Car-Parrinello Research Articles

High Li-ion conductivity in tetragonal LGPO: A comparative first-principles study against known LISICON and LGPS phases

We highlight fast Li-ion diffusion in hypothetical tetragonal ${\mathrm{Li}}_{10}{\mathrm{GeP}}_{2}{\mathrm{O}}_{12}$ (LGPO), as a counterpart to the well-known phases of orthorhombic (LISICON) LGPO, thio-LISICON, and tetragonal ${\mathrm{Li}}_{10}{\mathrm{GeP}}_{2}{\mathrm{S}}_{12}$ (LGPS). We use extended Car-Parrinello molecular dynamics in the canonical and isobaric-isothermal ensembles, finding first that tetragonal LGPO is dynamically stable, albeit 0.04 Ha/f.u. above LISICON LGPO. The calculated activation energy for Li-ion diffusion is 0.22 eV, well below the value calculated for LISICON LGPO (0.34 eV), and similar to those for thio-LISICON (0.23 eV) and tetragonal LGPS (0.18 eV). These results indicate that hypothetical tetragonal LGPO, although less stable than its orthorhombic allotrope, shows a room-temperature conductivity comparable to LGPS, and, if synthesized, could make a very attractive Li-ion conductor.

Modeling solvation effects on absorption and fluorescence spectra of indole in aqueous solution.

Modeling the optical spectra of molecules in solution presents a challenge, so it is important to understand which of the solvation effects (i.e., electrostatics, mutual polarization, and hydrogen bonding interactions between solute and solvent molecules) are crucial in reproducing the various features of the absorption and fluorescence spectra and to identify a sufficient theoretical model that accurately captures these effects with minimal computational cost. In this study, we use various implicit and explicit solvation models, such as molecular dynamics coupled with non-polarizable and polarizable force fields, as well as Car-Parrinello molecular dynamics, to model the absorption and fluorescence spectra of indole in aqueous solution. The excited states are computed using the equation of motion coupled cluster with single and double excitations combined with the effective fragment potential to represent water molecules, which we found to be a computationally efficient approach for modeling large solute-solvent clusters at a high level of quantum theory. We find that modeling mutual polarization, compared to other solvation effects, is a dominating factor for accurately reproducing the position of the peaks and spectral line shape of the absorption spectrum of indole in solution. We present an in-depth analysis of the influence that different solvation models have on the electronic excited states responsible for the features of the absorption spectra. Modeling fluorescence is more challenging since it is hard to reproduce even the correct emitting state, and force field parameters need to be re-evaluated.

Solvent effect on the 195Pt NMR properties in pyridonate-bridged PtIII dinuclear complex derivatives investigated by ab initio molecular dynamics and localized orbital analysis.

An ab initio molecular dynamics investigation of the solvent effect (water) on the structural parameters, 195Pt NMR spin-spin coupling constants (SSCCs) and chemical shifts of a series of pyridonate-bridged PtIII dinuclear complexes is performed using Kohn-Sham (KS) Car-Parrinello molecular dynamics (CPMD) and relativistic hybrid KS NMR calculations. The indirect solvent effect (via structural changes) has a dramatic effect on the 1JPtPt SSCCs. The complexes exhibit a strong trans influence in solution, where the Pt-Pt bond lengthens with increasing axial ligand σ-donor strength. In the diaqua complex, where the solvent effect is more pronounced, the SSCCs averaged for CPMD configurations with explicit plus implicit solvation agree much better with the experimental data, while the calculations for static geometry and CPMD unsolvated configurations show large deviations with respect to experiment. The combination of CPMD with hybrid KS NMR calculations provides a much more realistic computational model that reproduces the large magnitudes of 1JPtPt and 195Pt chemical shifts. An analysis of 1JPtPt in terms of localized and canonical orbitals shows that the SSCCs are driven by changes in the s-character of the natural atomic orbitals of Pt atoms, which affect the 'Fermi contact' mechanism.

Structure and solvation dynamics of the hydroxide ion in ice-like water clusters: a CCSD(T) and car-parrinello molecular dynamics study.

Using MP2, CCSD(T) electronic structure theory and ab initio molecular dynamics simulations, we explore the structure, solvation dynamics and vibrational spectra of OH-(H2O)n clusters. Our study reports new cubic and fused cubic global minima structures of OH-(H2O)n for n = 8-26 with surface and interior solvation arrangements. In the case of OH-(H2O)26, we show that MP2 and CCSD(T) calculations predict global minima structures with the hydroxide ion occupying the interior region of a densely packed cubic cluster that is secured by ionic hydrogen bonds. More importantly, results from ab initio molecular dynamics simulations of OH-(H2O)26 demonstrate that the hydroxide ion remains in the cluster interior and hexa-coordinated, irrespective of the temperature, up to around 175 K, then incrementally transitions from a surface-exposed penta- (170-200 K), to a tetra- (225 K) to a tri-coordinated OH-(H2O)3 structure at 300 K. Building on our temperature-dependent vibrational power spectra, we are also able to disentangle structure and temperature effects on individual spectral contributions arising from water molecules located in the inner and outer shell of OH-(H2O)26. Some of these theoretical results provide valuable guidance for the interpretation of IRMPD spectra of small hydroxide-water clusters, but there are also several intriguing implications of these results, in particular, for the solvation of the OH- ion at the surface of water nanodroplets and aqueous interfaces.

Deterministic quantum mechanics: The role of the Maxwell–Boltzmann distribution

AbstractTo be accepted by the community, the claim that nuclear motion has to be treated classically must be tested for all kinds of phenomena. For the moment we claim that in a quantum chemical calculation, a classical description of nuclear motion is superior to the use of the Schrödinger equation, and investigate how far we get with this statement. In the present paper we address the question what nuclear quantum statistics means in this context. We will show that the Maxwell–Boltzmann velocity distribution evolves quickly in any molecular dynamics simulation and this guarantees the physically correct behavior of molecular systems. Using first‐principles molecular dynamics simulations, or more precisely Car–Parrinello molecular dynamics, we investigate what this means for Bose‐Einstein condensates and for Cooper pairs. It turns out that our approach can explain all relevant phenomena. As a consequence, we can introduce a deterministic formulation of quantum mechanics and can get rid of all the paradoxa in traditional quantum mechanics. The basic idea is to treat electrons and nuclei differently.

Symmetry/Asymmetry of the NHN Hydrogen Bond in Protonated 1,8-Bis(dimethylamino)naphthalene

Experimental and theoretical results are presented based on vibrational spectra and motional dynamics of 1,8-bis(dimethylamino)naphthalene (DMAN) and its protonated forms (DMANH+ and the DMANH+ HSO4− complex). The studies of these compounds have been performed in the gas phase and solid-state. Spectroscopic investigations were carried out by infrared spectroscopy (IR), Raman, and incoherent inelastic neutron scattering (IINS) experimental methods. Density functional theory (DFT) and Car–Parrinello molecular dynamics (CPMD) methods were applied to support our experimental findings. The fundamental investigations of hydrogen bridge vibrations were accomplished on the basis of isotopic substitutions (NH → ND). Special attention was paid to the bridged proton dynamics in the DMANH+ complex, which was found to be affected by interactions with the HSO4− anion.

Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides

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.

Structural and quantitative analysis of water association in ethylammonium nitrate mixtures using soft modeling resolution of NIR spectra and molecular dynamics simulations

In this work we report on the structural and quantitative analysis of the water association in ethylammonium nitrate mixtures (EAN + H2O) using multivariate curve resolution based on alternate least squares (MCR-ALS) of Near Infrared (NIR) spectra and Car-Parrinello Molecular Dynamics (MD) simulations.MCR-ALS methodology was used to determine the concentration of the chemical species in the EAN + H2O mixtures, as well as the molar ratio between the coordinated EAN-H2O species. Measurements were performed over the entire range of IL mass fraction at three temperatures 298.15 K, 308.15 K and 318.15 K. The experimental results revealed the existence of three chemical environments, bulk water (H2O), neat ionic liquid (EAN), and solvated ionic liquid (EAN-H2O) in the mixtures. The hydration process of EAN was observed to be favorable for EAN mole fractions lower than 0.138.Car-Parrinello MD simulations were used to perform the structural analysis of selected mixtures. Simulations showed an increase of the water/EAN molar ratio in EAN-water complexes when the percentage of water in the mixtures was increased. In addition, they confirmed the reliability of previous classical MD simulations to analyze the interactions in the hydrogen-bonded network that is solvating EAN anions and cations.

Oxygen depletion in FLASH ultra-high-dose-rate radiotherapy: A molecular dynamics simulation.

We present a first-principles molecular dynamics (MD) simulation and expound upon a mechanism of oxygen depletion hypothesis to explain the mitigation of normal tissue injury observed in ultra-high-dose-rate (UHDR) FLASH radiotherapy. We simulated damage to a segment of DNA (also representing other biomolecules such as RNA and proteins) in a simulation box filled with O and molecules. Attoseconds physical interactions (ionizations, electronic, and vibrational excitations) were simulated by using the Monte Carlo track structure code Geant4-DNA. Immediately after ionization, ab initio Car-Parrinello molecular dynamics (CPMD) simulation was used to identify which O and molecules surrounding the DNA molecule were converted into reactive oxygen species (ROS). Subsequently, the femto- to nanosecond reactions of ROS were simulated by using MD with reactive force field (ReaxFF), to illustrate ROS merging into new types of non-reactive oxygen species (NROS) due to strong coupling among ROS. A coarse-grained model was constructed to describe the relevant collective phenomenon at the macroscopic level on ROS aggregation and formation of NROS agglomerates consistent with the underlying microscopic pathways obtained from MD simulations. Time-dependent molecular simulations revealed the formation of metastable and transient spaghetti-like complexes among ROS generated at UHDR. At the higher ROS densities produced under UHDR, stranded chains (i.e., NROS) are produced, mediated through attractive electric polarity forces, hydrogen bonds, and magnetic dipole-dipole interactions among hydroxyl radicals. NROS tend to be less mobile than cellular biomolecules as opposed to the isolated and sparsely dense ROS generated at conventional dose rates (CDR). We attribute this effect to the suppression of biomolecular damage induced per particle track. At a given oxygen level, as the dose rate increases, the size and number of NROS chains increase, and correspondingly the population of toxic ROS components decreases. Similarly, at a given high dose rate, as the oxygen level increases, so do the size and number of NROS chains until an optimum level of oxygen is reached. Beyond that level, the amount of oxygen present may be sufficient to saturate the production of NROS chains, thereby reversing the sparing effects of UHDRs. We showed that oxygen depletion, hypothesized to lead to lower normal-tissue toxicity at FLASH dose rates, takes place within femto- to nanoseconds after irradiation. The mechanism is governed by the slow dynamics of chains of ROS complexes (NROS). Under physoxic (≈ 4-5% oxygen) conditions (i.e., in normal tissues), NROS are more abundant than in hypoxic conditions (e.g., <0.3% in parts of tumors), suggesting that biomolecular damage would be reduced in an environment with physoxic oxygen levels. Hence irradiation at UHDRs would be more effective for sparing physoxic normal tissues but not tumors containing regions of hypoxia. At much higher levels of oxygen (e.g., >10-15%), oxygen depletion by UHDRs may not be sufficient for tissue sparing.

Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates.

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car–Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.

Estudo de Dinâmica Molecular da Reação do Intermediário Criegee CH2OO com o NO2 sob Efeito da Temperatura

Neste trabalho foram realizadas simulações computacionais da interação do intermediário Criegee CH2OO com o NO2, utilizando o modelo teórico da Dinâmica Molecular de Car-Parrinello, em temperaturas de 100 K, 300 K e 500 K. Através dos resultados obtidos, para as três temperaturas, foi possível observar a formação de novas moléculas. Os produtos são estáveis e diferentes, para cada temperatura, o que está diretamente associado ao efeito desta. Os comprimentos de ligação foram avaliados em termos do tempo médio de residência e demonstraram a formação das novas ligações.

Finite-temperature mechanical properties of nanostructures with first-principles accuracy

This article reports an original approach allowing to simulate the compression at finite temperature of nanostructures, based on the combination of external forces with Car-Parrinello molecular dynamics. An example of a successful application is described, the compression of buckminster-fullerene C60 at room temperature. It is shown that the C60 shell breaks at much lower strains than previously predicted, with a maximum contact force of 30 nN. This simple example demonstrates the potential of this approach, which can be especially useful to determine the mechanical properties of nanoparticles and clusters with an outstanding accuracy.

Hydration structure of As–III aqueous solutions from ab initio molecular dynamics simulations

A comprehensive study of aqueous arsenic acid (H3AsO3) and its deprotonated derivatives, namely H2AsO3− and HAsO32−, is carried out employing Car-Parrinello Molecular Dynamics (CPMD). Calculations are carried out with and without the incorporation of the dispersion correction, and critical comparison of its role on various structural and dynamical properties of the solute-solvent system are discussed. Aqueous H3AsO3 and H2AsO3− species solvated by 60 water molecules (which closely emulates normal pH conditions) are found to be stable, that is, without undergoing proton transfer with the solvent over the 50 ps of MD simulations performed. However, HAsO32− is found to be stable only in the basic media, emulated through the introduction of a hydroxyl ion (OH−) in lieu of one water molecule. The AsO33− species is not stable, and protonates quickly to HAsO32−, even under the basic environment of a hydroxyl ion (OH−) among 59 other water molecules simulated. Detailed analysis of the hydrogen bonding and vibrational spectra provide fresh microscopic insights on the hydration structure and dynamical characteristics of these species in aqueous environment. The spectroscopic insights derived, through comparison with their parent gas-phase species (H3AsO3), would be useful in the detection as well as quantification these species in various aqueous environments, for developing water remediation strategies of these environmentally hazardous species.

Some simple facts about water: CPMD simulation

The correct treatment of water and in particular liquid water is of central importance for the success of a quantum chemical method. The present study asks the question in how far the Car-Parrinello molecular dynamics method using the Becke-Lee-Yang-Parr functional is able to model liquid water. This question was asked before, but some recent publications contradict earlier work. The answer obtained in the present study supports a very conservative picture.

First-principles molecular dynamics investigation of ceria/silica sliding interface toward functional materials design for chemical mechanical polishing process

We report a form of chemical mechanical polishing (CMP) in which ceria abrasive particles polish a silicon wafer surface in a water environment. The Car-Parrinello molecular dynamics (CPMD) method, which enables chemical reaction dynamics in non-equilibrium systems to be treated non-empirically, was used. The first application of CPMD was to a model including a silica surface rubbed by a ceria cluster to ascertain the fundamental tribochemical phenomena in the CMP process. The model consisted of a hydrogen-terminated silica surface (a representative model of an oxidized wafer surface) and H4Ce6O12 cluster placed in the vicinity of an asperity in the silica surface. H2O molecules were explicitly considered in order to reflect the presence of slurry water. An external load and shear force were applied to the cluster. Under conditions of finite temperature and friction, a Ce-O-Si bridging bond formed at the interface between the silica surface and the ceria cluster. Subsequently, another Ce-O-Si bridging bond formed. These newly formed bridging bonds changed the silicon atom into a five-coordinated one. Because this state was probably unstable, a pyramid structure was rapidly restored by breaking the original Si-O bond in the asperity, meaning that the wafer surface became flattened. By referring to static density functional theory (DFT) calculations, we concluded that this bond dissociation event was due to multiple Ce-O-Si bonds forming. To discuss the effect of slurry water, a similar CPMD simulation, but without H2O molecules (i.e., dry friction), was performed. Here, the Si-O bond dissociation reaction did not take place even if multiple Ce-O-Si bonds formed. This means slurry water is needed for CMP to occur and it probably helps to weaken the Si-O bond. The second application of CPMD was to a model consisting of a thin water layer sandwiched between silica and ceria plates for studying the effect of the surface orientation of the ceria. Two low-index CeO2 surfaces, (100) and (111), were modeled. A chemical event wherein Ce-O-Si bridging bonds formed on the ceria/silica interface could be observed in both models. However, the bond dissociation reaction of the original Si-O bond on the silica surface proceeded only in the model with the (111) surface, and not on the (100) surface. This difference in reactivity could mainly be explained by the arrangement of atoms of each surface. The (111) surface provides hexagonal adsorption sites that inherently form a structure with five-coordinated silicon atoms, which are important intermediates in the CMP process. On the other hand, the (100) surface exhibits square adsorption sites which hardly form the required intermediate. We successfully examined the effect of the surface orientation of the ceria in addition to the fundamental CMP mechanism wherein multiple Ce-O-Si bonds initiate a chemical reaction including Si-O bond scission.

Ab Initio Molecular Dynamics Simulations of Aqueous Glucosamine Solutions: Solvation Structure and Mechanism of Proton Transfer from Water to Amino Group

Glucosamine is a component of many cellular glycoproteins that constitutes the cartilage, and it has several biological activities, such as anti-inflammatory, antioxidant, antifibrotic, and anticancer, and has been used in arthritis and dermatological treatments. Considering that the biological activities of glucosamine occur mainly in an aqueous environment, it is essential to understand the effects of an aqueous solvent on its geometric and electronic parameters using ab initio molecular dynamics. The Car-Parrinello molecular dynamics results show that the hydroxyl groups form stable hydrogen bonds with the water molecules with intensities ranging from weak (closed-shell interaction) to intermediate (partially covalent interactions). The H bonds formed between the amino group and the water molecule range from weak (closed-shell) to strong (covalent), and it shows an infinity residence time. The natural bonding orbital (NBO) approach was applied to analyze the effects of charge-transfer interactions on the behavior of the hydrogen bonds. The main contribution to stabilizing energies comes from n → σ* hyperconjugation and explains the stability of the H bonds. The energy barrier for the proton transfer from water to the amino group is 0.88 kcal/mol, and the van der Waals complex energy is 0.3 kcal/mol. The low protonation energy barrier shows that glucosamine can be protonated in an aqueous environment at room temperature, which helps to explain many of its biological activities.

Conformational diversity of the THF molecule in N2 matrix by means of FTIR matrix isolation experiment and Car-Parrinello molecular dynamics simulations.

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.

Synthesis, crystal structure and molecular modeling of a novel Chalcone-Quinolone Hybrid

Chalcones and their analogues have been found in nature or synthesized, and several biological activities have been reported to this class of compounds. A comprehensive study on molecular modeling and structural description were performed for a new chalcone-quinolinone hybrid 1-Benzenesulfonyl-3-(4-bromo-benzylidene)-2-(2-ethoxy-phenyl)-2,3-dihydro-1H-quinolin-4-one (CQH) in order to get a better understanding about its supramolecular arrangement and physicochemical properties. Moreover, the crystal structure, molecular interactions and supramolecular arrangement were described by X-ray diffraction with the contribution of Hirshfeld surfaces, and topological analysis to observed molecular interactions was performed by Quantum Theory of Atoms in Molecules (QTAIM). Finally, the electronic study for differences between the solid and gas phases was carried out by Car-Parrinello Molecular Dynamics (CPMD) using Density Functional Theory (DFT).

Ab Initio Molecular Dynamics Investigation of Beryllium Complexes.

Structures of aqueous [Be(H2O)4]2+, its outer-sphere and inner-sphere complexes with F-, Cl-, and SO42-, and dinuclear complexes with a [Be2(κ-OH)(κ-SO4)]+ core have been studied through Car-Parrinello molecular dynamics (CPMD) simulations with the BLYP functional. According to constrained CPMD/BLYP simulations and pointwise thermodynamic integration, the free energy of deprotonation of [Be(H2O)4]2+ and its binding free energy with F- are 9.6 and -6.2 kcal/mol, respectively, in good accord with available experimental data. The computed activation barriers for replacing a water ligand in [Be(H2O)4]2+ with F- and SO42-, 10.9 and 13.6 kcal/mol, respectively, are also in good qualitative agreement with available experimental data. These ligand-substitution reactions are indicated to follow associative interchange mechanisms with backside (SN2-like) attack of the anion relative to the aquo ligand it is displacing. Outperforming static density functional theory computations of the salient kinetic and thermodynamic quantities involving simple polarizable continuum solvent models, CPMD simulations are validated as a promising tool for studying the structures and speciation of beryllium complexes in aqueous solution.

Theoretical study of intramolecular hydrogen bond in selected symmetric "proton sponges" on the basis of DFT and CPMD methods.

"Proton sponges," derivatives of prototypic 1,8-bis(dimethylamino)naphthalene (DMAN), exhibit remarkable basicity, which made them interesting for various experimental and theoretical studies. The details of bridged proton dynamics in protonated DMAN and its derivative denoted as TMGN (1,8-bis(tetramethylguanidino)naphthalene) were investigated on the basis of density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) methods. Special attention was paid to the effects of symmetry of the molecular skeleton and the type of substituent on the bridged proton neighborhood statistics and dynamics. The metric parameter analyses of hydrogen bridge provided us with a conclusion that proton migration events in TMGNH+ are less numerous than in DMANH+, which can be rationalized by noticing the slower dynamics of large substituents of TMGN with respect to the smaller -N(Me)2 groups of DMAN. The atomic velocity power spectra served as computational models of the vibrational signatures associated with the presence of the intramolecular hydrogen bond. A broad feature was registered for hydrogen bonds present in both compounds. The computations were verified by experimental data available.