Static Density Functional Theory Calculations Research Articles

The combined inelastic neutron scattering and solid state DFT study of hydrogen atoms dynamics in a highly ordered kaolinite

The dynamics of the hydrogen atoms in the highly ordered kaolinite was studied by vibrational spectroscopy based on inelastic neutron scattering method with the focus on the spectral region of 100–1,250 cm−1. The experimental spectrum was interpreted by means of the solid state density functional theory calculations covering both normal mode analysis and molecular dynamics going beyond the harmonic approximation. The Al–O–H bending modes were found to be spread over the large interval of 100–1,100 cm−1, with the dominant contributions located between 800 and 1,100 cm-1. The shapes of the individual hydrogen spectra depend on the strengths of the individual interlayer O–H···O hydrogen bonds involving the inner surface hydroxyl groups. The modes assigned to the in-plane movements of the respective hydrogen atoms are well-defined and always appear on the top of the intervals of energy transfer. In contrast, the modes generated by the out-of-plane movements are spread over large intervals of energies spanning down to the region of external (lattice) modes.

Hydrolysis of cisplatin—a first-principles metadynamics study

Cisplatin, or cis-[Pt(NH(3))(2)Cl(2)], was the first member of a new revolutionary class of anticancer drugs that is still used today for the treatment of a wide variety of cancers. The mode of action of cisplatin starts inside the cell with the hydrolysis of Pt-Cl bonds to form a Pt-aqua complex. The solvent environment plays an essential role in many biochemical processes in general, and is expected to have a particular strong effect on the activation (hydrolysis) of cisplatin and cisplatin derivatives. To investigate these solvent effects, we have studied the explicit solvent structures during cisplatin hydrolysis by means of Car-Parrinello molecular dynamics simulations. Since hydrolysis is an activated process, and thus a rare event on the simulation timescale, we have applied the metadynamics sampling technique to map out the free energy landscape from which the reaction mechanism and activation free energy are obtained. Our simulations show that hydrogen bonding between solvent water molecules and metal complexes in the hydrolyzed product systems is stronger than that in the reactant cisplatin system. In addition, the free energy profiles from our metadynamics simulations for the cisplatin hydrolysis shows that the second hydrolysis of cisplatin is thermodynamically favourable, which is in good agreement with experimental results and previous static density functional theory calculations. The reactant channels for both hydrolysis steps are rather wide and flat, indicative of a continuous spectrum of allowed mechanisms with no strong preference for either concerted dissociative or concerted associative pathways. Three or five coordinated metastable intermediates do not exist in aqueous solution.

Electron-hole spectra created by adsorption on metals from density functional theory

Nonadiabaticity in adsorption on metal surfaces gives rise to a number of measurable effects such as chemicurrents and exoelectron emission. Here we present a quantitative theory of chemicurrents on the basis of ground-state density functional theory (DFT) calculations of the effective electronic potential and the Kohn-Sham band structure. Excitation probabilities are calculated both for electron-hole pairs and for electrons and holes separately from first-order time-dependent perturbation theory. This is accomplished by evaluating the matrix elements (between Kohn-Sham states) of the rate of change of the effective electronic potential between subsequent (static) DFT calculations. Our approach is related to the theory of electronic friction, but allows for direct access to the excitation spectra. The method is applied to adsorption of atomic hydrogen isotopes on the Al(111) surface. The results are compatible with the available experimental data (for noble metal surfaces); in particular, the observed isotope effect in H versus D adsorption is described by the present theory. Moreover, the results are in qualitative agreement with computationally elaborate calculations of the full dynamics within time-dependent density functional theory, with the notable exception of effects due to the spin dynamics. Being a perturbational approach, the method proposed here is simple enough to be applied to a wide class of adsorbates and surfaces, while at the same time allowing us to extract system-specific information.

Crystal structure and phonon instability of high-temperatureβ-Ca(BH4)2

$\text{Ca}{({\text{BH}}_{4})}_{2}$ is an interesting candidate for high-density hydrogen storage since it contains a large amount of hydrogen by weight and volume, and has been shown to reversibly release and absorb hydrogen, albeit at moderately high temperatures. $\text{Ca}{({\text{BH}}_{4})}_{2}$ undergoes a polymorphic transformation around 400--440 K from a low-temperature $\ensuremath{\alpha}\text{-Ca}{({\text{BH}}_{4})}_{2}$ phase to a high-temperature $\ensuremath{\beta}\text{-Ca}{({\text{BH}}_{4})}_{2}$ phase. The crystal structure of $\ensuremath{\beta}\text{-Ca}{({\text{BH}}_{4})}_{2}$ has only recently been resolved, and its thermodynamic phase stability is still not well understood. Using a combined experimental and theoretical approach, we have independently determined the structure of $\ensuremath{\beta}\text{-Ca}{({\text{BH}}_{4})}_{2}$ and assessed its thermodynamic stability in the quasiharmonic approximation. The space-group $P{4}_{2}/m$ gives an excellent agreement between experiment and theory, confirming the result of a recent study [Buchter et al., J. Phys. Chem. B 112, 8042 (2008)]. Using density-functional theory (DFT), we obtained a value of 10.9 kJ/mol for the static total-energy difference between the $\ensuremath{\beta}\text{-Ca}{({\text{BH}}_{4})}_{2}$ and the $\ensuremath{\alpha}\text{-Ca}{({\text{BH}}_{4})}_{2}$ phases at $T=0\text{ }\text{K}$ (without vibrations). Using DFT linear-response calculations, we find that the $[\frac{1}{2}\frac{1}{2}\ensuremath{\xi}]$ acoustic phonon branch of $\ensuremath{\beta}\text{-Ca}{({\text{BH}}_{4})}_{2}$ is dynamically unstable on the Brillouin-zone boundary at the $T=0\text{ }\text{K}$ lattice parameters predicted from static DFT calculations. This phonon branch is very sensitive to the lattice parameters and can be stabilized by including lattice expansion due to zero-point vibrational contributions in the quasiharmonic approximation. This expanded stable $\ensuremath{\beta}\text{-Ca}{({\text{BH}}_{4})}_{2}$ structure has a room-temperature vibrational entropy that is $16\text{ }\text{J}/\text{mol}\text{ }\text{K}$ higher than that of the $\ensuremath{\alpha}\text{-Ca}{({\text{BH}}_{4})}_{2}$ phase, qualitatively consistent with the observed stabilization of the former at elevated temperatures. The main contribution to the entropy difference between the $\ensuremath{\alpha}\text{-Ca}{({\text{BH}}_{4})}_{2}$ and $\ensuremath{\beta}\text{-Ca}{({\text{BH}}_{4})}_{2}$ phases comes from the low-frequency region dominated by translational and rotational phonon modes.

Insights into the chemical behavior of zinc dialkyldithiophosphate anti-wear additives in their isomeric and decomposed forms through molecular simulation

Ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory have been applied to study zinc dialkyldithiophosphate (ZDDP) engine oil anti-wear additives in their parent, isomeric and decomposed forms to identify differences in the basic finite temperature chemical behavior of these species that may be related to the formation of ZDDP anti-wear films. It was found that the isomers, which contain Zn–O bonds, exhibited finite temperature behavior leading to the dissociation of these bonds, while the parent ZDDP molecule, which contains only Zn–S bonds, did not. The dissociation of the Zn–O bonds improves the abilities of these molecules to participate in film formation reactions as electron donors and hence the transformation of the ZDDP molecule into species with Zn–O bonds, such as the isomers and decomposed species, may aid in anti-wear film formation. It was observed that the dissociation of the Zn–O bonds allowed the molecules to attain rearranged structures where the coordination at the zinc atom had significantly changed and it was found that these rearranged structures could decompose through the elimination of metathiophosphates (MTPs). The results of static density functional theory calculations on all species indicated that the elimination of MTPs was energetically favorable at high temperatures, however, the ability of the parent molecule to participate in rearrangement determines whether decomposition will occur. The fact that these species readily participate in reactions that lead to MTP formation is relevant within the context of ZDDP anti-wear film formation since the MTP molecules possess properties that make them ideal precursors to the thiophosphate networks that are thought to comprise these films. Overall, the results of this study indicate that differences between the ZDDP molecule, its isomers and decomposition products exist that may affect the abilities of these species to participate in the formation of anti-wear films. This information will be useful within the development of an overall mechanism for the formation of ZDDP anti-wear films.

Intramolecular SN2 Reaction Caused by Photoionization of Benzene Chloride−NH3 Complex: Direct ab Initio Molecular Dynamics Study

Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

AbstractThe decomposition reaction dynamics of 2,3,4,4′,5‐penta‐chlorinated biphenyl (2,3,4,4′,5‐PeCB), 3,3′,4,4′,5‐penta‐chlorinated biphenyl (3,3′,4,4′,5‐PeCB), and 2,3,7,8‐tetra‐chlorinated dibenzo‐p‐dioxin (2,3,7,8‐TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first‐principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first‐principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4′,5‐PeCB, 3,3′,4,4′,5‐PeCB, and 2,3,7,8‐TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

A scaled quantum mechanical force field and vibrational analysis for the gamma glycine crystal polymorph: Hydrogen bond stretching modes observed

A scaled quantum mechanical force field has been obtained from periodic solid state density functional theory calculations on the glycine crystal γ polymorph unit cell at the DNP/GGA/PBE level. The assignments here differ in some respects from those obtained earlier, primarily where a broad weak band observed in both Raman and IR spectra at 285 cm −1, previously assigned to an overtone of a lattice mode, is assigned here as a mix of Hydrogen bond stretching and CC torsion. The standard deviation of the error between experimentally observed and calculated frequencies, for calculations performed on both the optimized and neutron diffraction crystal structures, is 6 cm −1 for a total of 118 vibrational modes.

Simulations of the azimuthal distribution of low-energy H atoms scattered off Ag( [formula omitted]) at grazing incidence: DFT many-body versus model pair potentials

We compare the azimuthal distribution of H atoms after scattering off Ag(1 1 0) obtained by molecular dynamics with different H–Ag(1 1 0) potential energy surfaces (PES) and experimental results. We use grazing incident H atoms and low energies (up to 4 keV). Density functional theory (DFT) calculations are performed for the static case of an H atom in front of an Ag(1 1 0) surface. The surface is represented by an 8-atom slab, and the H atoms form 1×1 and 2×2 supercells. The generalized gradient approximation is used. Classical trajectories are evaluated on the obtained PES, and the azimuthal distribution of the scattered atoms is calculated. Good agreement with experiment is obtained which gives us some confidence in the correct description of the system at low energies by the static DFT calculations. These results are also compared with pair-potential calculations. The accuracy of trajectories may be important for the correct evaluation of charge transfer, energy loss and straggling during ion–surface collisions.

Ab initio simulation of molecular processes on oxide surfaces

Ab initio calculations based on both density functional theory (DFT) and Hartree–Fock (HF) methods are used to investigate the energetics and equilibrium structure of the stoichiometric and reduced TiO2 (110) surface, the adsorption of potassium on the (100) surface and of water on the (110) surface. It is shown that DFT and HF predictions of the relaxed ionic positions at the stoichiometric surface agree well with each other and fairly well with recent X-ray diffraction measurements. The inclusion of spin polarisation is shown to have a major effect on the energetics of the reduced surface formed by removal of bridging oxygens. The gap states observed to be induced by reduction are not reproduced unless spin polarisation is included. Static and dynamic DFT calculations on adsorbed water on TiO2 (110) confirm that dissociation of H2O leads to stabilisation at low coverages, but suggest a more complex picture at monolayer coverage, in which there is a rather delicate balance between molecular and dissociated geometries.

Application of time-dependent density functional response theory to Raman scattering

Recently, the first density functional theory (DFT) calculations on Raman intensities and depolarisation ratios were published. Those calculations were done in the static approximation. Here, we use time-dependent DFT in order to include the dependence of those properties on the frequency of the exciting light wave. By analytically calculating the frequency-dependent polarisability at different nuclear positions, our approach is closer to a fully analytic one than the previous DFT studies. Our results for five diatomics improve upon previous TDHF and SOPPA ab initio results and show that the frequency dependence cannot be ignored in quantitative comparisons to experiment. Our results for the important Q-branch differential Raman cross section of N 2 are closer to the experimental value than previous results. Inclusion of the frequency dependence has little effect on the depolarisation ratios, but improves the results for the cross sections obtained in static DFT calculations. Our results obtained with three different exchange-correlation potentials yield similar results.