Car-Parinello Molecular Dynamics Research Articles

Searching for Stable SinCn Clusters: Combination of Stochastic Potential Surface Search and Pseudopotential Plane-Wave Car-Parinello Simulated Annealing Simulations

To find low energy SinCn structures out of hundreds to thousands of isomers we have developed a general method to search for stable isomeric structures that combines Stochastic Potential Surface Search and Pseudopotential Plane-Wave Density Functional Theory Car-Parinello Molecular Dynamics simulated annealing (PSPW-CPMD-SA). We enhanced the Sunders stochastic search method to generate random cluster structures used as seed structures for PSPW-CPMD-SA simulations. This method ensures that each SA simulation samples a different potential surface region to find the regional minimum structure. By iterations of this automated, parallel process on a high performance computer we located hundreds to more than a thousand stable isomers for each SinCn cluster. Among these, five to 10 of the lowest energy isomers were further optimized using B3LYP/cc-pVTZ method. We applied this method to SinCn (n = 4–12) clusters and found the lowest energy structures, most not previously reported. By analyzing the bonding patterns of low energy structures of each SinCn cluster, we observed that carbon segregations tend to form condensed conjugated rings while Si connects to unsaturated bonds at the periphery of the carbon segregation as single atoms or clusters when n is small and when n is large a silicon network spans over the carbon segregation region.

Analysis of Infrared Spectra of Neat Liquid N-Methylpyrrole

The vibrational properties of neat liquid N-methylpyrrole were investigated. Quantitative near-infrared and mid-infrared spectra recordings including thin lm MIR transmission studies were performed. Basing on these data the optical constants of N-methylpyrrole in the 12500 560 cm−1 region were determined. The experiment was supported by an anharmonic analysis based on Moller Plesset perturbation theory and density functional theory level of theory, including the hybrid B2PLYP functional. Assignments of numerous bands observed in the liquid phase were proposed basing on potential energy distribution calculations and a comparison of experimental and simulated spectra was presented. The inaccuracy of static calculations in the reproduction of experimental spectrum in the C H stretching region has been observed and explained by the rotation of methyl group. A vibrational spectrum was therefore calculated by the use of Car Parinello molecular dynamics method for a better simulation of experimental spectrum. DOI: 10.12693/APhysPolA.124.115 PACS: 78.20.Bh, 78.20.Ci, 78.30.cb

Hydrogen bond lifetime for water in classic and quantum molecular dynamics

The lifetime of hydrogen bonds in water at T = 298 K and p = 0.1 MPa is computed by means of classic molecular dynamics with eight different potentials of pair lifetime interaction and Car-Parinello molecular dynamics. The results obtained using various computational techniques for hydrogen bond life-times are compared. It is shown that they can differ from one another by several times. The dependence for the hydrogen bond lifetime computed in our numerical experiment upon the method of its determination is found.

First-principles studies of the vibrational properties of amorphous carbon nitrides

Raman spectra of amorphous carbon nitride films (a-C:N) resemble those of typical amorphous carbon (a-C), and no specific features in the spectra are shown due to N doping. The present work provides a correlation between the microstructure and vibrational properties of a-C:N films from first principles. The six periodic model structures of 64 atoms with various mass densities and nitrogen contents are generated by the liquid-quench method using Car—Parinello molecular dynamics. By using Raman coupling tensors calculated with the finite electric field method, Raman spectra are obtained. The calculated results show that the vibrations of C=N could directly contribute to the Raman spectrum. The similarity of the Raman line shapes of N-doped and N-free amorphous carbons is due to the overlapping of C=N and C=C vibration bands. In addition, the origin of characteristic Raman peaks is also given.

The rotation of NO3−as a probe of molecular ion - water interactions

The hydration dynamics of aqueous nitrate, NO3 − (aq), is studied by 2D-IR spectroscopy, UV-IR- and UV-UV transient absorption spectroscopy. The experimental results are compared to Car-Parinello molecular dynamics (MD) simulations. The 2D-IR measurements and MD simulations of the non-degenerate asymmetric stretch vibrations of nitrate reveal an intermodal energy exchange occurring on a 0.2 ps time scale related to hydrogen bond fluctuations. The transient absorption measurements find that the nitrate ions rotate in 2 ps. The MD simulations indicate that the ion rotation is associated with the formation of new hydrogen bonds. The 2 ps rotation time thus indicates that the hydration shell of aqueous nitrate is rather labile.

Car-Parinello molecular dynamics simulations of thionitroxide and S-nitrosothiol in the gas phase, methanol, and water—A theoretical study of S-nitrosylation

A dilemma about whether thionitroxide radical (RSNHO) or S-nitrosothiol (RSNO) is observed in protein S-nitrosylation has arisen recently. To illustrate the effect of chemical environment on these structures, this paper presents quantum mechanical molecular dynamics of thionitroxide, and cis- and trans-S-nitrosothiols in the gas phase, methanol, and water. By using Car-Parrinello molecular dynamics (CPMD), we have observed that there is free rotation about the S-N bond at 300 K in thionitroxide, but no such rotation is observed for S-nitrosothiol. The C-S-N-O torsion angle distribution in thionitroxide is significantly dependent upon the surrounding environment, leading to either gauche-, cis-, or trans-conformation. In the case of S-nitrosothiol the C-S-N-O plane is twisted slightly by 5°–15° in the cis-isomer, while the periplanar structure is well-retained in the trans-isomer. The calculated results are in agreement with the X-ray crystallographic data of small molecular RSNO species. Interestingly, for both compounds, the CPMD simulations show that solvation can cause a decrease in the S-N bond length. Moreover, the oxygen atom of thionitroxide is found to be a good hydrogen-bond acceptor, forming an oxyanionhole-like hydrogen bonding network.

Classical Reactive Molecular Dynamics Implementations: State of the Art

Reactive molecular dynamics (RMD) implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein. We subdivide the RMD approaches developed during the last decade as well as older ones already reviewed in 1995 by Srivastava and Garrison and in 2000 by Brenner into two classes. The methods in the first RMD class rely on the use of a reaction cutoff distance and employ a sudden transition from the educts to the products. Due to their simplicity these methods are well suited to generate equilibrated atomistic or material-specific coarse-grained polymer structures. In connection with generic models they offer useful qualitative insight into polymerization reactions. The methods in the second RMD class are based on empirical reactive force fields and implement a smooth and continuous transition from the educts to the products. In this RMD class, the reactive potentials are based on many-body or bond-order force fields as well as on empirical standard force fields, such as CHARMM, AMBER or MM3 that are modified to become reactive. The aim with the more sophisticated implementations of the second RMD class is the investigation of the reaction kinetics and mechanisms as well as the evaluation of transition state geometries. Pure or hybrid ab initio, density functional, semi-empirical, molecular mechanics, and Monte Carlo methods for which no time evolution of the chemical systems is achieved are excluded from the present review. So are molecular dynamics techniques coupled with quantum chemical methods for the treatment of the reactive regions, such as Car-Parinello molecular dynamics.

Structural and Optical Properties of Oxygenated Silicon Quantum Dots

Silicon quantum dots of size as small as 1 nm in diameter were prepared by wet chemical route. These clusters are found to be covered with oxygen and hydrocarbon molecules. The optical measurements reveal strong absorption around 4.67 eV and weak absorption at lower energies. The clusters show a broad luminescence around 3.87 eV. These quantum dots are modeled using ab-initio Car Parinello Molecular Dynamics and computational studies explain the absorption spectrum of the clusters over observed energy range. In principle, these quantum dots can be useful as scintillating layer on crystalline silicon solar cells to enhance the photovoltaic efficiency.

Study of the atomic and electronic structures of amorphous silicon nitride and defects in it

The structure of amorphous silicon nitride obtained by cooling from a melt has been simulated by Car-Parinello molecular dynamics. Several types of Si-Si defect coordination have been revealed. It has been found that, in addition to normal Si-Si bonds, numerous double Si-Si bonds (Si-Si-Si defects) are present in the amorphous structure.

First-principles calculation of vibrational Raman spectra of tetrahedral amorphous carbon

The nonresonant vibrational Raman spectra of tetrahedral amorphous carbon are calculated from first principles. The structural model was generated using Car–Parinello molecular dynamics, the vibrational modes are determined using the linear response approach and Raman tensors are calculated using the finite electric field method. Our theoretical visible and reduced Raman spectra show an overall good agreement with experimental spectra, and better than previous calculated results. The analysis in terms of atomic vibrations shows that the Raman spectrum mainly comes from sp 2 contribution, G peak is due to the stretching vibration of any pair of sp 2 atoms and only a small sp 3 contribution can be noticed. The differences between peak intensities of reduced theoretical and experimental results mainly come from defects and the high sp 3 content in our simulated structure.

OD vibrations and hydration structure in an Al3+(aq) solution from a Car-Parrinello molecular-dynamics simulation

The optimized geometry, energetics, and vibrational properties of Al(D2O)n3+ clusters, with n = 1,2,4, and 6, have been studied using plane waves, different local basis sets, different methodologies [density-functional theory, MP2, CCSD(T)], and different functionals (BLYP, PBE). Moreover, Car-Parrinello molecular-dynamics (MD) simulations using the BLYP functional, plane waves, and the Vanderbilt ultrasoft pseudopotentials have been performed for an aqueous Al3+ solution with 1 ion and 32 D2O molecules in a periodic box at room temperature, studied for 10 ps. The cluster calculations were performed to pinpoint possible shortcomings of the electronic structure description used in the Car-Parinello MD (CPMD) simulation. For the clusters, the hydration structure and interaction energies calculated with the 'BLYP/plane-wave' approach agree well with high-level ab initio methods but the exchange-correlation functional introduces errors in the OD stretching frequencies (both in the absolute values and in the ion-induced shifts). For the aqueous solution, the CPMD simulation yields structural properties in good agreement with experimental data. The CPMD-simulated OD stretching vibrational band for the first-shell water molecules around Al3+ is strongly downshifted by the influence of the ion and is compared with experimental data from the literature. To make such a comparison meaningful, the influences of a number of systematic effects have been addressed, such as the exchange-correlation functional, the fictitious electron mass, anharmonicity effects, and the small box size in the simulation. Each of these factors (except the last one) is found to affect the OD frequency by 100 cm(-1) or more. The final "corrected" frequencies agree with experiment within approximately 30 cm(-1) for bulk water but are too little downshifted for the first-shell Al3+ (aq) water molecules (by approximately 200 cm(-1)).

Specific features of band structure in large-sized Si2−xCx (1.04 ≤ x < 1.10) nanocrystallites

The band structure of large-sized (20–35 nm) nanocrystallites (NCs) of Si2−xCx (1.04 < x < 1.10) has been investigated using different band energy approaches and a modified Car–Parinello molecular dynamics structure optimization of the NC interfaces. The excess of carbon favours the appearance of a thin prevailingly carbon-contained layer (with thickness of about 1 nm) covering the crystallites. As a consequence we observe a substantial structural reconstruction of near-the-interface SiC crystalline layers. Optical absorption spectra of the investigated sheets were performed. The numerical modelling shows that these NCs can be considered as SiC reconstructed crystalline films with a thickness of about 2 nm covering the SiC crystallites. The observed data are considered within different one-electron band structure methods. It was shown that the carbon sheet plays a key role in the modified band structure. The independent manifestation of the important role played by the reconstructed confined layers is due to the experimentally discovered excitonic-like resonances. Low-temperature absorption measurements confirm the existence of sharp-like absorption resonances originating from the reconstructed layers.

Linear Electro-Optics Effect in ZnO-F Film-Glass Interface

We have discovered large linear electro-optics (Pockels) effect in ZnO crystalline films doped with fluorine and deposited on bare glass. A complex approach including self-consistent band structure calculations together with a Car-Parinello molecular dynamics simulation of the film–glass interface structure was used. The non-centrosymmetric charge density distribution between the ZnO–F wurtzite-like crystalline films and the bare glass substrate causes the observed Pockels effect.

The Role of the Interfaces in the Optical Effects of Large-Sized SiCxO1-xN Nanocrystallites

ABSTRACTThe band energy structure of large-sized (10-25) nm nanocrystallites (NC) of SiCxO1-xN (0.96&lt;x&gt;1.06) was investigated using different band energy approaches, as well as modified Car Parinello molecular dynamics simulations of interfaces. A thin carbon sheet (of about 1e nm) appears, covering the crystallites. This sheet leads to substantial reconstruction of the near-the-interface SiCxO1-xN crystalline layers. Numerical modeling shows that these NC may be treated as quantum dot-like SiCxO1-xN reconstructed crystalline surfaces, covering the appropriate crystallites. All band energy calculation approaches (semi-empirical pseudopotential, fully augmented plane waves and norm-conserving self-consistent pseudopotential approaches) predicted the experimental spectroscopic data. In particular, it was shown that the near-the-surface carbon sheet plays a dominant role in the behavior of the reconstructed band energy structure. Independent evidence for the important role of the dot-like crystalline layers are the excitonic-like states, which are not dependent on the particular structure of the SiC, but are sensitive to the thickness of the carbon layer.

The role of the interfaces in the optical effects of large-sized SiCxO1-xN nanocrystallites

ABSTRACTThe band energy structure of large-sized (10-25) nm nanocrystallites (NC) of SiCxO1-xN (0.96&lt;x&lt;1.06) was investigated using different band energy approaches, as well as modified Car Parinello molecular dynamics simulations of interfaces. A thin carbon sheet (of about 1 nm) appears, covering the crystallites. This sheet leads to substantial reconstruction of the near-the-interface SiCxO1-xN crystalline layers. Numerical modeling shows that these NC may be treated as quantum dot-like SiCxO1-xN reconstructed crystalline surfaces, covering the appropriate crystallites. All band energy calculation approaches (semi-empirical pseudopotential, fully augmented plane waves and norm-conserving self-consistent pseudopotential approaches) predicted the experimental spectroscopic data. In particular, it was shown that the near-the-surface carbon sheet plays a dominant role in the behavior of the reconstructed band energy structure. Independent evidence for the important role of the dot-like crystalline layers are the excitonic-like states, which are not dependent on the particular structure of the SiC, but are sensitive to the thickness of the carbon layer.

Poly-amino-enolates: First examples of odd alternant conducting polymers

The molecular and electronic structure of a series of poly-amino-enolates is calculated ab initio within the density functional formalism using Car-Parinello molecular dynamics. Within this series, the bandgap is found to vary from 1 to 6.5 eV and the valence band is found to consist entirely of non-bonding orbitals. Both these features are essentially reproduced by a simple Hückel model. By variation of the Hückel parameters the important factors which determine the bandgap are identified. Hückel analysis furthermore demonstrates that the poly-amino-enolates are first examples of odd alternant conjugated polymers which allows the effects of the hetero atom substitution to be rationalised in terms of Dewar's colour rules for odd alternant systems.