Parrinello Molecular Dynamics Simulations Research Articles

Structural and bonding properties of small hydrocarbons inside Ca(squarate)-metal organic framework: ab-initio study

Ab−initio Molecular Dynamic (MD) and static Density Functional Theory (DFT) are used to study the structural and bonding properties of small hydrocarbon adsorbates inside Ca(squarate)−Metal Organic Framework (MOF). Car−Parrinello Molecular Dynamics (CPMD) simulations of a single−adsorbate−MOF structure are used to obtain the adsorbate most preferred site of adsorption. This site is used for further structural and bonding analyses using static DFT. Unlike many other MOFs; we found that the Ca(squarate)−MOF physisorbs and weakly binds small adsorbate molecules such as C2H2, C2H4, C2H6, and C3H8 with no observed charge transfer and minimal hybridization with the MOF orbitals. No covalent bonding is seen near the preferred site of adsorption. The calculated binding energies decreases as the H content in the adsorbate molecule increases and found to be −18.71 kJ/mol, −18.14 kJ/mol, −15.75 kJ/mol, and—4.47 kJ/mol for C2H2, C2H4, C2H6, and C3H8 molecules respectively. Density of State (DOS) and a Crystal Orbital Overlap Population (COOP) analyses show that the interactions between C and H atoms in the molecule and C and O atoms in the MOF have antibonding characteristics near the Fermi level. These antibonding states tend to destabilize the overall electronic structure of the combined adsorbate/MOF system and hence decrease the binding energies of these adsorbates inside the MOF.

Local proton hopping mechanism in imidazolium-based plastic crystal: an ab initio molecular dynamics study

Abstract Protic organic ionic plastic crystals (POIPCs) are promising solid-state proton conductor materials in anhydrous proton exchange membrane fuel cells, due to their mechanical flexibility and high ionic conductivity in the plastic crystal phase. In typical POIPCs, the ions are orientationally disordered while the centers of mass are ordered (positional order) like the crystal phase. The local disorder provides more degrees of freedom for the translational and rotational diffusion of ions, thus enhancing proton conduction either via the vehicle mechanism or the Grotthuss mechanism. Yet the local dynamics and the interactions of the cations and anions during the proton transfer process are far from being fully understood. Here, we performed Car–Parrinello molecular dynamics (CPMD) simulation on the imidazolium methanesulfate ([ImH][CH3SO3]) unit cell. By artificially creating one proton hole, we found that a proton can hop directly between the cations. Though the anion is not directly involved in proton hopping, the oxygen atom in the sulfonate group interacts with the proton and has a synergetic motion along with the proton hopping process. This indicates the structural disorder of imidazolium rings and the aid of an anion can facilitate Grotthuss-type proton hopping in imidazolium-based POIPCs.

Combined ReaxFF and Ab Initio MD Simulations of Brown Coal Oxidation and Coal-Water Interactions.

In this manuscript, we use a combination of Car–Parrinello molecular dynamics (CPMD) and ReaxFF reactive molecular dynamics (ReaxFF-MD) simulations to study the brown coal–water interactions and coal oxidation. Our Car–Parrinello molecular dynamics simulation results reveal that hydrogen bonds dominate the water adsorption process, and oxygen-containing functional groups such as carboxyl play an important role in the interaction between brown coal and water. The discrepancy in hydrogen bonds formation between our simulation results by ab initio molecular dynamics (CPMD) and that by ReaxFF-MD indicates that the ReaxFF force field is not capable of accurately describing the diffusive behaviors of water on lignite at low temperatures. The oxidations of brown coal for both fuel rich and fuel lean conditions at various temperatures were investigated using ReaxFF-MD simulations through which the generation rates of major products were obtained. In addition, it was observed that the density decrease significantly enhances the generation of gaseous products due to the entropy gain by reducing system density. Although the ReaxFF-MD simulation of complete coal combustion process is limited to high temperatures, the combined CPMD and ReaxFF-MD simulations allow us to examine the correlation between water adsorption on brown coal and the initial stage of coal oxidation.

Phase-transition behavior of (H2O) n=1-4 few-body systems from Car–Parrinello molecular dynamics

ABSTRACT Car–Parrinello molecular dynamics simulations were applied to investigate phase-transition behavior of (HO) few-body system for n=1−4 at BLYP-GGA level of density-functional theory. A number of important indicators including Lindemann index, ionic mean square displacements, radial distribution function, and shape deformation parameter were accordingly calculated as functions of temperature from 5 to 2000 K. All the four systems exhibited high thermal stabilities compared to bulk water with melting points estimated at , and 700 K for n=2,3, and 4, respectively. No obvious melting behavior was also observed for n=1 due to strong O–H covalent bonds. These values were also found to obey a decreasing trend as the size of the system increases, showing that a minimum size value can also be estimated for which characteristics of liquid water at the thermodynamic limit would consequently appear, in case of studying larger systems with .

Competition of Intra- and Intermolecular Forces in Anthraquinone and Its Selected Derivatives.

Intra- and intermolecular forces competition was investigated in the 9,10-anthraquinone (1) and its derivatives both in vacuo and in the crystalline phase. The 1,8-dihydroxy-9,10-anthraquinone (2) and 1,8-dinitro-4,5-dihydroxy-anthraquinone (3) contain Resonance-Assisted Hydrogen Bonds (RAHBs). The intramolecular hydrogen bonds properties were studied in the electronic ground and excited states employing Møller-Plesset second-order perturbation theory (MP2), Density Functional Theory (DFT) method in its classical formulation as well as its time-dependent extension (TD-DFT). The proton potential functions were obtained via scanning the OH distance and the dihedral angle related to the OH group rotation. The topological analysis was carried out on the basis of theories of Atoms in Molecules (AIM—molecular topology, properties of critical points, AIM charges) and Electron Localization Function (ELF—2D maps showing bonding patterns, calculation of electron populations in the hydrogen bonds). The Symmetry-Adapted Perturbation Theory (SAPT) was applied for the energy decomposition in the dimers. Finally, Car–Parrinello molecular dynamics (CPMD) simulations were performed to shed light onto bridge protons dynamics upon environmental influence. The vibrational features of the OH stretching were revealed using Fourier transformation of the autocorrelation function of atomic velocity. It was found that the presence of OH and NO substituents influenced the geometric and electronic structure of the anthraquinone moiety. The AIM and ELF analyses showed that the quantitative differences between hydrogen bonds properties could be neglected. The bridged protons are localized on the donor side in the electronic ground state, but the Excited-State Intramolecular Proton Transfer (ESIPT) was noticed as a result of the TD-DFT calculations. The hierarchy of interactions determined by SAPT method indicated that weak hydrogen bonds play modifying role in the organization of these crystal structures, but primary ordering factor is dispersion. The CPMD crystalline phase results indicated bridged proton-sharing in the compound 2.

Interfaces in Solid Electrolyte Interphase: Implications for Lithium-Ion Batteries

The existence of passivating layers at the interfaces is a major factor enabling modern lithium-ion (Li-ion) batteries. The properties of the passivation layers determine the cycle life, performance, and safety of batteries. One critical passivation layer is the solid electrolyte interphase (SEI), a heterogeneous multicomponent film formed due to the decomposition of the electrolyte at the surface of the anode. The multicomponent nature is critical for its functioning as the interfaces between these components play a critical role in determining performance and safety. In this work, we use first-principles simulations to investigate the thermodynamic, kinetic, and electronic properties of the interface between lithium fluoride (LiF) and lithium carbonate (Li2CO3), two common SEI components present in Li-ion batteries with organic liquid electrolytes. We construct a coherent interface between these components that restricts the strain in each of them to below 3%. We find that the interfacial structure has a formation energy of the Frenkel defect higher than bulk calculations and similar to pristine Li2CO3, generating Li vacancies in LiF and Li interstitials in Li2CO3 responsible for transport. On the other hand, the Li interstitial hopping barrier is reduced from 0.3 eV in bulk Li2CO3 to 0.10 or 0.22 eV in the interfacial structure considered, demonstrating the favorable role of the interface. Controlling these two effects in a heterogeneous SEI is crucial for maintaining fast ion transport in the SEI. We further perform Car–Parrinello molecular dynamics simulations to explore Li-ion conduction in our interfacial structure, which reveal an enhanced Li-ion diffusion in the vicinity of the interface. Understanding the interfacial properties of the multiphase SEI represents an important frontier to enable next-generation batteries.

Proton Acceptor near the Active Site Lowers Dramatically the O-O Bond Formation Energy Barrier in Photocatalytic Water Splitting.

The O–O bond formation process via water nucleophilic attack represents a thermodynamic and kinetic bottleneck in photocatalytic water oxidation because of the considerably high activation free energy barrier. It is therefore of fundamental significance and yet challenging to find strategies to facilitate this reaction. The microscopic details of the photocatalytic water oxidation step involving the O–O bond formation in a catalyst–dye supramolecular complex are here elucidated by density functional theory-based Car–Parrinello molecular dynamics simulations in the presence of an extra proton acceptor. Introducing a proton acceptor group (OH–) in the hydration shell near the catalytic active site accelerates the rate-limiting O–O bond formation by inducing a cooperative event proceeding via a concerted proton-coupled electron-transfer mechanism and thus significantly lowering the activation free energy barrier. The in-depth insight provides a strategy for facilitating the photocatalytic water oxidation and for improving the efficiency of dye-sensitized photoelectrochemical cells.

Prebiotic Soup Components Trapped in Montmorillonite Nanoclay Form New Molecules: Car-Parrinello Ab Initio Simulations.

The catalytic effects of complex minerals or meteorites are often mentioned as important factors for the origins of life. To assess the possible role of nanoconfinement within a catalyst consisting of montmorillonite (MMT) and the impact of local electric field on the formation efficiency of the simple hypothetical precursors of nucleic acid bases or amino acids, we performed ab initio Car–Parrinello molecular dynamics simulations. We prepared four condensed-phase systems corresponding to previously suggested prototypes of a primordial soup. We monitored possible chemical reactions occurring within gas-like bulk and MMT-confined four simulation boxes on a 20-ps time scale at 1 atm and 300 K, 400 K, and 600 K. Elevated temperatures did not affect the reactivity of the elementary components of the gas-like boxes considerably; however, the presence of the MMT nanoclay substantially increased the formation probability of new molecules. Approximately 20 different new compounds were found in boxes containing carbon monoxide or formaldehyde molecules. This observation and an analysis of the atom–atom radial distribution functions indicated that the presence of Ca2+ ions at the surface of the internal MMT cavities may be an important factor in the initial steps of the formation of complex molecules at the early stages of the Earth’s history.

A Car–Parrinello Molecular Dynamics Simulation Study of the Retro Diels–Alder Reaction for Partially Saturated 2-Pyrones in Water

2-Pyrones have been identified as potential platform molecules derived from biomass to produce high-value chemicals. Theoretical studies utilizing density functional theory (DFT) simulations have shown the partially saturated form of these molecules undergoing a retro Diels–Alder (rDA) reaction in both vapor and solvent conditions. Developing an understanding of the effect of solvent media is crucial to improve the processing of these biomass-derived compounds. In this context, DFT simulations had shown limited access due to either implicit solvent or static explicit solvent environment applied in the model, which did not account for the contribution from the dynamics. Herein, Car–Parrinello molecular dynamics (CPMD) simulations, in conjunction with metadynamics, were performed to understand the effect of dynamics of the solvent on the rDA reaction of partially saturated 2-pyrones. For this, compounds containing both electron-donating and -withdrawing groups as substituent were studied. It was observed th...

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car–Parrinello molecular dynamics

Crystal models of cellulose Iβ 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 Iβ 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).

Reaction dynamics of $$\hbox {CO}_2$$ CO 2 in aqueous amines from ab initio molecular dynamics: 2-amino-2-methyl-1,3-propanediol (AMPD) compared to monoethanolamine (MEA)

We present Car–Parrinello molecular dynamics simulations—combined with metadynamics—of the reactions accompanying the capture of $$\hbox {CO}_2$$ in an aqueous amine solution. The selected amine is 2-amino-2-methyl-1,3-propanediol, which has been investigated experimentally in the search for optimum absorbents. In analogy with the empirical search, we use as reference aqueous monoethanolamine (MEA) at 30 wt%, namely the chemical absorbent most frequently used for the removal of $$\hbox {CO}_2$$ from combustion gases. In particular, we refer to our own results which have led to a detailed characterization of several reaction paths for the absorption of $$\hbox {CO}_2$$ and the amine regeneration (Ma et al. in J Chem Theory Comput 11:3189, 2015). Our simulations refer to the zwitterion mechanism leading to the formation of a carbamate or carbamic acid and to the release of the molecule in solution. The scenario established for the reactions in MEA is confirmed, and in particular the role of the zwitterion mechanism also for $$\hbox {CO}_2$$ release. We find that the difference in the structure of the two molecules does not influence the dynamics of either the formation or the dissociation of the zwitterion. However, it affects its interaction with water in a significant way, thus reducing the probability of carbamate formation and its stability in solution.

Structural and dipolar fluctuations in liquid water: A Car–Parrinello molecular dynamics study

A Car–Parrinello molecular dynamics simulation was performed to investigate the local tetrahedral order, molecular dipole fluctuations and their interrelation with hydrogen bonding in liquid water. Water molecules were classified in three types, exhibiting low, intermediate and high tetrahedral order. Transitions from low to high tetrahedrally ordered structures take place only through transitions to the intermediate state. The molecular dipole moments depend strongly on the tetrahedral order and hydrogen bonding. The average dipole moment of water molecules with a strong tetrahedral order around them comes in excellent agreement with previous estimations of the dipole moment of ice Ih molecules.

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.

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.

Aqueous solvation of an amide molecule from first principles molecular simulations: Structure, hydrogen bond dynamics and spectral signature

Density functional theory (DFT) based Car–Parrinello molecular dynamics (CPMD) simulations were carried out to investigate the structure and dynamics of aqueous solvation shell of a single formamide (FA) molecule. Vibrational frequency through wavelet analysis and correlation function calculations have been performed to understand the spectral signature of water molecules in the first solvation shell and dynamics of solute–solvent hydrogen bonds, respectively. Structural aspects have been analyzed by calculating various pair correlation functions. FA takes part in more than two hydrogen bonds with water via carbonyl oxygen. Due to the presence of carbonyl group, the solvation through amine group hydrogen atoms is asymmetrical; each hydrogen participates in roughly one hydrogen bond. Carbonyl–water hydrogen bonds are stronger than the water–water hydrogen bonds; amine–water hydrogen bonds are much weaker than other two types of hydrogen bonds.

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.

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.

Equilibrium magnesium isotope fractionation between aqueous Mg2+ and carbonate minerals: Insights from path integral molecular dynamics

The theoretical determination of the isotopic fractionation between an aqueous solution and a mineral is of utmost importance in Earth sciences. While for crystals, it is well established that equilibrium isotopic fractionation factors can be calculated using a statistical thermodynamic approach based on the vibrational properties, several theoretical methods are currently used to model ions in aqueous solution. In this work, we present a systematic study to determine the reduced partition function ratio (β-factor) of aqueous Mg2+ using several levels of theory within the simulations. In particular, using an empirical force field, we compare and discuss the performance of the exact results obtained from path integral molecular dynamics (PIMD) simulations, with respect to the more traditional methods based on vibrational properties and the cluster approximation. The results show the importance of including configurational disorder for the estimation of the equilibrium isotope fractionation factor. We also show that using the vibrational frequencies computed from snapshots taken from equilibrated classical molecular dynamics represents a good approximation for the study of aqueous ions.Based on these conclusions, the β-factor of aqueous Mg2+ have been estimated from a Car–Parrinello molecular dynamics (CPMD) simulation with an ab initio force field, and combined with the β-factors of carbonate minerals (magnesite, dolomite, calcite and aragonite). Mg β-factor of Mg-bearing aragonite, calculated here for the first time, displays a lower value than the three other carbonate minerals. This is explained by a strong distortion of the cationic site leading to a decrease of the coordination number during Ca–Mg substitution. Overall, the equilibrium magnesium isotope fractionation factors between aqueous Mg2+ and carbonate minerals that derive from this methodological study support the previous theoretical results obtained from embedded cluster models.

UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations.

Pentaammine dioxido uranium(VI) dibromide ammonia (1/1), [UO2(NH3)5]Br2·NH3, was synthesized in the form of yellow crystals by the reaction of uranyl bromide, UO2Br2, with dry liquid ammonia. The compound crystallizes orthorhombic in space group Cmcm and is isotypic to [UO2(NH3)5]Cl2·NH3 with a = 13.2499(2), b = 10.5536(1), c = 8.9126(1) Å, V = 1246.29(3) Å(3) and Z = 4 at 123 K. The UO2(2+) cation is coordinated by five ammine ligands and the coordination polyhedron can be best described as pentagonal bipyramid. Car-Parrinello molecular dynamics simulations are reported for [UO2(NH3)5](2+) in the gas phase and in liquid NH3 solution (using the BLYP density functional). According to free-energy simulations, solvation by ammonia has only a small effect on the uranyl-NH3 bond strength.