systematically investigate its convergence with the number of explicitly included solvent shells with and without taking bulk solvation effects into account with the conductor-like screening model to represent implicit water beyond such explicit solute complexes. Concerning the static and time-resolved X-ray absorption spectra of pyrazine at the carbon K-edge as well as its UV-vis absorption spectrum in the gas phase, we find that these spectra obtained with Wigner and Maxwell-Boltzmann samplings substantially agree. For the UV-vis absorption spectrum in the aqueous solution, only the first two energetically low-lying bands converge quickly with the size of the explicitly included solvation shells, either with or without an additional continuum solvation taken into account. In stark contrast, calculations of the higher-lying excitations relying on finite microsolvated clusters without additional continuum solvation severely suffer from unphysical charge-transfer excitations into Rydberg-like orbitals at the cluster/vacuum interface. This finding indicates that computational UV-vis absorption spectra covering sufficiently high-lying states converge only if continuum solvation of the explicitly microsolvated solutes is included in the models.

Deciphering the Impact of Helium Tagging on Flexible Molecules: Probing Microsolvation Effects of Protonated Acetylene by Quantum Configurational Entropy

Helium, the lightest and most weakly interacting noble gas, is well-known for its unsurpassed chemical inertness. In many applications of helium in experimental techniques, such as tagging, messenger, or nanodroplet isolation action spectroscopy of molecules or complexes, it is assumed that the interaction of helium with the respective species, and thus the resulting interaction-induced perturbation, is small enough not to affect their structure and dynamics. Here, we probe the impact of one up to many attached helium atoms on protonated acetylene─an important nonclassical carbocation subject to three-center two-electron bonding in its ground state structure─using highly accurate interaction potentials in conjunction with entropy-based higher-order nonlinear correlation analysis. In particular, using neural network potentials at CCSD(T) accuracy, we disclose the specific structural perturbations due to the tagging of C₂H₃⁺ with up to 20 He atoms at a temperature of 1 K. Analysis reveals that microsolvation by helium influences the structure of C₂H₃⁺ noticeably, while our investigation of the quantum configurational information entropy additionally shows that correlations between individual orientational degrees of freedom are affected as a function of cluster size. In particular, it is found that the most probable bridge-like structure of the ro-vibrational quantum ground state of C₂H₃⁺, which is nonplanar and trans-bent in contrast to the perfectly planar equilibrium structure, becomes increasingly more localized upon adding helium atoms. The remarkably nonlinear behavior of the angular correlations as a function of cluster size is traced back to the buildup of the quantum microsolvation shell that enhances anisotropy up to N_He = 6 while more and more isotropic solvation takes over beyond six. Our approach is general and thus sets the stage to investigate the salient effects on the structure of flexible molecules due to tagging beyond the specific case.

Onset of Rotational Decoupling for a Molecular Ion Solvated in Helium: From Tags to Rings and Shells

Little is known about how rotating molecular ions interact with multiple ^{4}He atoms and how this relates to microscopic superfluidity. Here, we use infrared spectroscopy to investigate ^{4}He_{N}⋯H_{3}O^{+} complexes and find that H_{3}O^{+} undergoes dramatic changes in rotational behavior as ^{4}He atoms are added. We present evidence of clear rotational decoupling of the ion core from the surrounding helium for N>3, with sudden changes in rotational constants at N=6 and 12. In sharp contrast to studies on small neutral molecules microsolvated in helium, accompanying path integral simulations show that an incipient superfluid effect is not needed to account for these findings.

Deciphering the Properties of Nanoconfined Aqueous Solutions by Vibrational Sum Frequency Generation Spectroscopy

When confined between walls at nanometer distances, water exhibits surprisingly different properties with reference to bare interfacial water. Based on computer simulations, we demonstrate how vibrational sum frequency generation (VSFG) spectroscopy can be used-even with very mild symmetry breaking-to discriminate multilayer water in wide slit pores from both bilayer and monolayer water confined within molecularly narrow pores. Applying the technique, the VSFG lineshapes of monolayer, bilayer, and multilayer water are found to differ in characteristic ways, which is explained by their distinct density stratifications giving rise to different H-bonding patterns in the respective solvation layers.

Coupled Cluster Molecular Dynamics of Condensed Phase Systems Enabled by Machine Learning Potentials: Liquid Water Benchmark

Coupled cluster theory is a general and systematic electronic structure method, but in particular the highly accurate "gold standard" coupled cluster singles, doubles and perturbative triples, CCSD(T), can only be applied to small systems. To overcome this limitation, we introduce a framework to transfer CCSD(T) accuracy of finite molecular clusters to extended condensed phase systems using a high-dimensional neural network potential. This approach, which is automated, allows one to perform high-quality coupled cluster molecular dynamics, CCMD, as we demonstrate for liquid water including nuclear quantum effects. The machine learning strategy is very efficient, generic, can be systematically improved, and is applicable to a variety of complex systems.

State-resolved infrared spectrum of the protonated water dimer: revisiting the characteristic proton transfer doublet peak

The infrared (IR) spectra of protonated water clusters encode precise information on the dynamics and structure of the hydrated proton. However, the strong anharmonic coupling and quantum effects of these elusive species remain puzzling up to the present day. Here, we report unequivocal evidence that the interplay between the proton transfer and the water wagging motions in the protonated water dimer (Zundel ion) giving rise to the characteristic doublet peak is both more complex and more sensitive to subtle energetic changes than previously thought. In particular, hitherto overlooked low-intensity satellite peaks in the experimental spectrum are now unveiled and mechanistically assigned. Our findings rely on the comparison of IR spectra obtained using two highly accurate potential energy surfaces in conjunction with highly accurate state-resolved quantum simulations. We demonstrate that these high-accuracy simulations are important for providing definite assignments of the complex IR signals of fluxional molecules.

Infrared Spectra at Coupled Cluster Accuracy from Neural Network Representations

Infrared spectroscopy is key to elucidating molecular structures, monitoring reactions, and observing conformational changes, while providing information on both structural and dynamical properties. This makes the accurate prediction of infrared spectra based on first-principle theories a highly desirable pursuit. Molecular dynamics simulations have proven to be a particularly powerful approach for this task, albeit requiring the computation of energies, forces and dipole moments for a large number of molecular configurations as a function of time. This explains why highly accurate first-principles methods, such as coupled cluster theory, have so far been inapplicable for the prediction of fully anharmonic vibrational spectra of large systems at finite temperatures. Here, we push cutting-edge machine learning techniques forward by using neural network representations of energies, forces, and in particular dipoles to predict such infrared spectra fully at "gold standard" coupled cluster accuracy as demonstrated for protonated water clusters as large as the protonated water hexamer, in its extended Zundel configuration. Furthermore, we show that this methodology can be used beyond the scope of the data considered during the development of the neural network models, allowing for the computation of finite-temperature infrared spectra of large systems inaccessible to explicit coupled cluster calculations. This substantially expands the hitherto existing limits of accuracy, speed, and system size for theoretical spectroscopy and opens up a multitude of avenues for the prediction of vibrational spectra and the understanding of complex intra- and intermolecular couplings.

Neural network interaction potentials for para-hydrogen with flexible molecules

The study of molecular impurities in para-hydrogen ( pH2) clusters is key to push forward our understanding of intra- and intermolecular interactions, including their impact on the superfluid response of this bosonic quantum solvent. This includes tagging with only one or very few pH2, the microsolvation regime for intermediate particle numbers, and matrix isolation with many solvent molecules. However, the fundamental coupling between the bosonic pH2 environment and the (ro-)vibrational motion of molecular impurities remains poorly understood. Quantum simulations can, in principle, provide the necessary atomistic insight, but they require very accurate descriptions of the involved interactions. Here, we present a data-driven approach for the generation of impurity⋯ pH2 interaction potentials based on machine learning techniques, which retain the full flexibility of the dopant species. We employ the well-established adiabatic hindered rotor (AHR) averaging technique to include the impact of the nuclear spin statistics on the symmetry-allowed rotational quantum numbers of pH2. Embedding this averaging procedure within the high-dimensional neural network potential (NNP) framework enables the generation of highly accurate AHR-averaged NNPs at coupled cluster accuracy, namely, explicitly correlated coupled cluster single, double, and scaled perturbative triples, CCSD(T*)-F12a/aVTZcp, in an automated manner. We apply this methodology to the water and protonated water molecules as representative cases for quasi-rigid and highly flexible molecules, respectively, and obtain AHR-averaged NNPs that reliably describe the corresponding H2O⋯ pH2 and H3O+⋯ pH2 interactions. Using path integral simulations, we show for the hydronium cation, H3O+, that umbrella-like tunneling inversion has a strong impact on the first and second pH2 microsolvation shells. The automated and data-driven nature of our protocol opens the door to the study of bosonic pH2 quantum solvation for a wide range of embedded impurities.

Internal Electric Field-Induced Formation of Exotic Linear Acetonitrile Chains

The application of external electric and magnetic fields is a powerful tool for aligning molecules in a controlled way, if the thermal fluctuations are small. Here we demonstrate that the same holds for internal electric fields in a molecular cluster. The electric field of a single molecular dipole, HCl, is used to manipulate the aggregation mechanism of subsequently added acetonitrile molecules. As a result, we could form exotic linear acetonitrile (CH₃CN) chains at 0.37 K, as confirmed by infrared spectroscopy in superfluid helium nanodroplets. These linear chains are not observed in the absence of HCl and can be observed only when the internal electric field created by an HCl molecule is present. The accompanying simulations provide mechanistic insights into steric control, explain the selectivity of the process, and show that non-additive electronic polarization effects systematically enhance the dipole moment of these linear chains. Thus, adding more CH₃CN monomers even supports further quasi-linear chain growth.

Zwitter Ionization of Glycine at Outer Space Conditions due to Microhydration by Six Water Molecules

We investigate glycine microsolvation with water molecules, mimicking astrophysical conditions, in our laboratory by embedding these clusters in helium nanodroplets at 0.37 K. We recorded mass selective infrared spectra in the frequency range 1500-1800  cm^{-1} where two bands centered at 1630 and 1724  cm^{-1} were observed. By comparison with the extensive accompanying calculations, the band at 1630  cm^{-1} was assigned to the COO^{-} asymmetric stretching mode of the zwitter ion and the band at 1724  cm^{-1} was assigned to redshifted C=O stretch within neutral clusters. We show that zwitter ion formation of amino acids readily occurs with only few water molecules available even under extreme conditions.

Nanoconfinement Effects on Water in Narrow Graphene-based Slit Pores as Revealed by THz Spectroscopy

The properties of water at interfaces are known since long to differ from those of bulk water in many distinctive ways. More recently, specific confinement effects different from mere interfacial...

Competition between Coulomb and van der Waals Interactions in Xe-Cs^{+} Aggregates on Cu(111) Surfaces

Microscopic insight into interactions is a key for understanding the properties of heterogenous interfaces. We analyze local attraction in noncovalently bonded Xe-Cs^{+} aggregates and monolayers on Cu(111) as well as repulsion upon electron transfer. Using two-photon photoemission spectroscopy, scanning tunneling microscopy, and coupled cluster calculations combined with an image-charge model, we explain the intricate impact Xe has on Cs^{+}/Cu(111). We find that attraction between Cs^{+} and Xe counterbalances the screened Coulomb repulsion between Cs^{+} ions on Cu(111). Furthermore, we observe that the Cs 6s electron is repelled from Cu(111) due to xenon's electron density. Together, this yields a dual, i.e., attractive or repulsive, response of Xe depending on the positive or negative charge of the respective counterparticle, which emphasizes the importance of the Coulomb interaction in these systems.

A Joint Venture of Ab Initio Molecular Dynamics, Coupled Cluster Electronic Structure Methods, and Liquid-State Theory to Compute Accurate Isotropic Hyperfine Constants of Nitroxide Probes in Water

The isotropic hyperfine coupling constant (HFCC, Aiso) of a pH-sensitive spin probe in a solution, HMI (2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water, is computed using an ensemble of state-of-the-art computational techniques and is gauged against X-band continuous wave electron paramagnetic resonance (EPR) measurement spectra at room temperature. Fundamentally, the investigation aims to delineate the cutting edge of current first-principles-based calculations of EPR parameters in aqueous solutions based on using rigorous statistical mechanics combined with correlated electronic structure techniques. In particular, the impact of solvation is described by exploiting fully atomistic, RISM integral equation, and implicit solvation approaches as offered by ab initio molecular dynamics (AIMD) of the periodic bulk solution (using the spin-polarized revPBE0-D3 hybrid functional), embedded cluster reference interaction site model integral equation theory (EC-RISM), and polarizable continuum embedding (using CPCM) of microsolvated complexes, respectively. HFCCs are obtained from efficient coupled cluster calculations (using open-shell DLPNO-CCSD theory) as well as from hybrid density functional theory (using revPBE0-D3). Re-solvation of "vertically desolvated" spin probe configuration snapshots by EC-RISM embedding is shown to provide significantly improved results compared to CPCM since only the former captures the inherent structural heterogeneity of the solvent close to the spin probe. The average values of the Aiso parameter obtained based on configurational statistics using explicit water within AIMD and from EC-RISM solvation are found to be satisfactorily close. Using either such explicit or RISM solvation in conjunction with DLPNO-CCSD calculations of the HFCCs provides an average Aiso parameter for HMI in aqueous solution at 300 K and 1 bar that is in good agreement with the experimentally determined one. The developed computational strategy is general in the sense that it can be readily applied to other spin probes of similar molecular complexity, to aqueous solutions beyond ambient conditions, as well as to other solvents in the longer run.

Dielectric relaxation of water: assessing the impact of localized modes, translational diffusion, and collective dynamics

A multitude of distinct physical processes and molecular mechanisms have been introduced in the past in an effort to understand the unusual dielectric loss spectrum of water with its pronounced peak at roughly 20 GHz. Our computer simulations including ab initio molecular dynamics provide no evidence for a major impact of cage dynamics or local-diffusive motion on the lineshape below 200 GHz. We also show that the collective motion of hundreds of water molecules and/or their significant diffusive displacements are not required. Instead, the dielectric relaxation of water up to about 200 GHz can be quantitatively described in terms of two unimodal and smoothly decaying spectral contributions.

Confinement-Controlled Aqueous Chemistry within Nanometric Slit Pores

In this Focus Review, we put the spotlight on very recent insights into the fascinating world of wet chemistry in the realm offered by nanoconfinement of water in mechanically rather rigid and chemically inert planar slit pores wherein only monolayer and bilayer water lamellae can be hosted. We review the effect of confinement on different aspects such as hydrogen bonding, ion diffusion, and charge defect migration of H⁺(aq) and OH^-(aq) in nanoconfined water depending on slit pore width. A particular focus is put on the strongly modulated local dielectric properties as quantified in terms of anisotropic polarization fluctuations across such extremely confined water films and their putative effects on chemical reactions therein. The stunning findings disclosed only recently extend wet chemistry in particular and solvation science in general toward extreme molecular confinement conditions.

POS0472 COMPARATIVE METABOLOMIC ANALYSIS OF SERUM SAMPLES FROM PATIENTS WITH COINCIDENTAL RHEUMATOLOGICAL AND MALIGNANT DISEASES

Background:

Rheumatic and musculoskeletal diseases (RMDs) and malignancies are both caused by a dysfunctional immune system and the probability of their coincidence in one individual is rising due to advances in cancer treatment and demographic changes. However, the lack of understanding of the complex interrelationship of both conditions often leads to undertreatment and high level of suffering in affected patients. Herein, the MalheuR project breaks new ground by systematic analysis of concomitant malignant and rheumatic diseases and closes the knowledge gaps on the clinical and molecular level.

Objectives:

To enable early diagnosis of concomitant malignancy and/or identification of patients at risk in the future, changes in serum metabolome were explored in order to create a diagnostic classification model.

Methods:

Serum samples from patients with concomitant RMD and cancer or obligate precancerous lesions (n=78, breast cancer (23), melanoma (14), MGUS (12), prostate cancer (8) and others (21)) were collected as a pilot study within the MalheuR project, a registry-based study initiated in 2018 at the university hospital Heidelberg, Germany. The following groups were defined by the underlying RMD: rheumatoid arthritis (n=42), psoriasis arthritis (n=23), spondylarthritis (n=9) and systemic lupus erythematosus (n=4). RMD patients without any malignancies were used as controls (n=280: 122 RA, 81 PsA, 46 SpA, 31 SLE).

Samples were analyzed by 1H NMR spectroscopy. For all samples, regular 1H acquisition with presaturation and Carr-Purcell-Meiboom-Gill (CPMG) spectra were acquired using a 600 MHz Bruker NMR spectrometer. Spectra were processed with TopSpin using 0.2 Hz of line broadening and manual phasing. Molar concentrations of 26 metabolites were acquired by integration of NMR spectra. With GraphPad Prism, univariate and ANOVA statistical analysis was performed to find significant differences between each malignant group and their control group as well as between all four malignant groups.

Results:

Mean disease duration was 11.8 ±10.5 years for cancer and 12.8±10.8 years for RMDs since diagnosis. 1.4% received cancer treatment (6.4% of malignancy group), 69.3% csDMARDs, 42.3% b/tsDMARDs and 46.4% glucocorticoids at the time of sample collection.

Most metabolites tested were significantly lower in the malignancy groups versus associated controls: Concentrations of amino acids V and L were significantly reduced in all malignancy samples. Additionally, T, D, N, Q, E, A, I were altered in RA, SpA and PsA, changes in G were seen in RA, PsA and SLE and P was altered in RA and PsA only. Furthermore, lower concentrations of short chain fatty acids and tricarboxylic acid cycle intermediates were present in the malignancy groups. In no case was a metabolite concentration significantly higher in the malignancy group than in the associated control. When comparing the metabolome within the four malignancy groups, only the concentrations of creatine, threonine and isoleucine were found higher in RA patients with malignancy.

Conclusion:

Significant differences between the metabolomic fingerprints of RMD patients with and without malignancies could be observed. These changes might be characteristic for cancer burden, as in most cases the underlying RMD was not relevant when comparing the concentrations between the malignancy groups. Our results may promote understanding of the interrelationships of both disease entities as well as prove useful as biomarkers for diagnostic and therapeutic purposes.

Acknowledgements:

Grant/research support from medical faculty (Olympia Morata Programme) and foundations commission (Herbert Daus estate) of University of Heidelberg

Disclosure of Interests:

None declared

Aqueous TMAO solution under high hydrostatic pressure

Trimethylamine N-oxide (TMAO) is a well known osmolyte in nature, which is used by deep sea fish to stabilize proteins against High Hydrostatic Pressure (HHP). We present a combined ab initio molecular dynamics, force field molecular dynamics, and THz absorption study of TMAO in water up to 12 kbar to decipher its solvation properties upon extreme compression. On the hydrophilic oxygen side of TMAO, AIMD simulations at 1 bar and 10 kbar predict a change of the coordination number from a dominating TMAO·(H₂O)₃ complex at ambient conditions towards an increased population of a TMAO·(H₂O)₄ complex at HHP conditions. This increase of the TMAO-oxygen coordination number goes in line with a weakening of the local hydrogen bond network, spectroscopic shifts and intensity changes of the corresponding intermolecular THz bands. Using a pressure-dependent HHP force field, FFMD simulations predict a significant increase of hydrophobic hydration from 1 bar up to 4-5 kbar, which levels off at higher pressures up to 10 kbar. THz spectroscopic data reveal two important pressure regimes with spectroscopic inflection points of the dominant intermolecular modes: The first regime (1.5-2 kbar) is barely recognizable in the simulation data. However, it relates well with the observation that the apparent molar volume of solvated TMAO is nearly constant in the biologically relevant pressure range up to 1 kbar as found in the deepest habitats on Earth in the ocean. The second inflection point around 4-5 kbar is related to the amount of hydrophobic hydration as predicted by the FFMD simulations. In particular, the blueshift of the intramolecular CNC bending mode of TMAO at about 390 cm^-1 is the spectroscopic signature of increasingly pronounced pressure-induced changes in the solvation shell of TMAO. Thus, the CNC bend can serve as local pressure sensor in the multi-kbar pressure regime.

Unveiling Zwitterionization of Glycine in the Microhydration Limit

Charge separation under solvation stress conditions is a fundamental process that comes in many forms in doped water clusters. Yet, the mechanism of intramolecular charge separation, where constraints due to the molecular structure might be intricately tied to restricted solvation structures, remains largely unexplored. Microhydrated amino acids are such paradigmatic molecules. Ab initio simulations are carried out at 300 K in the frameworks of metadynamics sampling and thermodynamic integration to map the thermal mechanisms of zwitterionization using Gly(H₂O) _n with n = 4 and 10. In both cases, a similar water-mediated proton transfer chain mechanism is observed; yet, detailed analyses of thermodynamics and kinetics demonstrate that the charge-separated zwitterion is the preferred species only for n = 10 mainly due to kinetic stabilization. Structural analyses disclose that bifurcated H-bonded water bridges, connecting the cationic and anionic sites in the fluctuating microhydration network at room temperature, are enhanced in the transition-state ensemble exclusively for n = 10 and become overwhelmingly abundant in the stable zwitterion. The findings offer potential insights into charge separation under solvation stress conditions beyond the present example.

Probing Local Electrostatics of Glycine in Aqueous Solution by THz Spectroscopy

Based upon precise terahertz (THz) measurements of the solvated amino acid glycine and accompanying ab-initio molecular-dynamics simulations, we show that the N-C-C-O open/close mode at 315 cm-1 serves as a sensitive, label-free probe for the local protonation of the amide group. Experimentally, we can show that this holds not only for glycine but also for diglycine and valine. The approach is more general, since the changes due to protonation result in intensity changes which can be probed by THz time domain (0-50 cm-1 ) as well as by precise THz-FT spectroscopy (50-400 cm-1 ). A detailed analysis allows us to directly correlate the titration spectra with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of a natural amino acid in water in a label-free manner.

Experimental demonstration of novel beam characterization using a polarizable X-band transverse deflection structure

The PolariX TDS (Polarizable X-Band Transverse Deflection Structure) is an innovative TDS-design operating in the X-band frequency-range. The design gives full control of the streaking plane, which can be tuned in order to characterize the projections of the beam distribution onto arbitrary transverse axes. This novel feature opens up new opportunities for detailed characterization of the electron beam. In this paper we present first measurements of the Polarix TDS at the FLASHForward beamline at DESY, including three-dimensional reconstruction of the charge-density distribution of the bunch and slice emittance measurements in both transverse directions. The experimental results open the path toward novel and more extensive beam characterization in the direction of multi-dimensional-beam-phase-space reconstruction.

Improving the Yield and Rate of Acid-Catalyzed Deconstruction of Lignin by Mechanochemical Activation

Lignin is a potential biomass feedstock from plant material, but it is particularly difficult to economically process. Inspired by recent ball-milling results, state-of-the-art quantum mechanochemistry calculations have been performed to isolate and probe the purely mechanochemical stretching effect alone upon acid-catalyzed deconstruction of lignin. Effects upon cleavage of several exemplary simple ethers are examined first, and with low stretching force they all are predicted to cleave substantially faster, allowing for use of milder acids and lower temperatures. Effects upon an experimentally known lignin fragment model (containing the ubiquitous β-O-4 linkage) are next examined; this first required a mechanism refinement (3-step indirect cleavage, 1-step side reaction) and identification of the rate-limiting step under zero-force (thermal) conditions. Mechanochemical activation using very low stretching forces improves at first only yield, by fully shutting off the ring-closure side reaction. At only somewhat larger forces, in stark contrast, a switch in mechanism is found to occur, from 3-step indirect cleavage to the direct cleavage mechanism of simple ethers, finally strongly enhancing the cleavage rate of lignin. It is concluded that mechanochemical activation of the common β-O-4 link in lignin would improve the rate of its acidolysis via a mechanism switch past a low force threshold. Relevance to ball-milling experiments is discussed.

On the Adaptability of the Chemical Reaction of Hairpin Ribozyme to High Pressures

The discovery of RNA enzymes, ribozymes, provided strong support to the RNA world hypothesis suggesting that early life evolved from RNAs able to both store genetic information and catalyze biochemical reactions. Moreover, evidence is accumulating that primitive life might have emerged in deep-sea environments and, thus, at high hydrostatic pressures. If true, ribozymes should be able to function under those pressures. In this work, we ask if and possibly how ribozymes could function at high pressures. To this end, we specifically focus on the chemical reaction steps of the self-cleavage catalysis of hairpin ribozyme by employing extensive QM/MM metadynamics simulations. We find that the reaction scenario at high pressures is vastly different than that at ambient conditions, yet the rate-limiting reaction barrier and, thus, the reaction rate are only marginally affected. Therefore, the results indeed suggest that ribozymes would function at high pressures but by following a vastly different reaction scenario.

Supercritical Water is not Hydrogen Bonded

Thinking about water is inextricably linked to hydrogen bonds, which are highly directional in character and determine the unique structure of water, in particular its tetrahedral H-bond network. Here, we assess if this common connotation also holds for supercritical water. We employ extensive ab initio molecular dynamics simulations to systematically monitor the evolution of the H-bond network mode of water from room temperature, where it is the hallmark of its fluctuating three-dimensional network structure, to supercritical conditions. Our simulations reveal that the oscillation period required for H-bond vibrations to occur exceeds the lifetime of H-bonds in supercritical water by far. Instead, the corresponding low-frequency intermolecular vibrations of water pairs as seen in supercritical water are found to be well represented by isotropic van-der-Waals interactions only. Based on these findings, we conclude that water in its supercritical phase is not a H-bonded fluid.

Generating Excess Protons in Microsolvated Acid Clusters under Ambient Conditions: An Issue of Configurational Entropy versus Internal Energy

Acid dissociation, and thus liberation of excess protons in small water droplets, impacts on diverse fields such as interstellar, atmospheric or environmental chemistry. At cryogenic temperatures below 1 K, it is now well established that as few as four water molecules suffice to dissociate the generic strong acid HCl, yet temperature-driven recombination sets in simply upon heating that cluster. Here, the fundamental question is posed of how many more water molecules are required to stabilize a hydrated excess proton at room temperature. Ab initio path integral simulations disclose that not five, but six water molecules are needed at 300 K to allow for HCl dissociation independently from nuclear quantum effects. In order to provide the molecular underpinnings of these observations, the classical and quantum free energy profiles were decomposed along the dissociation coordinate in terms of the corresponding internal energy and entropy profiles. What decides in the end about acid dissociation, and thus ion pair formation, in a specific microsolvated water cluster at room temperature is found to be a fierce competition between classical configurational entropy and internal energy, where the former stabilizes the undissociated state whereas the latter favors dissociation. It is expected that these are generic findings with broad implications on acid-base chemistry depending on temperature in small water assemblies.

How Can Protons Migrate in Extremely Compressed Liquid Water?

Compression of liquid water up to multi-kbar pressures is known to perturb dramatically its local structure required for charge defects to migrate as topological defects in the hydrogen-bonded network. Our ab initio simulations show that the migration of excess protons is not much affected at 10 kbar, whereas that of proton holes is significantly reduced. Non-Markovian analyses show that this is not due to modifying the free energy barriers of both charge transfer and migration. It is rather pressure-induced modifications of the population of activated states, depending on interstitial water, which rules charge migration at extreme compression.

Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme

Hairpin ribozyme catalyzes the reversible self-cleavage of phosphodiester bonds which plays prominent roles in key biological processes involving RNAs. Despite impressive advances on ribozymatic self-cleavage, critical aspects of its molecular reaction mechanism remain controversially debated. Here, we generate and analyze the multidimensional free energy landscape that underlies the reaction using extensive QM/MM metadynamics simulations to investigate in detail the full self-cleavage mechanism. This allows us to answer several pertinent yet controversial questions concerning activation of the 2'-OH group, the mechanistic role of water molecules present in the active site, and the full reaction pathway including the structures of transition states and intermediates. Importantly, we find that a sufficiently unrestricted reaction subspace must be mapped using accelerated sampling methods in order to compute the underlying free energy landscape. It is shown that lower-dimensional sampling where the bond formation and cleavage steps are coupled does not allow the system to sufficiently explore the landscape. On the basis of a three-dimensional free energy surface spanned by flexible generalized coordinates, we find that 2'-OH is indirectly activated by adjacent G8 nucleobase in conjunction with stabilizing H-bonding involving water. This allows the proton of the 2'-OH group to directly migrate toward the 5'-leaving group via a nonbridging oxygen of the phosphodiester link. At variance with similar enzymatic processes where water wires connected to protonable side chains of the protein matrix act as transient proton shuttles, no such de/reprotonation events of water molecules are found to be involved in this ribozymatic transesterification. Overall, our results support an acid-catalyzed reaction mechanism where A38 nucleobase directly acts as an acid whereas G8, in stark contrast, participates only indirectly via stabilizing the nascent nucleophile for subsequent attack. Moreover, we conclude that self-cleavage of hairpin ribozyme follows an A_N + D_N two-step associative pathway where the rate-determining step is the cleavage of the phosphodiester bond. These results provide a major advancement in our understanding of the unique catalytic mechanism of hairpin ribozyme which will fruitfully impact on the design of synthetic ribozymes.

Assessing the properties of supercritical water in terms of structural dynamics and electronic polarization effects

Evolution of water's structural dynamics from ambient liquid to supercritical dense liquid-like and dilute gas-like conditions.

Quantifying anisotropic dielectric response properties of nanoconfined water within graphene slit pores

Water presents puzzling properties once it gets confined, in particular its dielectric response becomes highly anisotropic. Here, we analyze the dielectric response of water within graphene slit pores based on molecular dynamics simulations.

Mechanochemical disulfide reduction reveals imprints of noncovalent sulfur⋯oxygen chalcogen bonds in protein-inspired mimics in aqueous solution

Chalcogen bonds in proteins are found to impact on the mechanochemical reduction of disulfide bridges in aqueous environments.

Quantum Microsolvation of Protonated Methane with ^{4}He: Large-Amplitude Motion Heavily Influences Bosonic Exchange

Quantum simulations of small CH_{5}^{+}·^{4}He_{n} complexes disclose significant and antagonistic impact of small-amplitude local vibrational motion vs large-amplitude global fluxional motion within the CH_{5}^{+} impurity on helium in real and permutation space. While the former significantly enhances bosonic exchange in the surrounding ^{4}He microsolvation shell compared to the rigid-body reference, the latter greatly suppresses long permutation cycles, which is traced back to the different nature of these quantum fluctuations. Therefore, it is expected that the resulting impact on local superfluidity is generic for fluctuating impurities in bosonic environments.