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Nanoporous membranes promise energy-efficient water desalination. Hexagonal boron nitride (h-BN), like graphene, exhibits outstanding physical and chemical properties, making it a promising candidate for water treatment. We employed Car-Parrinello molecular dynamics simulations to establish an accurate modeling of Na+ and Cl- permeation through hydrogen passivated nanopores in graphene and h-BN membranes. We demonstrate that ion separation works well for the h-BN system by imposing a barrier of 0.13 eV and 0.24 eV for Na+ and Cl- permeation, respectively. In contrast, for permeation of the graphene nanopore, the Cl- ion faces a minimum of energy of 0.68 eV in the nanopore plane and is prone toward blockade of the nanopore, while the Na+ ion experiences a slight minimum of 0.03 eV. Overall, the desalination performance of h-BN nanopores surpasses that of their graphene counterparts.

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NMR spectroscopy has become a standard technique in studies both on carbon capture and storage. 13 C NMR allows the detection of two peaks for carbonated aqueous samples: one for CO2(aq) and another one for the species H2 CO3 , HCO3 - , and CO3 2- -herein collectively named Hx CO3 x-2 . The chemical shift of this second peak depends on the molar fraction of the three species in equilibrium and has been used to assess the equilibrium between HCO3 - and CO3 2- . The detection of H2 CO3 at low pH solutions is hindered, because of the concurrent liberation of CO2 when the medium is acidified. Herein, a valved NMR tube facilitates the detection of the Hx CO3 x-2 peak across a wide pH range, even at pH 1.8 where the dominant species is H2 CO3 . The method employed the formation of frozen layers of NaH13 CO3 and acid solutions within the tube, which are mixed as the tube reaches room temperature. At this point, the tube is already securely sealed, preventing any loss of CO2 to the atmosphere. A spectrophotometry approach allowed the measurement of the actual pH inside the pressurized NMR tube. The chemical shift for H2 CO3 was determined as 160.33 ± 0.03 ppm, which is in good agreement with value obtained by DFT calculations combined with Car-Parrinello molecular dynamics. The H2 CO3 pKa value determined by the present method was 3.41 ± 0.03, for 15% D2 O aqueous medium and 0.8 mol/L ionic strength. The proposed method can be extended to studies about analogs such as alkyl carbonic and carbamic acids.

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The assumption that nuclear motion is classical explains many phenomena. The problems of Schrödinger's cat and the EPR paradoxon do not exist in a perfectly deterministic theory. All it needs is to describe nuclear motion classically right from the beginning. To establish this simple idea, it must be tested for as many examples as possible. In the present paper, we use ab initio molecular dynamics to investigate the infrared spectrum of a 'magic' protonated water cluster H3O+(H2O)20 which exhibits some features that were believed to afford a quantum treatment of nuclear motion. The role of the temperature in contrast to a quantum mechanical description is discussed.

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We demonstrate how to fully ascribe Raman peaks simulated using ab initio molecular dynamics to specific vibrations in the structure at finite temperatures by means of Wannier functions. Here, we adopt our newly introduced method for the simulation of the Raman spectra in which the total polarizability of the system is expressed as a sum over Wannier polarizabilities. The assignment is then based on the calculation of partial Raman activities arising from self- and/or cross-correlations between different types of Wannier functions in the system. Different types of Wannier functions can be distinguished based on their spatial spread. To demonstrate the predictive power of this approach, we applied it to the case of a cyclohexane molecule in the gas phase and were able to fully assign the simulated Raman peaks.

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Electrolysis is a potential candidate for a quick method of wastewater cleansing. However, it is necessary to know what compounds might be formed from bioorganic matter. We want to know if there are toxic intermediates and if it is possible to influence the product formation by the variation in initial conditions. In the present study, we use Car-Parrinello molecular dynamics to simulate the fastest reaction steps under such circumstances. We investigate the behavior of amino acids and peptides under anodic conditions. Such highly reactive situations lead to chemical reactions within picoseconds, and we can model the reaction mechanisms in full detail. The role of the electric current is to discharge charged species and, hence, to produce radicals from ions. This leads to ultra-fast radical reactions in a bulk environment, which can also be seen as redox reactions as the oxidation states change. In the case of amino acids, the educts can be zwitterionic, so we also observe complex acid-base chemistry. Hence, we obtain the full spectrum of condensed-phase chemistry.

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Tetrahydrofuran (THF) is a widely used chemical compound, in particular as a solvent in organic and inorganic synthesis. The THF molecule has also an interesting property, namely, undergoes pseudorotation, similar to the case of the cyclopentane. Low energy difference between the envelope (Cs symmetry) and twisted (C2 symmetry) conformations of the THF molecule leads to the interconversion between the two conformers. We study the influence of the molecular environment (N2) on the Cs-C2 equilibrium of tetrahydrofuran in the THF@N2 system utilizing nitrogen matrix isolation infrared spectroscopy. We observe a different ratio between envelope (Cs) and twisted (C2) conformations with respect to a change of the temperature. FTIR experimental studies are supported by the results of the static density functional theory calculations and Car-Parrinello molecular dynamics simulations. We focus on the dynamics of the pseudorotation process, in particular, the lifetime of the THF conformations and their mutual rearrangements. On the basis of the THF@N2 matrix model, with explicit nitrogen molecules, the anharmonic infrared spectra are generated from the Fourier transformation of the dipole moment autocorrelation function.

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The impact of condensed-phase and finite-temperature effects on the theoretical X-ray absorption spectra of transition metal complexes is assessed. The former are included in terms of the all-electron Gaussian and augmented plane-wave approach, whereas the latter are taken into account by extensive ensemble averaging along second-generation Car-Parrinello ab initio molecular dynamics trajectories. We find that employing the periodic boundary conditions and including finite-temperature effects systematically improves the agreement between our simulated X-ray absorption spectra and experimental measurements. © 2018 Wiley Periodicals, Inc.

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We present an accurate computational study of the electronic structure and lattice dynamics of solid molecular hydrogen at high pressure. The band-gap energies of the C2/c, Pc, and P63/m structures at pressures of 250, 300, and 350 GPa are calculated using the diffusion quantum Monte Carlo (DMC) method. The atomic configurations are obtained from ab initio path-integral molecular dynamics (PIMD) simulations at 300 K and 300 GPa to investigate the impact of zero-point energy and temperature-induced motion of the protons including anharmonic effects. We find that finite temperature and nuclear quantum effects reduce the band-gaps substantially, leading to metallization of the C2/c and Pc phases via band overlap; the effect on the band-gap of the P63/m structure is less pronounced. Our combined DMC-PIMD simulations predict that there are no excitonic or quasiparticle energy gaps for the C2/c and Pc phases at 300 GPa and 300 K. Our results also indicate a strong correlation between the band-gap energy and vibron modes. This strong coupling induces a band-gap reduction of more than 2.46 eV in high-pressure solid molecular hydrogen. Comparing our DMC-PIMD with experimental results available, we conclude that none of the structures proposed is a good candidate for phases III and IV of solid hydrogen. © 2017 Wiley Periodicals, Inc.

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Crystal models of cellulose Iß and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iß allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A).

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Sulfur mustard (SM) is one of the most dangerous chemical compounds used against humans, mostly at war conditions but also in terrorist attacks. Even though the sulfur mustard has been synthesized over a hundred years ago, some of its molecular properties are not yet resolved. We investigate the structural flexibility of the SM molecule in the gas phase by Car-Parrinello molecular dynamics simulations. Thorough conformation analysis of 81 different SM configurations using density functional theory is performed to analyze the behavior of the system at finite temperature. The conformational diversity is analyzed with respect to the formation of intramolecular blue-shifting CH⋯S and CH⋯Cl hydrogen bonds. Molecular dynamics simulations indicate that all structural rearrangements between SM local minima are realized either in direct or non-direct way, including the intermediate structure in the last case. We study the lifetime of the SM conformers and perform the population analysis. Additionally, we provide the anharmonic dynamical finite temperature IR spectrum from the Fourier Transform of the dipole moment autocorrelation function to mimic the missing experimental IR spectrum.

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The interplay between electrostatic and van der Waals (vdW) interactions in porphyrin-C60 dyads is still under debate despite its importance in influencing the structural characteristics of such complexes considered for various applications in molecular photovoltaics. In this article, we sample the conformational space of a porphyrin-C60 dyad using Car-Parrinello molecular dynamics simulations with and without empirical vdW corrections. Long-range vdW interactions, which are poorly described by the commonly used density functional theory functionals, prove to be essential for a proper dynamics of the dyad moieties. Inclusion of vdW corrections brings porphyrin and C60 close together in an orientation that is in agreement with experimental observations. The structural differences arising from the vdW corrections are shown to be significant for several properties and potentially less important for others. Additionally, our Mulliken population analysis reveals that contrary to the common belief, porphyrin is not the primary electron donating moiety for C60 . In the considered dyad, fullerene's affinity for electrons is primarily satisfied by charge transfer from the amide group of the linker. However, we show that in the absence of another suitable bound donor, C60 can withdraw electrons from porphyrin if it is sufficiently close.

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The aim of this study was to perform calculations using the method of Car-Parrinello molecular dynamics, leading to the optimized geometry of the molecules of 1,4-benzenedicarboxylic acid (terephthalic acid) in crystals, for the hydrogen form and three variants of substitution of deuterium atoms inside a carboxyl group. Based on the results, trajectories and dipole moments were calculated, what makes possible to simulate vibrations in different systems, and to make calculation of theoretical infrared spectra and atomic power spectra. Theoretical results were compared with the experimental spectra, which verifies the correctness of the method and also was compared with the results obtained by quantum-mechanical calculations using DFT for the isolated dimer. Comparison of the spectra of different forms, allowed for in-depth analysis of the effect of isotopic substitution on the frequency of vibrations and shapes of bands, and confirm the presence of possible coupling effects and intra- and intermolecular interactions. Comparison with the DFT results for the dimer show influence of the crystal structure on the spectra.

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