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arXiv2018

Binary Mixtures of Novel Sulfoxides and Water: Intermolecular Structure, Dynamic Properties, Thermodynamics, and Cluster Analysis

Senior dialkyl sulfoxides constitute interest in the context of biomedical sciences due to their abilities to penetrate phospholipid bilayers, dissolve drugs, and serve as cryoprotectants. Intermolecular interactions with water, a paramount component of the living cell, determine performance the sulfoxide-based artificial systems in their prospective applications. Herein, we simulated a wide composition range of the sulfoxide/water mixtures, up to 85 w/w% sulfoxide using classical molecular dynamics to determine structure, dynamics, and thermodynamics as a function of the mixture composition. As found, both diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) are strongly miscible with water. DESO and EMSO based aqueous mixtures exhibit similar structure and thermodynamic properties, however, quite different dynamic properties over an entire range of compositions. Strong deviations from an ideal mixture between 30 50 mol% of sulfoxide content leads to relatively high shear viscosities of the mixtures. Free energy of mixing with water is only slightly more favorable for EMSO than for DESO. The results, for the first time, quantify high miscibilities of both sulfoxides with water and motivate comprehensive in vivo investigation of the proposed mixtures.

cond-mat.soft↗

arXiv2018

Multi-scale theoretical approach to X-ray absorption spectra in disordered systems: an application to the study of Zn(II) in water

We develop a multi-scale theoretical approach aimed at calculating from first principles X-ray absorption spectra of liquid solutions and disordered systems. We test the method by considering the paradigmatic case of Zn(II) in water which, besides being relevant in itself, is also of interest for biology. With the help of classical molecular dynamics simulations we start by producing bunches of configurations differing for the Zn(II)-water coordination mode. Different coordination modes are obtained by making use of the so-called dummy atoms method. From the collected molecular dynamics trajectories, snapshots of a more manageable subsystem encompassing the metal site and two solvation layers are cut out. Density functional theory is used to optimize and relax these reduced system configurations employing a uniform dielectric to mimic the surrounding bulk liquid water. On the resulting structures, fully quantum mechanical X-ray absorption spectra calculations are performed by including core-hole effects and core-level shifts. The proposed approach does not rely on any guessing or fitting of the force field or of the atomic positions of the system. The comparison of the theoretically computed spectrum with the experimental Zn K-edge XANES data unambiguously demonstrates that among the different a priori possible geometries, Zn(II) in water lives in an octahedral coordination mode.

cond-mat.soft↗

arXiv2018

The low temperature D$^+$ + H$_2$ $\rightarrow$ HD + H$^+$ reaction rate coefficient: a ring polymer molecular dynamics and quasi-classical trajectory study

The reaction between D$^+$ and H$_2$ plays an important role in astrochemistry at low temperatures and also serves as a prototype for simple ion-molecule reaction. Its ground $\tilde{X}~^1A^{\prime}$ state has a very small thermodynamic barrier (up to 1.8$\times 10^{-2}$ eV) and the reaction proceeds through the formation of an intermediate complex lying within the potential well of depth of at least 0.2 eV thus representing a challenge for dynamical studies. In the present work, we analyze the title reaction within the temperature range of 20 $-$ 100 K by means of ring polymer molecular dynamics (RPMD) and quasi-classical trajectory (QCT) methods over the full-dimensional global potential energy surface developed by Aguado et al. [A. Aguado, O. Roncero, C. Tablero, C. Sanz, and M. Paniagua, J. Chem. Phys., 2000, 112, 1240]. The computed thermal RPMD and QCT rate coefficients are found to be almost independent of temperature and fall within the range of 1.34 $-$ 2.01$\times$10$^{-9}$ cm$^3$ s$^{-1}$. They are also in a very good agreement with the previous time-independent quantum mechanical and statistical quantum method calculations. Furthermore, we observe that the choice of asymptotic separation distance between the reactants can markedly alter the rate coefficient in the low temperature regime (20 $-$ 50 K). Therefore it is of utmost importance to correctly assign the value of this parameter for dynamical studies, particularly at very low temperatures of astrochemical importance. We finally conclude that experimental rate measurements for the title reaction are highly desirable in future.

physics.chem-ph↗

arXiv2018

Automated Calculation of Thermal Rate Coefficients using Ring Polymer Molecular Dynamics and Machine-Learning Interatomic Potentials with Active Learning

We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials actively learning on-the-fly. Based on the original computational procedure implemented in the RPMDrate code, our methodology gradually and automatically constructs the potential energy surfaces (PESs) from scratch with the data set points being selected and accumulated during the RPMDrate simulation. Such an approach ensures that our final machine-learning model provides reliable description of the PES which avoids artifacts during exploration of the phase space by RPMD trajectories. We tested our methodology on two representative thermally activated chemical reactions studied recently by RPMDrate at temperatures within the interval of 300--1000~K. The corresponding PESs were generated by fitting to only a few thousands automatically generated structures (less than 5000) while the RPMD rate coefficients retained the deviation from the reference values within the typical convergence error of RPMDrate. In future, we plan to apply our methodology to chemical reactions which proceed via complex-formation thus providing a completely general tool for calculating RPMD thermal rate coefficients for any polyatomic gas phase chemical reaction.

physics.chem-ph↗

arXiv2018

Excited-State Solvation Structure of Transition Metal Complexes from Molecular Dynamics Simulations and Assessment of Partial Atomic Charge Methods

In this work, we investigate the excited-state solute and solvation structure of $\mathrm{[Ru(bpy)_3]^{2+}}$, $\mathrm{[Fe(bpy)_3]^{2+}}$, $\mathrm{[Fe(bmip)_2]^{2+}}$ and $\mathrm{[Cu(phen)_2]^{+}}$ (bpy=2,2'-pyridine; bmip=2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine; phen=1,10-phenanthroline) transition metal complexes (TMCs) in terms of solute-solvent radial distribution functions (RDFs) and evaluate the performance of some of the most popular partial atomic charge (PAC) methods for obtaining these RDFs by molecular dynamics (MD) simulations. To this end, we compare classical MD of a frozen solute in water and acetonitrile (ACN) with quantum mechanics/molecular mechanics Born-Oppenheimer molecular dynamics (QM/MM BOMD) simulations. The calculated RDFs show that the choice of a suitable PAC method is dependent on the coordination number of the metal, denticity of the ligands, and type of solvent. It is found that this selection is less sensitive for water than ACN. Furthermore, a careful choice of the PAC method should be considered for TMCs that exhibit a free direct coordination site, such as $\mathrm{[Cu(phen)_2]^{+}}$. The results of this work show that fast classical MD simulations with ChelpG/RESP or CM5 PACs can produce RDFs close to those obtained by QM/MM MD and thus, provide reliable solvation structures of TMCs to be used, e.g. in the analysis of scattering data.

physics.chem-ph↗

arXiv2018

Modelling Strategies for the Covalent Functionalization of 2D Phosphorene

The paper is an excursus on potential acid-base adducts formed by an unsaturated main group or transition metal species and P atoms of phosphorene (P n ), which derives from the black phosphorus exfoliation. Various possibilities of attaining a realistic covalent functionalization of the 2D material have been examined via DFT solid state calculations. The distribution of neighbor P atoms at one side of the sheet and the reciprocal directionalities of their lone pairs must be clearly understood to foreshadow the best possible acceptor reactants. Amongst the latter, the main group BH3 or I2 species have been examined for their intrinsic acidity, which favors the periodic mono-hapto anchoring at Pn atoms. The corresponding adducts are systematically compared with other molecular P donors from a phosphine to white phosphorus, P4. Significant variations emerge from the comparison of the band gaps in the adducts and the naked phosphorene with a possible electronic interpretation being offered. Then, the Pn covalent functionalization has been analyzed in relation to unsaturated metal fragments, which, by carrying one, two or three vacant sigma hybrids, may interact with a different number of adjacent P atoms. For the modelling, the concept of isolobal analogy is important for predicting the possible sets of external coligands at the metal, which may allow the anchoring at phosphorene with a variety of hapticities. Structural, electronic, spectroscopic and energy parameters underline the most relevant pros and cons of some new products at the 2D framework, which have never been experimentally characterized but appear to be reasonably stable.

physics.chem-ph↗

arXiv2019

Photodetachment and Photoreactions of Substituted Naphthalene Anions in a Tandem Ion Mobility Spectrometer

Substituted naphthalene anions (deprotonated 2-naphthol and 6-hydroxy-2-naphthoic acid) are spectroscopically probed in a tandem drift tube ion mobility spectrometer (IMS). Target anions are selected according to their drift speed through nitrogen buffer gas in the first IMS stage before being exposed to a pulse of tunable light that induces either photodissociation or electron photodetachment, which is conveniently monitored by scavenging the detached electrons with trace \ce{SF6} in the buffer gas. The photodetachment action spectrum of the 2-naphtholate anion exhibits a band system spanning 380-460\,nm~with a prominent series of peaks spaced by 440\,\cme, commencing at 458.5\,nm, and a set of weaker peaks near the electron detachment threshold corresponding to transitions to dipole-bound states. The two deprotomers of 6-hydroxy-2-naphthoic acid are separated and spectroscopically probed independently. The molecular anion formed from deprotonation of the hydroxy group possesses a photodetachment action spectrum similar to that of the 2-naphtholate anion with an onset at 470\,nm and a maximum at 420\,nm. Near threshold, photoreaction with \ce{SF6} is observed with displacement of an OH group by an F atom. In contrast, the anion formed from deprotonation of the carboxylic acid group features a photodissociation action spectrum, recorded on the \ce{CO2} loss channel, lying to much shorter wavelength with an onset at 360\,nm and maximum photoresponse at 325\,nm.

astro-ph.IM↗

arXiv2018

Root-Growth of Boron Nitride Nanotubes: Experiments and \textit{Ab Initio} Simulations

We have synthesized boron nitride nanotubes (BNNTs) in an arc in presence of boron and nitrogen species only, without transition metals. We find that BNNTs are often attached to pure boron nanoparticles, suggesting that root-growth is a likely mechanism for their formation. To gain further insight into this process we have studied key mechanisms for root growth of BNNTs on the surface of a liquid boron droplet by ab initio molecular dynamics simulations. We find that nitrogen atoms reside predominantly on the droplet surface where they organize to form boron nitride islands below 2400 K. To minimize contact with the liquid particle underneath, the islands assume non-planar configurations that are likely precursors for the thermal nucleation of cap structures. Once formed, the caps are stable and can easily incorporate nitrogen and boron atoms at their base, resulting in further growth. Our simulations support the root-growth mechanism of BNNTs and provide comprehensive evidence of the active role played by liquid boron.

physics.chem-ph↗

arXiv2016

Experimental and Computational Study of Isomerically Pure Soluble Aza-phthalocyanines and Azasubphthalocyanines of Varying Number of Aza Units

Herein, we present a series of isomerically pure, peripherically alkyl substituted, soluble and low aggregating azaphthalocyanines as well as their new, smaller hybrid homologues, the azasubphthalocyanines. The focus lies on the effect of the systematically increasing number of aza building blocks [-N=] replacing the non peripheral [-CH=] units and its influence on physical and photophysical properties of these chromophores. The absolute and relative HOMO-LUMO energies of azaphthalocyanines was analyzed using UV-Vis, CV and compared to density functional theory calculations (B3LYP, TD-DFT). Crystals of substituted subphthalocyanine, N2-Pc*H2 and N4-[Pc*Zn$\cdot$H2O] were obtained out of DCM. For the synthesis of the valuable tetramethyltetraline phthalocyanine building block a new highly efficient synthesis involving a nearly quantitative CoII catalyzed aerobic autoxidation step is introduced replacing inefficient KMnO4/pyridine as oxidant. The lowering of the HOMO level is revealed as the determining factor for the trend in the adsorption energies by electronic structure analysis.

physics.chem-ph↗

arXiv2017

Experimental evidence for a second hydrogen ordered phase of ice VI

In the last decade five new ice phases were experimentally prepared. Two of them are empty clathrate hydrates and three of them represent hydrogen ordered counterparts of previously known disordered ice phases. Here, we report on hydrogen ordering in ice VI samples upon cooling at pressures up to 1.8 GPa. Using calorimetry, dielectric relaxation spectroscopy, Raman spectroscopy, and powder X-ray diffraction we provide evidence for the existence of a second hydrogen ordered phase related to ice VI, that we call ice β-XV. This phase is more ordered than ice XV by 14% and directly transforms to ice XV above 103K and to ice VI above 129K. That is, upon heating an order->order->disorder transition is experienced. The new phase is thus thermodynamically more stable than ice XV requiring a new stability region in the phase diagram of water. Raman spectroscopy indicates ice XV and ice β-XV to be different in terms of symmetry and space group. The activation energies for dielectric relaxation are 45 kJ mol-1 in ice β-XV compared to 18 kJ mol-1 in ice XV. Powder X-ray data show the oxygen network to be the one of ice VI. The ordering of hydrogen atoms induces a significant peak shift to lower d-spacings at d=0.265 nm in ice β-XV, whereas for ice XV shifts to higher d-spacings are found. This present work represents a unique experimental realization of a second electric ordering in an ice phase.

cond-mat.mtrl-sci↗

arXiv2018

Charge Regulating Macro-ions in Salt Solutions: Screening Properties and Electrostatic Interactions

We revisit the charge-regulation mechanism of macro-ions and apply it to mobile macro-ions in a bathing salt solution. In particular, we examine the effects of correlation between various adsorption/desorption sites and analyze the collective behavior in terms of the solution effective screening properties. We show that such a behavior can be quantified in terms of the charge {\em asymmetry} of the macro-ions, defined by their preference for a non-zero effective charge, and their {\em donor/acceptor} propensity for exchanging salt ions with the bathing solution. Asymmetric macro-ions tend to increase the screening, while symmetric macro-ions can in some cases decrease it. Macro-ions that are classified as donors display a rather regular behavior, while those that behave as acceptors exhibit an anomalous non-monotonic Debye length. The screening properties, in their turn, engender important modifications to the disjoining pressure between two charged surfaces. Our findings are in particular relevant for solutions of proteins, whose exposed amino acids can undergo charge dissociation/association processes to/from the bathing solution, and can be considered as a solution of charged regulated macro-ions, as analyzed here.

cond-mat.soft↗

arXiv2018

Modeling the relative dynamics of DNA-coated colloids

We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over the fast DNA dynamics leads to an evolution equation for the particle in isolation, which contains both friction and diffusion. The DNA-induced friction coefficient depends on the physical properties of the DNA, and substituting parameter values typical of a 1$μ$m colloid coated densely with weakly interacting DNA gives a coefficient about 100 times larger than the corresponding coefficient of hydrodynamic friction. We use a mean-field extension of the model to higher dimensions to estimate the friction tensor for a disc rotating and translating horizontally along a line. When the DNA strands are very stiff and short, the friction coefficient for the disc rolling approaches zero while the friction for the disc sliding remains large. Together, these results could have significant implications for the dynamics of DNA-coated colloids or other ligand-receptor systems, implying that DNA-induced friction between colloids can be stronger than hydrodynamic friction and should be incorporated into simulations, and that it depends nontrivially on the type of relative motion, possibly causing the particles to assemble into out-of-equilibrium metastable states governed by the pathways with the least friction.

cond-mat.soft↗

arXiv2018

Electrostatic interaction of particles trapped at fluid interfaces: Effects of geometry and wetting properties

The electrostatic interaction between pairs of spherical or macroscopically long, parallel cylindrical colloids trapped at fluid interfaces is studied theoretically for the case of small inter-particle separations. Starting from the effective interaction between two planar walls and by using the Derjaguin approximation, we address the issue of how the electrostatic interaction between such particles is influenced by their curvatures and by the wetting contact angle at their surfaces. Regarding the influence of curvature, our findings suggest that the discrepancies between linear and nonlinear Poisson-Boltzmann theory, which have been noticed before for planar walls, also occur for spheres and macroscopically long, parallel cylinders, though their magnitude depends on the wetting contact angle. Concerning the influence of the wetting contact angle $θ$ simple relations are obtained for equally sized particles which indicate that the inter-particle force varies significantly with $θ$ only within an interval around $90^\circ$. This interval depends on the Debye length of the fluids and on the size of the particles but not on their shape. For unequally sized particles, a more complicated relation is obtained for the variation of the inter-particle force with the wetting contact angle.

cond-mat.soft↗

arXiv2018

The viscoelastic signature underpinning polymer deformation under shear flow

Entangled polymers are deformed by a strong shear flow. The shape of the polymer, called the form factor, is measured by small angle neutron scattering. However, the real-space molecular structure is not directly available from the reciprocal-space data, due to the phase problem. Instead, the data has to be fitted with a theoretical model of the molecule. We approximate the unknown structure using piecewise straight segments, from which we derive an analytical form factor. We fit it to our data on a semi-dilute entangled polystyrene solution under in situ shear flow. The character of the deformation is shown to lie between that of a single ideal chain (viscous) and a cross-linked network (elastic rubber). Furthermore, we use the fitted structure to estimate the mechanical stress, and find a fairly good agreement with rheology literature.

cond-mat.soft↗

arXiv2018

Incipient spin-dipole coupling in a 1D helical-chain metal-organic hybrid

Low dimensional magnetic systems (such as spin-chain) are extensively studied due to their exotic magnetic properties. Here, we would like to address that such systems should also be interesting in the field of dielectric, ferroelectricity and magnetodielectric coupling. As a prototype example, we have investigated a one-dimensional (1D) helical-chain metal-organic hybrid system with a chiral structure which shows a broad hump in magnetic susceptibility around 55 K (Tmax). The complex dielectric constant exactly traces this feature, which suggests intrinsic magnetodielectric coupling in this chiral system. The dipolar ordering at Tmax occurs due to lattice-distortion which helps to minimize the magnetic energy accompanied by 1D-magnetic ordering or vice-versa. This experimental demonstration initiates a step to design and investigate hybrid organic-inorganic magnetic systems consisting of chiral structure towards ferroelectricity and magnetodielectric coupling.

cond-mat.mtrl-sci↗

arXiv2021

X-ray induced desorption and photochemistry in CO ice

We report an investigation of X-ray induced desorption of neutrals, cations and anions from CO ice. The desorption of neutral CO, by far the most abundant, is quantified and discussed within the context of its application to astrochemistry. The desorption of many different cations, including large cations up to the mass limit of the spectrometer, are observed. In contrast, the only desorbing anions detected are O$^-$ and C$^-$. The desorption mechanisms of all these species are discussed with the aid of their photodesorption spectrum. The evolution of the X-ray absorption spectrum shows significant chemical modifications of the ice upon irradiation, which along with the desorption of large cations gives a new insight into X-ray induced photochemistry in CO ice.

physics.chem-ph↗

arXiv2022

Photoelectron circular dichroism in angle-resolved photoemission from liquid fenchone

We present an experimental X-ray photoelectron circular dichroism (PECD) study of liquid fenchone at the C 1s edge. A novel setup to enable PECD measurements on a liquid microjet [Malerz et al., Rev. Sci. Instrum., 2022, 93, 015101] was used. For the C 1s line assigned to fenchone's carbonyl carbon, a non-vanishing asymmetry is found in the intensity of photoelectron spectra acquired under a fixed angle in the backward-scattering plane. This experiment paves the way towards a novel probe of the chirality of organic/biological molecules in aqueous solution.

physics.chem-ph↗

arXiv2021

Phase coherent excitation of SABRE permits simultaneous hyperpolarization of multiple targets at high magnetic field

Hyperpolarization methods in magnetic resonance overcome sensitivity limitations, especially for low-γ nuclei such as 13C and 15N. Signal Amplification By Reversible Exchange (SABRE) and extended SABRE (X-SABRE) are efficient and low-cost methods for generating large polarizations on a variety of nuclei, but they most commonly use low magnetic fields (μT-mT). High field approaches, where hyperpolarization is generated directly in the spectrometer, are potentially much more convenient but have been limited to selectively hyperpolarize single targets. Here we introduce a new pulse sequence-based approach that affords broadband excitation of SABRE hyperpolarization at high magnetic fields without having to tailor pulse sequence parameters to specific targets. This permits simultaneous hyperpolarization of multiple targets for the first time at high field and offers a direct approach to integration of high-field SABRE hyperpolarization into routine NMR applications, such as NMR-based metabonomics and biomolecular NMR.

physics.chem-ph↗