Space-Resolved OH Vibrational Spectra of the Hydration Shell around CO2.

The CO2 molecule is weakly bound in water. Here we analyze the influence of a dissolved CO2 molecule on the structure and OH vibrational spectra of the surrounding water. From the analysis of ab initio molecular dynamics simulations (BLYP-D3) we present static (structure, coordination, H-bonding, tetrahedrality) and dynamical (OH vibrational spectra) properties of the water molecules as a function of distance from the solute. We find a weakly oscillatory variation ("ABBA") in the 'solution minus bulk water' spectrum. The origin of these features can largely be traced back to solvent-solute hard-core interactions which lead to variations in density and tetrahedrality when moving from the solute's vicinity out to the bulk region. The high-frequency peak in the solute-affected spectra is specifically analyzed and found to originate from both water OH groups that fulfill the geometric H-bond criteria, and from those that do not (dangling ones). Effectively, neither is hydrogen-bonded.

PiNN: A Python Library for Building Atomic Neural Networks of Molecules and Materials.

Atomic neural networks (ANNs) constitute a class of machine learning methods for predicting potential energy surfaces and physicochemical properties of molecules and materials. Despite many successes, developing interpretable ANN architectures and implementing existing ones efficiently are still challenging. This calls for reliable, general-purpose, and open-source codes. Here, we present a python library named PiNN as a solution toward this goal. In PiNN, we designed a new interpretable and high-performing graph convolutional neural network variant, PiNet, as well as implemented the established Behler-Parrinello neural network. These implementations were tested using datasets of isolated small molecules, crystalline materials, liquid water, and an aqueous alkaline electrolyte. PiNN comes with a visualizer called PiNNBoard to extract chemical insight "learned" by ANNs. It provides analytical stress tensor calculations and interfaces to both the atomic simulation environment and a development version of the Amsterdam Modeling Suite. Moreover, PiNN is highly modularized, which makes it useful not only as a standalone package but also as a chain of tools to develop and to implement novel ANNs. The code is distributed under a permissive BSD license and is freely accessible at https://github.com/Teoroo-CMC/PiNN/ with full documentation and tutorials.

Fifty Shades of Water: Benchmarking DFT Functionals against Experimental Data for Ionic Crystalline Hydrates.

We propose that crystalline ionic hydrates constitute a valuable resource for benchmarking theoretical methods for aqueous ionic systems. Many such structures are known from the experimental literature, and they contain a large variety of water-water and ion-water structural motifs. Here we have collected a data set (CRYSTALWATER50) of 50 structurally unique "in-crystal" water molecules, involved in close to 100 nonequivalent O-H···O hydrogen bonds. A dozen well-known DFT functionals were benchmarked with respect to their ability to describe these experimental structures and their OH vibrational frequencies. We find that the PBE, RPBE-D3, and optPBE-vdW methods give the best H-bond distances and that anharmonic OH frequencies generated from B3LYP//optPBE-vdW energy scans outperform the other methods, i.e., here we performed B3LYP energy scans along the OH stretching coordinate while the rest of the structure was kept fixed at the optPBE-vdW-optimized positions.

Maximally resolved anharmonic OH vibrational spectrum of the water/ZnO(101¯0) interface from a high-dimensional neural network potential.

Unraveling the atomistic details of solid/liquid interfaces, e.g., by means of vibrational spectroscopy, is of vital importance in numerous applications, from electrochemistry to heterogeneous catalysis. Water-oxide interfaces represent a formidable challenge because a large variety of molecular and dissociated water species are present at the surface. Here, we present a comprehensive theoretical analysis of the anharmonic OH stretching vibrations at the water/ZnO(101¯0) interface as a prototypical case. Molecular dynamics simulations employing a reactive high-dimensional neural network potential based on density functional theory calculations have been used to sample the interfacial structures. In the second step, one-dimensional potential energy curves have been generated for a large number of configurations to solve the nuclear Schrödinger equation. We find that (i) the ZnO surface gives rise to OH frequency shifts up to a distance of about 4 Å from the surface; (ii) the spectrum contains a number of overlapping signals arising from different chemical species, with the frequencies decreasing in the order ν(adsorbed hydroxide) > ν(non-adsorbed water) > ν(surface hydroxide) > ν(adsorbed water); (iii) stretching frequencies are strongly influenced by the hydrogen bond pattern of these interfacial species. Finally, we have been able to identify substantial correlations between the stretching frequencies and hydrogen bond lengths for all species.

Red-shifting and blue-shifting OH groups on metal oxide surfaces - towards a unified picture.

We analyse the OH vibrational signatures of 56 structurally unique water molecules and 34 structurally unique hydroxide ions in thin water films on MgO(001) and CaO(001), using DFT-generated anharmonic potential energy surfaces. We find that the OH stretching frequencies of intact water molecules on the surface are always downshifted with respect to the gas-phase species while the OH- groups are either upshifted or downshifted. Despite these differences, the main characteristics of the frequency shifts for all three types of surface OH groups (OHw, OsH and OHf) can be accounted for by one unified expression involving the in situ electric field from the surrounding environment, and the gas-phase molecular properties of the vibrating species (H2O or OH-). The origin behind the different red- and blueshift behaviour can be traced back to the fact that the molecular dipole moment of a gas-phase water molecule increases when an OH bond is stretched, but the opposite is true for the hydroxide ion. We propose that familiarity with the relations presented here will help surface scientists in the interpretation of vibrational OH spectra for thin water films on ionic crystal surfaces.

CO2 Hydration Shell Structure and Transformation.

The hydration-shell of CO2 is characterized using Raman multivariate curve resolution (Raman-MCR) spectroscopy combined with ab initio molecular dynamics (AIMD) vibrational density of states simulations, to validate our assignment of the experimentally observed high-frequency OH band to a weak hydrogen bond between water and CO2. Our results reveal that while the hydration-shell of CO2 is highly tetrahedral, it is also occasionally disrupted by the presence of entropically stabilized defects associated with the CO2-water hydrogen bond. Moreover, we find that the hydration-shell of CO2 undergoes a temperature-dependent structural transformation to a highly disordered (less tetrahedral) structure, reminiscent of the transformation that takes place at higher temperatures around much larger oily molecules. The biological significance of the CO2 hydration shell structural transformation is suggested by the fact that it takes place near physiological temperatures.

Comparing van der Waals DFT methods for water on NaCl(001) and MgO(001).

In this work, a range of van der Waals type density functionals are applied to the H2O/NaCl(001) and H2O/MgO(001) interface systems to explore the effect of an explicit dispersion treatment. The functionals we use are the self-consistent vdW functionals vdW-DF, vdW-DF2, optPBE-vdW, optB88-vdW, optB86b-vdW, and vdW-DF-cx, as well as the dispersion-corrected PBE-TS and PBE-D2 methods; they are all compared with the standard PBE functional. For both NaCl(001) and MgO(001), we find that the dispersion-flavoured functionals stabilize the water-surface interface by approximately 20%-40% compared to the PBE results. For NaCl(001), where the water molecules remain intact for all overlayers, the dominant contribution to the adsorption energy from "density functional theory dispersion" stems from the water-surface interactions rather than the water-water interactions. The optPBE-vdW and vdW-DF-cx functionals yield adsorption energies in good agreement with available experimental values for both NaCl and MgO. To probe the strengths of the perturbations of the adsorbed water molecules, we also calculated water dipole moments and found an increase up to 85% for water at the MgO(001) surface and 70% at the NaCl(001) surface, compared to the gas-phase dipole moment.

Efficacy and safety of electrochemotherapy combined with peritumoral IL-12 gene electrotransfer of canine mast cell tumours.

Electrochemotherapy combined with peritumoral interleukin-12 (IL-12) gene electrotransfer was used for treatment of mast cell tumours in 18 client-owned dogs. Local tumour control, recurrence rate, as well as safety of combined therapy were evaluated. One month after the therapy, no side effects were recorded and good local tumour control was observed with high complete responses rate which even increased during the observation period to 72%. IL-12 gene electrotransfer resulted in 78% of patients with detectable serum IFN-γ and/or IL-12 levels. In the treated tumours vascular changes as well as minimal T-lymphocytes infiltration was observed. After 1 week, the plasmid DNA was not detected intra- or peritumorally and no horizontal gene transfer was observed. In summary, our study demonstrates high antitumour efficacy of electrochemotherapy combined with IL-12 electrotransfer, which also prevented recurrences or distant metastases, as well as its safety and feasibility in treatment of canine mast cell tumours.

Vibrational models for a crystal with 36 water molecules in the unit cell: IR spectra from experiment and calculation.

We present experimental and calculated IR spectra of the water molecules in crystalline aluminium nitrate nonahydrate and a method to generate a realistic and well resolved isotope-isolated spectrum from periodic DFT calculations. Our sample crystal contains 18 structurally different OH groups and is a perfect benchmark compound to validate vibrational models and the structure-property relationship of bound water molecules. FTIR spectra (ATR technique) were recorded for the Al(NO3)3·9H2O crystal at 138 and 298 K, and due to a multitude of OH contributions and couplings, they are naturally poorly resolved and yield a broad OH band in the range 3500 to 2700 cm(-1) at both temperatures. Isotope-isolated IR spectra have the clear advantage over non-deuterated spectra that they are better resolved and easier to interpret - here we have extended the experimental study by simulating the isotope-isolated IR spectrum, using PBE-D2 and auxiliary B3LYP calculations and an anharmonic OH vibrational model. We find excellent agreement between the shapes and frequency ranges of the experimental and calculated OH spectral bands. We make use of four different vibrational models: (i) a harmonic lattice-dynamical model for the isotope-isolated crystal with 1 H among 71 D, (ii) a harmonic lattice-dynamical model for the normal undeuterated crystal involving all the vibrational couplings, (iii) a harmonic 1-dimensional uncoupled OH vibrational model, and (iv) the anharmonic variant of the previous model, which yields the final spectrum. We also use the individual frequencies, resolved by the calculations, to quantify new or extended relationships involving OH frequencies versus local electric fields and H-bond distances. We explore the correlation between OH frequency and molecular dipole moment for bound water molecules.

Large polarization but small electron transfer for water around Al(3+) in a highly hydrated crystal.

Precise molecular-level information on the water molecule is precious, since it affects our interpretation of the role of water in a range of important applications of aqueous media. Here we propose that electronic structure calculations for highly hydrated crystals yield such information. Properties of nine structurally different water molecules (19 independent OO hydrogen bonds) in the Al(NO3)3·9H2O crystal have been calculated from DFT calculations. We combine the advantage of studying different water environments using one and the same compound and method (instead of comparing a set of independent experiments, each with its own set of errors) with the advantage of knowing the exact atomic positions, and the advantage of calculating properties that are difficult to extract from experiment. We find very large Wannier dipole moments for H2O molecules surrounding the cations: 4.0-4.3 D (compared to our calculated value of 1.83 D in the gas phase). These are induced by the ions and the H-bonds, while other water interactions and the relaxation of the internal water geometry in fact decrease the dipole moments. We find a good correlation between the water dipole moment and the OO distances, and an even better (non-linear) correlation with the average electric field over the molecule. Literature simulation data for ionic aqueous solutions fit quite well with our crystalline 'dipole moment vs. OO distance' curve. The progression of the water and cation charges from 'small clusters ⇒ large clusters ⇒ the crystal' helps explain why the net charges on all the water molecules are so small in the crystal.

Different structures give similar vibrational spectra: the case of OH- in aqueous solution.

We have calculated the anharmonic OH(-)(aq) vibrational spectrum in aqueous solution with a "classical Monte Carlo simulation + QM/MM + vibrational" sequential approach. A new interaction model was used in the Monte Carlo simulations: a modified version of the charged-ring hydroxide-water model from the literature. This spectrum is compared with experiment and with a spectrum based on CPMD-generated structures, and the hydration structures and H-bonding for the two models are compared. We find that: (i) the solvent-induced frequency shift as well as the absolute OH(-) frequency are in good agreement with experiment using the two models; (ii) the Raman and IR bands are very similar, in agreement with experiment; (iii) the hydration structure and H-bonding around the ion are very different with the two ion-water interaction models (charged-ring and CPMD); (iv) a cancellation effect between different regions of the hydration shell makes the total spectra similar for the two interaction models, although their hydration structures are different; (v) the net OH(-) frequency shift is a blueshift of about +80 cm(-1) with respect to frequency of the gas-phase ion.

A gold cyano complex in nitromethane: MD simulation and X-ray diffraction.

The solvation structure around the dicyanoaurate(I) anion (Au(CN)2-) in a dilute nitromethane (CH3NO2) solution is presented from X-ray diffraction measurements and molecular dynamics simulation (NVT ensemble, 460 nitromethane molecules at room temperature). The simulations are based on a new solute-solvent force-field fitted to a training set of quantum-chemically derived interaction energies. Radial distribution functions from experiment and simulation are in good agreement. The solvation structure has been further elucidated from MD data. Several shells can be identified. We obtain a solvation number of 13-17 nitromethane molecules with a strong preference to be oriented with their methyl groups towards the solute.

Calculation of anharmonic OH phonon dispersion curves for the Mg(OH)2 crystal.

Anharmonic OH phonon dispersion curves have been calculated for the Mg(OH)(2) crystal. A crystal Hamiltonian was set up for the vibrational problem, where the coordinates consists of the bond lengths of two hydroxide ions in the central unit cell. Its two-dimensional potential energy surface was constructed from first principle calculations within the density functional theory approximation. Dispersion curves were calculated by diagonalizing the Hamiltonian in a basis of singly excited crystal functions. The single particle functions used to construct the crystal states were taken from a Morse oscillator basis set. These well chosen functions made it possible to restrict calculations to include only very few functions, which greatly contributed to a transparent presentation of the underlying theory. All calculations could be done analytically except for the calculation of a few integrals. We have compared our results with those of a series of harmonic lattice dynamics calculations and have found that the anharmonicity shifts the IR and Raman dispersion curves downward appreciably and slightly changes the energy differences between both curves. From an analysis of the harmonic results we conclude that incorporating the coupling between OH stretching motion and the motion of their centers of mass will appreciably change the overall features of the dispersion curves. Extension of the anharmonic model along these lines will cause no problem to the theoretical approach presented in this paper.

Anharmonic OH vibrations in Mg(OH)2 (brucite): two-dimensional calculations and crystal-induced blueshift.

A two-dimensional quantum-mechanical vibrational model has been used to calculate the anharmonic OH vibrational frequencies in the layered Mg(OH)(2) (brucite) crystal. The underlying potential energy surface was generated by density functional theory (DFT) calculations. The resulting OH frequencies are upshifted (blueshifted) by about +75 cm(-1) with respect to the gas-phase OH frequency (+120 cm(-1) in experiments; the discrepancy is mainly due to inadequacies in the DFT and pseudopotential models). The Raman-IR split is about 50 cm(-1), both in the calculations and in experiments. We find that the blueshift phenomenon in brucite can qualitatively be explained by a parabolalike "OH frequency versus electric field" correlation curve pertaining to an OH(-) ion exposed to an electric field. We also find that it is primarily the neighbors within the Mg(OH)(2) layer that induce the blueshift while the interlayer interaction gives a smaller (and redshifting) contribution.

Origin of the OH vibrational blue shift in the LiOH crystal.

The O-H vibrational frequency in crystalline hydroxides is either upshifted or downshifted by its crystalline surroundings. In the LiOH crystal, the experimental gas-to-solid O-H frequency upshift ("blue shift") is approximately +115 cm(-1). Here plane-wave DFT calculations for the isotope-isolated LiOH crystal have been performed and we discuss the origin of the OH frequency upshift, and the nature of the OH group and the interlayer interactions. We find that (1) the vibrational frequency upshift originates from interactions within the LiOH layer; this OH upshift is slightly lessened by the interlayer interactions; (2) the interlayer O-H - - - H-O interaction is largely electrostatic in character (but there is no hydrogen bonding); (3) the gas-to-solid vibrational shift for OH in LiOH(s) and its subsystems qualitatively adheres to a parabola-like "frequency vs electric field strength" correlation curve, which has a maximum for a positive electric field, akin to the correlation curve earlier found in the literature for an isolated OH(-) ion in an electric field.

2D calculation of anharmonic OH vibrations in a layered hydroxide crystal.

Anharmonic vibrational frequencies for the Raman-active (A(1g)) and the IR-active (A(2u)) modes have been calculated for the LiOH crystal within a plane-wave density functional theory (DFT) framework. We find that a two-dimensional quantum-mechanical vibrational approach, allowing for anharmonic coupling between symmetric and antisymmetric OH stretching modes, produces OH frequencies--both absolute frequencies and gas-to-solid frequency shifts--in good agreement with experiment. Remaining errors in the absolute frequencies are largely a consequence of the DFT model chosen. A one-dimensional normal-mode following vibrational treatment, on the other hand, fails to reproduce both absolute anharmonic frequencies and gas-to-solid frequency shifts.

Efficient electrotransfection into canine muscle.

Two different types of electroporation protocols have been developed for efficient electrotransfer of plasmid DNA into skeletal muscle of experimental animals. At first, only low voltage electric pulses have been used, but lately, a combination of high and low voltage pulses has been suggested as more efficient. Up to date, in dogs, this type of electroporation protocol has never been used for muscle targeted plasmid DNA electrotransfection. In this study, we used two different DNA plasmids, one encoding green fluorescent protein and one encoding human interleukin-12. Five different electroporation protocols were evaluated. Three of them featured different combinations of high and low voltage pulses, and two were performed with delivery of low voltage pulses only. Our study shows that combination of 1 high voltage pulse (600 V/cm, 100 mus), followed by 4 low voltage pulses (80 V/cm, 100 ms, 1 Hz) yielded in the same transfection efficiency as the standard trains of low voltage pulses. However, this protocol is performed quicker and, thus, more suitable for potential use in clinical practice. In addition, it yielded in detectable systemic expression of human interleukin-12. Electrotransfer of either of the plasmids was associated with only mild and transitory local side effects, without clinically detectable systemic side effects. The results indicate that electrotransfection is a feasible, effective, and safe method for muscle targeted gene therapy in dogs, which could have potential for clinical applications in veterinary medicine of small animals.

The effect of the histological properties of tumors on transfection efficiency of electrically assisted gene delivery to solid tumors in mice.

Uniform DNA distribution in tumors is a prerequisite step for high transfection efficiency in solid tumors. To improve the transfection efficiency of electrically assisted gene delivery to solid tumors in vivo, we explored how tumor histological properties affected transfection efficiency. In four different tumor types (B16F1, EAT, SA-1 and LPB), proteoglycan and collagen content was morphometrically analyzed, and cell size and cell density were determined in paraffin-embedded tumor sections under a transmission microscope. To demonstrate the influence of the histological properties of solid tumors on electrically assisted gene delivery, the correlation between histological properties and transfection efficiency with regard to the time interval between DNA injection and electroporation was determined. Our data demonstrate that soft tumors with larger spherical cells, low proteoglycan and collagen content, and low cell density are more effectively transfected (B16F1 and EAT) than rigid tumors with high proteoglycan and collagen content, small spindle-shaped cells and high cell density (LPB and SA-1). Furthermore, an optimal time interval for increased transfection exists only in soft tumors, this being in the range of 5-15 min. Therefore, knowledge about the histology of tumors is important in planning electrogene therapy with respect to the time interval between DNA injection and electroporation.

MEPE expression in osteocytes during orthodontic tooth movement.

UNLABELLED: MEPE and DMP1 may play a role in mineralisation and demineralisation within the osteocyte microenvironment. Our earlier studies showed that DMP1 is mechanically responsive [Gluhak-Heinrich J, Ye L, Bonewald LF, Feng JQ, MacDougall M, Harris SE, et al. Mechanical loading stimulates dentin matrix protein 1 (DMP1) in osteocytes in vivo. J Bone Min Res 2003;18(5):807-17]. OBJECTIVES: To examine the effect of mechanical loading on the expression of MEPE using mouse tooth movement model, and compare this effect to that on DMP1. METHODS: In situ hybridisation and immunohistochemistry was performed on 38 treated and 38 control bone sites loaded 6-72 h. ImageJ was used for quantification of mRNA expression in osteocytes. RESULTS: Alveolar osteocytes showed high basal level of MEPE that decreased during the first day of loading, followed by 2.8-fold stimulation at day 3, and returning to a control level by day 7. CONCLUSION: The osteocyte specific mechanical stimulation of MEPE was delayed and different, compared to that of DMP1. This suggests a distinct role of MEPE and DMP1 in the response of osteocytes to mechanical loading in vivo.

Catastrophizing: a risk factor for postsurgical pain.

OBJECTIVE: This research was designed to test the hypothesis that presurgery "catastrophizing" would predict postsurgical pain and postsurgical analgesic consumption. METHODS: A sample of 48 individuals who underwent anterior cruciate ligament repair participated in the study. All participants completed the Pain Catastrophizing Scale (described by Sullivan et al in 1995) prior to surgery. Measures of pain (pain scores on a scale of 0-10) were obtained in the postanesthetic care unit, as well as 1, 2, and 7 days after surgery. Opioid and nonopioid analgesic consumption was tabulated while patients were in the hospital and after discharge. RESULTS: Results showed that the Pain Catastrophizing Scale was a significant predictor of acute postsurgical pain in the postanesthetic care unit (r = 0.48, P = 0.004 for maximum pain in the postanesthetic care unit). Maximum pain ratings in patients with high Pain Catastrophizing Scale scores (> median of 13) were 33% to 74% higher numerically than in patients with low Pain Catastrophizing Scale scores (< or = median), and the duration of moderate-severe pain (>3/10) was more prolonged (45 minutes versus 28 minutes in patients with high and low Pain Catastrophizing Scale scores, respectively; P < 0.05). The Pain Catastrophizing Scale was also predictive of pain with activity at 24 hours (r = 0.65 for pain on walking, P < or = 0.0001). The Pain Catastrophizing Scale did not predict postoperative analgesic use. CONCLUSION: The pattern of findings suggests that high catastrophizing scores may be a risk factor for heightened pain following surgery. Clinical and theoretical implications of the findings are addressed.