Car-Parrinello Molecular Dynamics Trajectories Research Articles

Unraveling the Nature of Hydrogen Bonds of "Proton Sponges" Based on Car-Parrinello and Metadynamics Approaches.

The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as "proton sponges". Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted "proton sponge" served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car-Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in "proton sponges" are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces.

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, B97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm–1700 cm and 2300 cm–3400 cm in the gas phase and 600 cm–1800 cm and 2200 cm–3400 cm in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm–1700 cm and 2300 cm–3300 cm for the gas phase and one broad absorption region in the solid state between 700 cm and 3100 cm. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

Dynamical Rashba Band Splitting in Hybrid Perovskites Modeled by Local Electric Fields

We report a computational method for evaluating the dynamical Rashba interaction coefficient of tetragonal and cubic methylammonium lead iodide (MAPbI3) perovskite, at various size scales, through Car–Parrinello molecular dynamics trajectories. This strategy involves the calculation of a time-dependent band structure of the target systems using periodic boundary conditions and the evaluation of the amplitude of band-splitting due to the spin–orbit coupling (SOC) with the computation of a local electric field. This model, physically motivated by a rewriting of the SOC Hamiltonian according to the heterogeneity of three-dimensional systems and our choice of k-space sampling, involves directly the methylammonium configuration space sampling. Originally applied to tetragonal and cubic unit cells with static point-charges, this model is further ameliorated in order to take into account the replication of this unit cell through space and to account for the dynamical nature of charge distribution. Once our proto...

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).

Uranyl Carbonate Complexes in Aqueous Solution and Their Ligand NMR Chemical Shifts and 17O Quadrupolar Relaxation Studied by ab Initio Molecular Dynamics.

Dynamic structural effects, NMR ligand chemical shifts, and 17O NMR quadrupolar relaxation rates are investigated in the series of complexes UO22+, UO2(CO3)34-, and (UO2)3(CO3)66-. Car-Parrinello molecular dynamics (CPMD) is used to simulate the dynamics of the complexes in water. NMR properties are computed on clusters extracted from the CPMD trajectories. In the UO22+ complex, coordination at the uranium center by water molecules causes a decrease of around 300 ppm for the uranyl 17O chemical shift. The final value of this chemical shift is within 40 ppm of the experimental range. The UO2(CO3)34- and (UO2)3(CO3)66- complexes show a solvent dependence of the terminal carbonate 17O and 13C chemical shifts that is less pronounced than that for the uranyl oxygen atom. Corrections to the chemical shift from hybrid functionals and spin-orbit coupling improve the accuracy of chemical shifts if the sensitivity of the uranyl chemical shift to the uranyl bond length (estimated at 140 ppm per 0.1 Å from trajectory data) is taken into consideration. The experimentally reported trend in the two unique 13C chemical shifts is correctly reproduced for (UO2)3(CO3)66-. NMR relaxation rate data support large 17O peak widths, but remain below those noted in the experimental literature. Comparison of relaxation data for solvent-including versus solvent-free models suggest that carbonate ligand motion overshadows explicit solvent effects.

NMR J-Coupling Constants of Tl-Pt Bonded Metal Complexes in Aqueous Solution: Ab Initio Molecular Dynamics and Localized Orbital Analysis.

The influence of solvent (water) coordination and dynamics on the electronic structure and nuclear magnetic resonance (NMR) indirect spin-spin coupling (J-coupling) constants in a series of Tl-Pt bonded complexes is investigated using Kohn-Sham (KS) Car-Parrinello molecular dynamics (CPMD) and relativistic hybrid KS NMR calculations with and without coordination to water. Coordination of the Tl center by water molecules has a dramatic impact on 1J(Tl-Pt) and other J-coupling constants. It is shown that a previous computational study of the same complexes using static optimized structures and nonhybrid functionals was correct about the important role of the solvent but obtained reasonable agreement with experimental NMR data because of a cancellation of substantial errors. For example, the CPMD trajectories show that on average the inner coordination shell of Tl is not saturated, as previously assumed, which leads to poor agreement with experiment when the J-coupling constants are averaged over the CPMD trajectories using NMR calculations with nonhybrid functionals. The combination of CPMD with hybrid KS NMR calculations provides a much more realistic computational model that reproduces the large magnitudes of 1J(Tl-Pt) and the correct trends for other coupling constants. An analysis of 1J(Tl-Pt) in terms of localized orbitals shows that the presence of coordinating water molecules increases the capacity for covalent interactions between Tl and Pt. There is pronounced multicenter bonding along the metal-metal axis of the complexes.

Effect of Structural Dynamics on the Opto-Electronic Properties of Bare and Hydrated ZnS QDs

Quantum mechanical calculations on the structural and optoelectronic features of two realistic wurtzite-like ZnS quantum dot (QD) models, namely, (ZnS)33 and (ZnS)116, are presented both in vacuo and in an explicit water solution environment. Car–Parrinello molecular dynamics (CPMD) simulation and excited-state, Time-Dependent Density Functional Theory (DFT/TDDFT) calculations on extended models are combined to unravel hitherto inaccessible atomistic features of the investigated systems. Ultrasmall QDs are predicted to exhibit strong dynamical fluctuations. Accordingly, the bare (ZnS)33 model undergoes a drastic structural rearrangement and evolves from the starting bulk-like structure to an amorphous phase. The geometrical changes occurring over the time are reflected on the opto-electronic properties. The band-edge states and the optical absorption onset both sizably vary along the CPMD trajectory. Eventually, the optical gap decreases due to the emergence of high-lying occupied orbitals. These midgap s...

Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solu-tion: How Geometric Parameters Influence the Hydrogen Bond Strength

Chemometric statistical approaches involving multiple linear regression (MLR) and principal component analysis (PCA) were employed on a set of 42 distinct snapshot structures of the physiological histamine monocation in aqueous solution along the Car-Parrinello molecular dynamics trajectory, in order to obtain a better insight into the relationship between the geometry parameters of the system and the resulting νNH stretching frequencies. A simple 2D linear regression of νNH with Namino···Owater distances gave a very poor correlation (R2 = 0.42), but both MLR and PCA with the inclusion of four directly bonded water molecules offered a notably predictive model that is even able to distinguish two classes of structures based on the Cl- counterion position. Taking into account waters from the first, second and third solvation shells, sequentially diminished the overall predictive ability of the model, yet increased the number of useful predictors that, in the largest model with 51 solvent molecules, all correspond to bulk water, implying that both chemometric methods are consistent in suggesting that fundamental histamine N–H stretching vibrations are very complex in nature and strongly coupled to the fluctuating environment.

EXAFS Debye-Waller factors issued from Car-Parrinello molecular dynamics: Application to the fit of oxaliplatin and derivatives

One of the main pitfalls in EXAFS fitting is correlation among parameters, which can lead to unreliable fits. The use of theoretical Debye-Waller factors (DWs) is a promising way to reduce the number of fitted parameters. When working with molecular dynamics, it is not only possible to evaluate DWs from the statistical distributions issued from the trajectory but also to estimate the distribution anharmonicity, and to compute simulated average EXAFS spectra that can be fitted as experimental ones, in order to assess the ability of EXAFS fitting to recover information on DWs, as well as other structural and spectroscopical parameters. The case studied is oxaliplatin, a third generation anticancer drug. The structural information and the simulated average spectra were derived from a Car-Parrinello molecular dynamics (CP-MD) trajectory of a compound closely related to oxaliplatin. We present the DWs issued from this simulation and their use, by taking their theoretical absolute values (no DW fitted) or their ratios (one DW fitted). In this second approach, the fit of oxaliplatin experimental spectra leads to DWs values very close to the theoretical ones. This shows that the CP-MD trajectory provides a good representation of the distance distributions for oxaliplatin. Transferability of oxaliplatin DWs, for all relevant single and multiple scattering paths, to closely related compounds is proven for the case of bis(oxalato)platinum(II) and bis(ethylene diamine)platinum(II).

The initial stages of bioglass dissolution: a Car–Parrinello molecular-dynamics study of the glass–water interface

The initial dissolution stages following implantation of a biomaterial in a physiological environment are critical for its bioactive properties. Car–Parrinello molecular-dynamics (CPMD) simulations of the interface between the 45S5 bioglass surface and liquid water have been carried out to investigate these processes. The analysis of a 40 ps CPMD trajectory has highlighted the potential mechanism of Na + /H + exchange, leading to formation of surface silanols through water dissociation. Moreover, by comparing the properties of water layers arranged at different distances from the glass surface, we discuss the way in which the particular structure and composition of the bioglass surface affects the hydrogen-bond network and orientation of water in its close proximity.

Car–Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate

We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.

Ab initio static and molecular dynamics study of the absorption spectra of the 4-styrylpyridine photoswitch in its cis and trans forms

We report a thorough investigation of the absorption spectra of the cis and trans isomers of the 4-styrylpyridine photoswitch based on TDDFT calculations. The spectra of both isomers were analysed first from the results of excitation calculations performed on their optimised geometries. The main absorption band of the cis isomer is thus predicted to be due to the S(0)--> S(1) and S(0)--> S(2) transitions, while the main absorption band of the trans isomer is predicted to originate exclusively from the S(0)--> S(1) transition. The convolution of the calculated oscillator strengths with Gaussians helped mimic the broadening of the electronic transitions. However, it proved necessary to use Gaussians with a large full width at half maximum of 5000 cm(-1); and, compared to experiment, the calculated main absorption bands of the two isomers are significantly red-shifted and far too symmetric. Consequently, as required for the detailed analysis of the finite-temperature absorption spectrum of a molecule as flexible as 4-styrylpyridine, the influence of the thermal fluctuations has been taken into account by calculating the spectra as time averages over Car-Parrinello molecular dynamics trajectories. For both isomers, this led to a noticeable improvement in the relative positions of the calculated and experimental main absorption bands, and the asymmetry of the calculated bands brings them in better agreement with the experimental ones. Furthermore, these last results show that, actually, the S(0)--> S(1) and S(0)--> S(2) transitions both contribute significantly to the finite-temperature main absorption bands of the two isomers. Finally, in order to also take the vibrational broadening into account, the Franck-Condon factors of the relevant vibrations were calculated within the displaced harmonic oscillator approximation. By thus taking both the thermal and the vibrational broadening into account for the calculation of the absorption bands, the agreement between experiment and theory could be further improved.

Vibrational frequencies in Car–Parrinello molecular dynamics

Car-Parrinello molecular dynamics (CPMD) are widely used to investigate the dynamical properties of molecular systems. An important issue in such applications is the dependence of dynamical quantities such as molecular vibrational frequencies upon the fictitious orbital mass μ. Although it is known that the correct Born-Oppenheimer dynamics are recovered at zero μ, it is not clear how these dynamical quantities are to be rigorously extracted from CPMD calculations. Our work addresses this issue for vibrational frequencies. We show that when the system is sufficiently close to the ground state the calculated ionic vibrational frequencies are ω(M) = ω(0M)[1 -C(μ/M)] for small μ/M, where ω(0M) is the Born-Oppenheimer ionic frequency, M the ionic mass, and C a constant that depends upon the ion-orbital coupling force constants. Our analysis also provides a quantitative understanding of the orbital oscillation amplitudes, leading to a relationship between the adiabaticity of a system and the ion-orbital coupling constants. In particular, we show that there is a significant systematic dependence of calculated vibrational frequencies upon how close the CPMD trajectory is to the Born-Oppenheimer surface. We verify our analytical results with numerical simulations for N(2), Sn(2), and H/Si(100)-(2×1).

Modeling the Water−Bioglass Interface by Ab Initio Molecular Dynamics Simulations

The hydration of the surface of a highly bioactive silicate glass was modeled using ab initio (Car-Parrinello) molecular dynamics (CPMD) simulations, focusing on the structural and chemical modifications taking place at the glass-water interface immediately after contact and on the way in which they can affect the bioactivity of these materials. The adsorption of a water dimer and trimer on the dry surface was studied first, followed by the extended interface between the glass and liquid water. The CPMD trajectories provide atomistic insight into the initial stages relevant to the biological activity of these materials: following contact of the glass with an aqueous (physiological) medium, the initial enrichment of the surface region in Na+ cations establishes dominant Na+-water interactions at the surface, which allow water molecules to penetrate into the open glass network and start its partial dissolution. The model of a Na/H-exchanged interface shows that Ca2+-water interactions are mainly established after the dominant fraction of Na is leached into the solution. Another critical role of modifier cations was highlighted: they provide the Lewis acidity necessary to neutralize OH(-) produced by water dissociation and protonation of nonbridging oxygen (NBO) surface sites. The CPMD simulations also highlighted an alternative, proton-hopping mechanism by which the same process can take place in the liquid water film. The main features of the bioactive glass surface immediately after contact with an aqueous medium, as emerged from the simulations, are (a) silanol groups formed by either water dissociation at undercoordinated Si sites or direct protonation of NBOs, (b) OH(-) groups generally stabilized by modifier cations and coupled with the protonated NBOs, and (c) small rings, relatively stable and unopened even after exposure to liquid water. The possible role and effect of these sites in the bioactive process are discussed.

Molecular Properties Investigation of a Substituted Aromatic Mannich Base: Dynamic and Static Models

An analysis of the hydrogen bridge of a Mannich base-type compound [3,5,6-trimethyl-2(N,N-dimethylaminomethyl)phenol, TMM] was performed according to the Car-Parrinello molecular dynamics (CPMD) scheme. A classical treatment of nuclei coupled with a first-principle potential energy surface was obtained from molecular dynamics simulation. Dipole moment values were collected during CPMD trajectory acquisition and subsequently used for the data analysis. The vibrational features and the intramolecular hydrogen-bond properties in the gas phase and solid state of the TMM compound were analyzed on the basis of widely used approaches: Fourier transformation of the autocorrelation function of both the atomic velocities and dipole moments. In addition, the time evolution of the structural parameters related to the hydrogen bond was carried out. The optimally localized Wannier functions served to describe the electronic structure of the Mannich base studied. The second part of the TMM compound study was performed in vacuo on the basis of density functional theory and second-order Møller-Plesset perturbation theory. The potential energy functions were used to solve the 1-D vibrational Schroedinger equation for the proton motion. This enabled a prediction of the anharmonic vibrational levels of the intramolecular hydrogen bond. The description of the electron density topology of the TMM molecule was carried out using the atoms in molecules theoretical framework. The computational results were further compared with the infrared spectra in the solid state.

Nuclear magnetic shielding and quadrupole coupling tensors in liquid water: a combined molecular dynamics simulation and quantum chemical study.

Nuclear magnetic resonance (NMR) shielding tensors for the oxygen and hydrogen nuclei, as well as nuclear quadrupole coupling tensors for the oxygen and deuterium nuclei of water in the liquid and gaseous state, are calculated using Hartree-Fock and density functional theory methods, for snapshots sampled from Car-Parrinello molecular dynamics trajectories. Clusters representing local liquid structures and instantaneous configurations of a single molecule representing low-density gas are fed into a quantum chemical program for the calculation of the NMR tensors. The average isotropic and anisotropic tensorial properties of 400 samples in both states, averaged using a common Eckart coordinate frame, are calculated from the data. We report results for the gas-to-liquid chemical shifts of (17)O and (1)H nuclei, as well as the corresponding change in the nuclear quadrupole couplings of (17)O and (2)H. Full thermally averaged shielding and quadrupole coupling tensors are reported for the gaseous and liquid-state water, for the first time in the case of liquid. Electron correlation effects, the difference of classical vs quantum mechanical rovibrational averaging, and different methods of averaging anisotropic properties are discussed.

Ab initio molecular dynamics simulations and g-tensor calculations of aqueous benzosemiquinone radical anion: effects of regular and "T-stacked" hydrogen bonds.

Car-Parrinello molecular dynamics (CP-MD) simulations of the benzosemiquinone radical anion in aqueous solution have been performed at ambient conditions. Analysis of the trajectory shows not only extensive hydrogen bonding to the carbonyl oxygen atoms (ca. 4-5.6 water molecules depending on distance criteria), but also relatively long-lived "T-stacked" hydrogen bonds to the semiquinone pi-system. These results are discussed in the context of recent findings on semiquinone-protein interactions in photosynthetic reaction centers, and of EPR and vibration spectroscopical data for the aqueous system. Snapshots from the CP-MD trajectory are used for the first quantum chemical analyses of dynamical effects on electronic g-tensors, using cluster models and a recently developed density functional method. In particular, the effects of intermolecular hydrogen-bond dynamics on the g-tensor components are examined, in comparison with recent EPR and ENDOR studies.

Solvation Structure and Mobility Mechanism of OH-: A Car−Parrinello Molecular Dynamics Investigation of Alkaline Solutions

The hydroxide ion (OH-) has an unusually high mobility in water, comparable to that of the proton. However, a consensus view of the OH- mobility mechanism and its solvation structure has yet to emerge. In addition, X-ray and spectroscopic experiments reveal significant changes in the structural and dynamical properties of water in the presence of OH-. To gain insight into these questions, we have carried out Car−Parrinello molecular dynamics (CPMD) calculations for aqueous NaOH and KOH solutions under ambient conditions over a wide range of concentrations. These simulations are able to reproduce many puzzling phenomena, in particular, the loss of tetrahedral coordination of water (interpreted from a recent neutron diffraction with isotopic substitution experiment) and the appearance of new spectroscopic features at high concentrations. Furthermore, it is demonstrated that the observed behavior is a result of the formation of a variety of compact hydroxide−water complexes. The distribution of these complexes is dependent upon the concentration and the counterion. The present results reconcile conflicting structural interpretations from previous experimental and theoretical studies on hydroxide solutions. Analysis of the CPMD trajectories supports the view that the transport mechanism of the hydroxide ion is distinct from that of the proton.