Car-Parrinello Molecular Dynamics Simulations Research Articles

Force-field parameters for vanadium ions (+ 2, + 3, + 4, + 5) to investigate their interactions within the vanadium redox flow battery electrolyte solution

With a long term objective of investigating the molecular interactions of vanadium ions with different moieties in the conventional vanadium redox flow battery (VRFB) aqueous electrolyte solution, as well as with the additives in the electrolyte, force-field parameters for vanadium ions are proposed. The parameterization of vanadium ions is performed on the basis of first solvation shell structure for vanadium ions in water obtained by density functional theory (DFT) calculations. Car-Parrinello molecular dynamics (CPMD) simulations were performed to benchmark the proposed force field parameters in the condensed phase environment. The water–vanadium interactions obtained by the proposed parameters are also compared with the extended X-ray absorption fine structure (EXAFS) data in the literature. (Krakowiak et al., Inorganic Chemistry. 51, 2012, 9598–9609.) The regular octahedral structure of oxygen atoms around V2+ and V3+ and distorted octahedral structure of oxygen atoms around V4+ and V5+, as revealed by EXAFS, are reproduced accurately by the suggested force-field parameters. These validated parameters can now be used to perform molecular dynamics simulations on the VRFB electrolyte solution to obtain fundamental understanding of the effect of different additives on solubility and thermal stability of vanadium ions within the VRFB electrolyte.

Growth of metalloid aluminum clusters on graphene vacancies.

Ab initio simulations are used to show that graphene vacancy sites may offer a means of templated growth of metalloid aluminum clusters from their monohalide precursors. We present density functional theory and ab initio molecular dynamics simulations of the aluminum halide AlCl interacting with a graphene surface. Unlike a bare Al adatom, AlCl physisorbs weakly on vacancy-free graphene with little charge transfer and no hybridization with carbon orbitals. The barrier for diffusion of AlCl along the surface is negligible. Covalent bonding is seen only with vacancies and results in strong chemisorption and considerable distortion of the nearby lattice. Car-Parrinello molecular dynamics simulations of AlCl liquid around a graphene single vacancy show spontaneous metalloid cluster growth via a process of repeated insertion reactions. This suggests a means of templated cluster nucleation and growth on a carbon substrate and provides some confirmation for the role of a trivalent aluminum species in nucleating a ligated metalloid cluster from AlCl and AlBr solutions.

Structural flexibility of the sulfur mustard molecule at finite temperature from Car–Parrinello molecular dynamics simulations

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.

A Serendipitous Rendezvous with a Four-Center Two-Electron Bonded Intermediate in the Aerial Oxidation of Hydrazine.

Oxidation by dioxygen has a rich repertoire of mechanistic intricacies. Herein, we report a hitherto unknown paradigm of dioxygen activation reaction which propagates through a four center two electron (4c-2e) bound species. Using static DFT and ab initio quantum chemical techniques we have unraveled the oxidation pathway for hydrazine and its methylated analogues by dioxygen which involves formation of this unconventional 4c-2e bonded species en route to the oxidation products. Inconvertible evidence in favor of such an unprecedented dioxygen activation route is provided by capturing the events of formation of the 4c-2e species in aqueous phase for hydrazine and its congeners and the experimentally observed products from the respective 4c-2e species, like H2O2 and N2H2 , diazene in the case of hydrazine using Car-Parrinello molecular dynamics simulations.

Alloy counter electrodes in dye-sensitized solar cells

Dye-sensitized solar cells (DSSCs) have gained widespread attention of researchers in recent years due to their unique advantages, such as low cost of production, ease of manufacturing and relatively high power conversion efficiency. Traditionally, a DSSC has several components including photoanode material, dyes, electrolytes and the counter electrode (CE), which must cooperate intimately to transform incident light into current. As a crucial part of DSSCs, designing CE with excellent properties is a key to improve the power conversion efficiency of DSSCs. As the good CE material, noble metal Pt material exhibiting high catalytic activity and electrical conductivity has obtained high power conversion efficiency in DSSCs. However, some problems of Pt, especially high scarcity in the nature and the corrosivity of I–/I3– electrolyte, limit its further application in DSSCs. Meanwhile, lots of Pt-free materials involving carbon materials, transition metal compounds, polymers, and hybrids have been developed as CE materials to solve the challenges of the Pt-based DSSCs, and achieved favorable power conversion efficiency. Recently, another novel type of alloy materials, which include Pt-based and Pt-free alloys, show superior catalytic activity and have achieved significant power conversion efficiency when applied as CEs in DSSCs. The alloy materials have the merits of simple preparation process and low cost and are the outstanding candidate to replace Pt in DSSCs. The present review gives a summary of the alloy materials as CE in DSSCs. We stress the advantages and disadvantages of alloy CE materials, and put forward ideas for preparation methods, DSSCs’ designing, ab-initio Car-Parrinello molecular dynamics simulations, first-principle density functional theory calculations and stability evaluations in future research for DSSCs featuring alloy CEs. Also, some crucial issues in alloy-based DSSCs and the further applications of the alloy materials in other field of catalysis are discussed.

Hydrogen bonds in quinoline N-oxide derivatives: first-principle molecular dynamics and metadynamics ground state study

Car–Parrinello molecular dynamics simulations were carried out for 8-hydroxyquinoline N-oxide (1) and 2-carboxyquinoline N-oxide (2) in vacuo and in the solid state. The first-principle approach was employed to intramolecular hydrogen bond features present in the studied quinoline N-oxides. Grimme’s dispersion correction was employed throughout the study. Special attention was devoted to the solid-state computations knowing that in the molecular crystals, strong and weak interactions are responsible for spatial organization and molecular properties of molecules. On the basis of Car–Parrinello molecular dynamics, it was possible to reproduce the hydrogen bond dynamics as well as to investigate the vibrational features on the basis of Fourier transform of the atomic velocity autocorrelation function. The free energy surfaces for proton motion were reproduced by unconstrained CPMD runs as well as by metadynamics. Larger flexibility of the bridge proton in 2 was noticed. The computations are verified by experimental X-ray and IR data available.

Ab Initio MD Simulations of the Brønsted Acidity of Glutathione in Aqueous Solutions: Predicting pKa Shifts of the Cysteine Residue.

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.

Revisiting the Aqueous Solutions of Dimethyl Sulfoxide by Spectroscopy in the Mid- and Near-Infrared: Experiments and Car-Parrinello Simulations.

The infrared and near-infrared spectra of the aqueous solutions of dimethyl sulfoxide are revisited. Experimental and computational vibrational spectra are analyzed and compared. The latter are determined as the Fourier transformation of the velocity autocorrelation function of data obtained from Car-Parrinello molecular dynamics simulations. The experimental absorption spectra are deconvolved, and the excess spectra are determined. The two-dimensional excess contour plot provides a means of visualizing and identifying spectral regions and concentration ranges exhibiting nonideal behavior. In the binary mixtures, the analysis of the SO stretching band provides a semiquantitative picture of the formation and dissociation of hydrogen-bonded DMSO-water complexes. A maximum concentration of these clusters is found in the equimolar mixture. At high DMSO concentration, the formation of rather stable 3DMSO:1water complexes is suggested. The formation of 1DMSO:2water clusters, in which the water oxygen atoms interact with the sulfoxide methyl groups, is proposed as a possible reason for the marked depression of the freezing temperature at the eutectic point.

Infrared absorption spectra of liquid water and deuterated water by Car-Parrinello molecular dynamics

Infrared (IR) absorption spectra plays a key role in the study of thermodynamic and dynamic properties of liquid water. Car-Parrinello molecular dynamics simulations within the framework of density-functional theory are used to study the IR absorption, dielectric function and optical properties of liquid water and deuterated water. Using the energy minimization model to obtain the input structure, we calculate the molecular dipole moment of water and deuterated water at ambient temperature, and then obtain the IR absorption spectra by Fourier transforming the autocorrelated function of dipole moment. As the numerical analysis indicates, the calculated results fit well with previous literature experiments. The absorption peak represents the stretching mode of oxygen-hydrogen covalent bond and shows a slight red shift. The dielectric functions and optical constants of water and deuterated water at the temperature of 303 K are extracted from IR absorption spectrum.

Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car–Parrinello molecular dynamics study

The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car–Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

Identification of Di(oxymethylene)glycol in the Raman Spectrum of Formaldehyde Aqueous Solutions by ab Initio Molecular Dynamics Simulations and Quantum Chemistry Calculations.

Di(oxymethylene)glycol forms in formaldehyde aqueous solutions by polymerization of methanediol. The structure and hydrogen bond interactions of di(oxymethylene)glycol with water were characterized by performing Car-Parrinello molecular dynamics simulations. The anharmonic vibrational frequencies of di(oxymethylene)glycol in solution were determined with ab initio calculations considering explicitly the hydrogen-bonded water molecules, while other interactions with solvent were described within a polarizable continuum model approach. The calculations allow for a detailed interpretation of the experimental Raman spectrum of formaldehyde aqueous solutions, leading to the assignment of the band at 920 cm(-1) to the symmetric CO stretching mode of di(oxymethylene)glycol.

From Saturated BN Compounds to Isoelectronic BN/CC Counterparts: An Insight from Computational Perspective.

In the present study, the inorganic analogues of alkanes as well as their isoelectronic BN/CC counterparts that bridge the gap between organic and inorganic chemistry are comparatively studied on the grounds of static DFT and Car-Parrinello molecular dynamics simulations. The BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 were considered and compared with their isoelectronic counterparts NH3 BH2 NH2 BH3 and CH3 CH2 CH2 CH3 . In addition, systematical replacement of the NH2 BH2 fragment by the isoelectronic CH2 CH2 moiety is studied in the molecules H3 N(NH2 BH2 )3-m (CH2 CH2 )m BH3 (for m=0, 1, 2, or 3) and H3 N(NH2 BH2 )2-m (CH2 CH2 )m BH3 (for m=0, 1, or 2). The DFT and Car-Parrinello simulations show that the isosteres of the BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 and of larger oligomers of the type (BN)k (CC)l where k≥l are stable compounds. The BN/CC butane H3 NCH2 CH2 BH3 spontaneously produces molecular hydrogen at room temperature. The reaction, prompted by very strong dihydrogen bonding NH⋅⋅⋅HB, undergoes through the neutral, hypervalent, pentacoordinated boron dihydrogen complex RBH2 (H2 ) [R=(CH2 CH2 )n NH2 ]. The calculations suggest that such intermediate and the other BN/CC butanes CH3 CH2 BH2 NH3 , BH3 CH2 NH2 CH3 , and NH3 CH2 BH2 CH3 as well as larger BN/CC oligomers are viable experimentally. A simple recipe for the synthesis of CH3 CH2 BH2 NH3 is proposed. The strength of the dihydrogen bonding appeared to be crucial for the overall stability of the saturated BN/CC derivatives.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pKa Values from Metadynamics Sampling.

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation-deprotonation reaction of the 20 canonical α amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metadynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pKa values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error, with respect to experimental results, of 0.2 pKa units.

Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations.

The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

Influence of Temperature on the Rotameric Forms of the Propyl Acetate Molecule: Raman and FTIR Spectroscopic Studies Aided by ab Initio and Car-Parrinello Molecular Dynamics Simulations.

The conformational preferences of the industrially and biologically significant propyl acetate (PA) molecule have been investigated by Raman and FTIR spectra, aided by ab initio and Car-Parrinello molecular dynamics (CPMD) simulation studies. The PA molecule can exist in various rotameric forms at room temperature, trans-trans [TT], trans-gauche [(TG(+))/(TG(-))], gauche-trans [(G(+)T)/(G(-)T)], and gauche-gauche [(G(+)G(-))/(G(-)G(+))], depending upon the rotation about the O3-C4 and C4-C5 bonds of the molecule. The vibrational signatures of different rotameric forms of the PA molecule have been assigned for the first time. Raman and temperature-dependent FTIR spectra of the PA molecule envisage the coexistence of the TT, TG(+)/TG(-), G(+)T/G(-)T, and G(+)G(-)/G(-)G(+) forms of the PA molecule at room temperature. However, at low (ca. -95 °C) and high temperatures (ca. 65 °C), the TG(+) form of the PA molecule is estimated to be preponderant. These results are substantiated by the CPMD simulations, together with the estimation of fwhm values of the vibrational signatures of the PA molecule recorded at high-, room-, and low-temperature domains.

Structural Properties and Dynamics of Thiophene in Sub/Supercritical Carbon Dioxide from Car-Parrinello Molecular Dynamics Simulations.

Structrual and dynamic properties of thiophene (C4H4S) in supercritical carbon dioxide were studied using Car-Parrinello molecular dynamics simulations. The geometries and energies optimized for the thiophene-CO2 complex show a stable C-H···O hydrogen bond interactions both in gas phase and in supercritical CO2. The radial distribution functions of CO2 around thiophene in the supercritical phase state show a correlation suggesting C-H···O hydrogen bond and S···C interaction. Local structural properties of the mixtures were investigated by angular-radial distributions and spatial distribution functions. The results show a mutually parallel arrangement between the thiophene plane and CO2 molecules at short distances and a high probability of the thiophene being located in the radial directions of the CO2 molecules. The decay of orientational correlations at 318.15 K shows slower relaxation compared to those of 298.15 K for first and second rank correlations. The vibrations of CO2 and thiophene molecules have been examined through an analysis of the velocity autocorrelation functions of the atoms. The C-H stretching modes of thiophene in the isolated configuration are less red-shifted and have a much narrower frequency range than that in the mixtures.

Visualizing the mixed bonding properties of liquid boron with high-resolution x-ray Compton scattering.

Bonding characteristics of liquid boron at 2500K are studied by using high-resolution Compton scattering. An excellent agreement is found between the measurements and the corresponding Car-Parrinello molecular dynamics simulations. Covalent bond pairs are clearly shown to dominate in liquid boron along with the coexistence of diffuse pairs. Our study reveals the complex bonding pattern of liquid boron and gives insight into the unusual properties of this high-temperature liquid.

A computational study of intramolecular hydrogen bonds breaking/formation: impact on the structural flexibility of the ranitidine molecule.

Ranitidine is a histamine H2-receptor antagonist that reduces gastric acid secretion. We studied the flexibility of the ranitidine molecule with the special focus on the network of diverse intramolecular hydrogen bonds: N-H⋯O, N-H⋯N, C-H⋯O, C-H⋯N and N-H⋯S. We performed static density functional theory calculations of global and local minima and analyzed their stability at finite temperature in the Car-Parrinello molecular dynamics simulations. We observed intramolecular H-bonds breaking/formation crucial for the structural rearrangements leading to the folding process. The lifetimes of the closed structures of ranitidine were also estimated. The existence of hydrogen bonds and their strength were confirmed on the basis of topological parameters in the bond critical points utilizing Quantum Theory of Atoms in Molecules.

1H Nuclear Spin Relaxation of Liquid Water from Molecular Dynamics Simulations

We have investigated the nuclear spin relaxation properties of (1)H in liquid water with the help of molecular dynamics simulations. We have computed the (1)H nuclear spin relaxation times T1 and T2 and determined the contribution of the different interactions to the relaxation at different temperatures and for different classical water models (SPC/E, TIP3P, TIP4P, and TIP4P/2005). Among the water models considered, the TIP4P/2005 model exhibits the best agreement with the experiment. The same analysis was performed with Car-Parrinello ab initio molecular dynamics simulations of bulk water at T = 330 K, which provided results close to the experimental values at room temperature. To complete the study, we have successfully accounted for the temperature-dependence of T1 and T2 in terms of a simplified model, which considers the reorientation in finite angle jumps and the diffusive translation of water molecules.

Van der Waals interactions are critical in Car-Parrinello molecular dynamics simulations of porphyrin-fullerene dyads.

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.