Re-examining the properties of the aqueous vapor-liquid interface using dispersion corrected density functional theory

First-principles molecular dynamics simulations, in which the forces are computed from electronic structure calculations, have great potential to provide unique insight into structure, dynamics, electronic properties, and chemistry of interfacial systems that is not available from empirical force fields. The majority of current first-principles simulations are driven by forces derived from density functional theory with generalized gradient approximations to the exchange-correlation energy, which do not capture dispersion interactions. We have carried out first-principles molecular dynamics simulations of air-water interfaces employing a particular generalized gradient approximation to the exchange-correlation functional (BLYP), with and without empirical dispersion corrections. We assess the utility of the dispersion corrections by comparison of a variety of structural, dynamic, and thermodynamic properties of bulk and interfacial water with experimental data, as well as other first-principles and force field-based simulations.     

Hydrated hydride anion clusters

On the basis of density functional theory (DFT) and high level ab initio theory, we report the structures, binding energies, thermodynamic quantities, IR spectra, and electronic properties of the hydride anion hydrated by up to six water molecules. Ground state DFT molecular dynamics simulations (based on the Born-Oppenheimer potential surface) show that as the temperature increases, the surface-bound hydride anion changes to the internally bound structure. Car-Parrinello molecular dynamics simulations are also carried out for the spectral analysis of the monohydrated hydride. Excited-state ab initio molecular dynamics simulations show that the photoinduced charge-transfer-to-solvent phenomena are accompanied by the formation of the excess electron-water clusters and the detachment of the H radical from the clusters. The dynamics of the detachment process of a hydrogen radical upon the excitation is discussed.     

Ab Initio simulations of nonstoichiometric Cd(x)Te(1-x) liquids

We present ab initio molecular-dynamics simulations for Cd(x)Te(1-x) liquids where the composition is nonstoichiometric. The simulations are performed following Born-Oppenheimer molecular dynamics. The required forces are obtained from a solution of the Kohn-Sham equation using ab initio pseudopotentials. We consider stoichiometries of the form: Cd(x)Te(1-x), where x=0.2, 0.4, 0.6, and 0.8. For each composition of the melt, we consider a range of temperatures near the experimentally determined liquid temperatures. We examine the microstructural properties of the melt, the viscosity, and self-diffusion properties of the liquid as a function of the stoichiometry and temperature. We also perform an analysis of the distribution of the electronic density of states in these liquids. We find that structural changes in the local order, experimentally predicted to occur when the concentration of Cd is increased, are closely related to changes in the electronic properties of the melt.     

Tight-binding molecular dynamics simulation of ZnSe liquid within the local environment dependence

We investigate the structural, electronic and dynamical properties of ZnSe liquid using tight-binding molecular dynamics (TBMD) simulations. We report the TBMD calculations for the solid and liquid forms of the ZnSe compound. To produce more realistic results the TB model includes the local environment dependence in the Hamiltonian matrix at finite temperature for ZnSe. To further demonstrate the efficiency of the TBMD approach, we present results for finite temperature physical properties of ZnSe liquid. We are able to show good agreement with experiment for the atomic mean-squared displacement and melting point.     

Ab initio molecular dynamics of protonated dialanine and comparison to infrared multiphoton dissociation experiments

Finite temperature Car-Parrinello molecular dynamics simulations are performed for the protonated dialanine peptide in vacuo, in relation to infrared multiphoton dissociation experiments. The simulations emphasize the flexibility of the different torsional angles at room temperature and the dynamical exchange between different conformers which were previously identified as stable at 0 K. A proton transfer occurring spontaneously at the N-terminal side is also observed and characterized. The theoretical infrared absorption spectrum is computed from the dipole time correlation function, and, in contrast to traditional static electronic structure calculations, it accounts directly for anharmonic and finite temperature effects. The comparison to the experimental infrared multiphoton dissociation spectrum turns out very good in terms of both band positions and band shapes. It does help the identification of a predominant conformer and the attribution of the different bands. The synergy shown between the experimental and theoretical approaches opens the door to the study of the vibrational properties of complex and floppy biomolecules in the gas phase at finite temperature.     

First principles calculation of the thermodynamic properties of silicon clusters

The thermodynamic properties of Si clusters are calculated using first principles quantum methods combined with molecular dynamics for simulating the trajectories of clusters. A plane wave basis is used with ab initio pseudo potentials and the local density approximation for determining the electronic energies and forces. Langevin molecular dynamics simulates thermal contact with a constant temperature reservoir. Vibrational spectra, moments of inertia, anharmonic corrections, and free energies are predicted for Si₂ through Si₅. The translational contribution is based on the ideal gas limit. The rotation contribution is approximated using a classical rigid rotator. Vibrational modes are determined from the dynamical matrix in the harmonic approximation. Corrections due to anharmonicity and coupling between rotational and vibrational modes are fit from the molecular dynamics simulations. Received: 17 September 1997 / Accepted: 14 October 1997     

Polarizability versus mobility: atomistic force field for ionic liquids

Based on classical molecular dynamics simulations, we discuss the impact of Coulombic interactions on a comprehensive set of properties of room temperature ionic liquids (RTILs) containing 1,3-dimethylimidazolium (MMIM(+)), N-butylpyridinium (BPY(+)), and bis(trifluoromethane sulfonyl)imide (TFSI(-)) ions. Ionic transport is found to be noticeably hindered by the excessive Coulombic energy, originating from the neglect of electronic polarization in the condensed phase of these RTILs. Starting from the models, recently suggested by Lopes and Padua, we show that realistic ionic dynamics can be achieved by the uniform scaling of electrostatic charges on all interaction sites. The original model systematically overestimates density and heat of vaporization of RTILs. Since density linearly depends on charge scaling, it is possible to use it as a convenient beacon to promptly derive a correct scaling factor. Based on the simulations of [BPY][TFSI] and [MMIM][TFSI] over a wide temperature range, we conclude that the suggested technique is feasible to greatly improve quality of the already existing non-polarizable FFs for RTILs.     

Quantum effects on adsorption and diffusion of hydrogen and deuterium in microporous materials

Monte Carlo and molecular dynamics simulations and neutron scattering experiments are used to study the adsorption and diffusion of hydrogen and deuterium in zeolite Rho in the temperature range of 30-150 K. In the molecular simulations, quantum effects are incorporated via the Feynman-Hibbs variational approach. We suggest a new set of potential parameters for hydrogen, which can be used when Feynman-Hibbs variational approach is used for quantum corrections. The dynamic properties obtained from molecular dynamics simulations are in excellent agreement with the experimental results and show significant quantum effects on the transport at very low temperature. The molecular dynamics simulation results show that the quantum effect is very sensitive to pore dimensions and under suitable conditions can lead to a reverse kinetic molecular sieving with deuterium diffusing faster than hydrogen.     

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) method for a large number of configurations generated from MD simulations. The method includes electron correlation effects at the coupled cluster singles and doubles level and the use of a large correlation consistent basis set. A polarizable force field has been used for the molecular dynamics part in both the CC/MM method and in the MD simulation. We describe how the methodology can be optimized with respect to computational costs while maintaining the quality of the results. Using the optimized method we study the energetic properties including the heat of vaporization and electronic excitation energies as well as electric dipole and quadrupole moments, the frequency dependent electric (dipole) polarizability, and electric-field-induced second harmonic generation first and second hyperpolarizabilities. Comparisons with experiments are performed where reliable data are available. Furthermore, we discuss the important issue on how to compare the calculated microscopic nonlocal properties to the experimental macroscopic measurements.     

Theoretical studies of solid bicyclo-HMX: effects of hydrostatic pressure and temperature

On the basis of density functional theory (DFT) and molecular dynamics (MD), the structural, electronic, and mechanical properties of the energetic material bicyclo-HMX have been studied. The crystal structure optimized by the LDA/CA-PZ method compares well with the experimental data. Band structure and density of states calculations indicate that bicyclo-HMX is an insulator with the band gap of ca. 3.4 eV and the N-NO(2) bond is the reaction center. The pressure effect on the bulk structure and properties has been investigated in the range of 0-400 GPa. The crystal structure and electronic character change slightly as the pressure increases from 0 to 10 GPa; when the pressure is over 10 GPa, further increment of the pressure determines significant changes of the structures and large broadening of the electronic bands together with the band gap decreasing sharply. There is a larger compression along the c-axis than along the a- and b-axes. To investigate the influence of temperature on the bulk structure and properties, isothermal-isobaric MD simulations are performed on bicyclo-HMX in the temperature range of 5-400 K. It is found that the increase of temperature does not significantly change the crystal structure. The thermal expansion coefficients calculated for the model indicate anisotropic behavior with slightly larger expansion along the a- and c-axes than along the b-axis.     

Excess electron localization sites in neutral water clusters

We present approximate pseudopotential quantum-mechanical calculations of the excess electron states of equilibrated neutral water clusters sampled by classical molecular dynamics simulations. The internal energy of the clusters are representative of those present at temperatures of 200 and 300 K. Correlated electronic structure calculations are used to validate the pseudopotential for this purpose. We find that the neutral clusters support localized, bound excess electron ground states in about 50% of the configurations for the smallest cluster size studied (n = 20), and in almost all configurations for larger clusters (n > 66). The state is always exterior to the molecular frame, forming typically a diffuse surface state. Both cluster size and temperature dependence of energetic and structural properties of the clusters and the electron distribution are explored. We show that the stabilization of the electron is strongly correlated with the preexisting instantaneous dipole moment of the neutral clusters, and its ground state energy is reflected in the electronic radius. The findings are consistent with electron attachment via an initial surface state. The hypothetical spectral dynamics following such attachment is also discussed.     

Ab initio and molecular dynamics studies of crystalline TNAD (trans-1,4,5,8-tetranitro-1,4,5,8-tetraazadecalin)

The structural and electronic properties of the energetic crystal TNAD (trans-1,4,5,8-tetranitro-1,4,5,8- tetraazadecalin) have been studied using plane-wave ab initio calculations based on the density function theory method with the ultrasoft pseudopotentials. It is found that the predicted crystal structure is in good agreement with experimental data and there are strong inter- and intramolecular interactions in bulk TNAD. Band structure calculations indicate that TNAD is an insulator with the band gap of ca. 3.3 eV. The hydrostatic compression effect on TNAD has been studied in the pressure range of 0-600 GPa. The results show that a pressure less than 10 GPa does not significantly change the geometric parameters, charge distributions, and electronic bands. When the pressure is over 10 GPa, increasing the pressure determines significant changes of the geometrical and electronic structures and large broadening of the electronic bands together with a sharp decrease of the band gap. Isothermal-isobaric molecular dynamics simulations at atmospheric pressure were further performed on the TNAD crystal in the temperature range 5-500 K. Average equilibrium lattice parameters and elastic properties as functions of temperature were determined. The thermal expansion coefficients calculated for the crystal indicate anisotropic behavior with the largest expansion along the b axis.     

Influence of Intermolecular Vibrations on the Electronic Coupling in Organic Semiconductors: The Case of Anthracene and Perfluoropentacene

We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure.     

Preferential binding of peptides to graphene edges and planes

Peptides identified from combinatorial peptide libraries have been shown to bind to a variety of abiotic surfaces. Biotic-abiotic interactions can be exploited to create hybrid materials with interesting electronic, optical, or catalytic properties. Here we show that peptides identified from a combinatorial phage display peptide library assemble preferentially to the edge or planar surface of graphene and can affect the electronic properties of graphene. Molecular dynamics simulations and experiments provide insight into the mechanism of peptide binding to the graphene edge.     

The effects of electronic structure and charged state on thermodynamic properties: an ab initio molecular dynamics investigations on neutral and charged clusters of Na(39), Na(40), and Na(41)

In this paper we explore the effects of the electronic structure, the charge state, and the nature of energy distribution of isomers on the thermodynamic properties of sodium clusters. The focus of the work is to isolate the effects of these ingredients on thermodynamic behavior by choosing specific clusters. Toward this end we investigate Na(39) (-), Na(40), and Na(41) (+), which are the electronic closed shell systems which differ in number of atoms and charge state. We also examine Na(39), Na(39) (+), Na(40) (+), and Na(41) clusters having different charges of these clusters. Our density functional molecular dynamics simulations show that all electronic shell-closing clusters have similar melting temperature of approximately 310 K. Remarkably, it is observed that an addition of even one electron to Na(39) increases the melting temperature by about 40 K and makes the specific heat curve sharper. All the cationic clusters show broadened specific heat curves.     

Conformational and electronic properties of a microperoxidase in aqueous solution: a computational study.

A theoretical study of the conformational properties of a small heme peptide in aqueous solution is carried out by classical, long-timescale molecular dynamics simulations. The electronic properties of this species, that is, the relative energies of its excited electronic states and the redox potential, are reproduced and related to the conformational behavior using the perturbed matrix method and basic statistical mechanics. Our results show an interesting coupling between the conformational transitions and the electronic properties. These investigations, beyond the biophysically relevant results addressing the long-standing question of the actual role of the enzyme structure on the enzyme activity, are also of some methodological interest since they offer a further computational perspective for including the electronic degrees of freedom into the modeling of rather complex molecular systems.     

Molecular simulation of excimer fluorescence in polystyrene and poly(vinylcarbazole)

In fluorescence emission spectra of poly(vinylcarbazole) (PVK), two types of excimers are observed, the fully and the partially overlapped excimers, namely, excimers and exciplexes. In this work, we investigated the structural changes induced by the transition between electronic levels S(0) and S(1). Furthermore, the widely used assumption of similar potential energy surfaces in the S(0) and S(1) states and its use in molecular dynamics simulations are thoroughly examined for PVK and polystyrene (PS). The ground-state and excited-state intermolecular potentials between phenyl or carbazyl substituents in PS or PVK, respectively, are computed from high-level ab initio calculations and fit to analytic potentials. Finally, molecular dynamics simulations are performed at room temperature for PS and for isotactic and syndiotactic PVK. This treatment enabled the decoupling of excimer and exciplex contributions from the simulated spectra.     

Liquid crystalline metal-free phthalocyanines designed for charge and exciton transport

A joint theoretical and experimental study of the electronic and structural properties of liquid crystalline metal-free phthalocyanines bearing a strong potential for charge and exciton transport has been performed. The synthesis of such compounds has been triggered by quantum chemical calculations showing that: (i) hole transport is favored in metal-free phthalocyanines by their extremely low reorganization energy (0.045 eV) and large electronic splittings; and (ii) the efficiency of energy transfer along the one-dimensional discotic stacks is weakly affected by rotational disorder due to the two-dimensional character of the molecules. We have synthesized two metal-free phthalocyanines with different branched aliphatic chains on the gram scale to allow for a full characterization of their solid-state properties. The two compounds self-organize in liquid crystalline mesophases, as evidenced by optical microscopy, differential scanning calorimetry, X-ray powder diffraction, and molecular dynamics simulations. They exhibit a columnar rectangular mesophase at room temperature and a columnar hexagonal mesophase at elevated temperature.     

Investigation of nanocomposite PNIPAm-g-graphene with pre-lower critical solution temperature rapid thermal response function for chip adaptive cooling: A molecular dynamics and computational fluid dynamics simulations

Temperature-sensitive hydrogels have been widely used for rapid adaptive cooling in electronic device thermal management with promising applications. However, existing temperature-sensitive hydrogels can only regulate the flow in the chip cooling system after the ambient temperature reaches their lower critical solution temperature (LCST). Before reaching LCST, effective rapid heat dissipation for electronic chips is not achievable. This study aims to develop a temperature-sensitive hydrogel that can provide assisted adaptive cooling for electronic chips before reaching its LCST. This requires the hydrogel to have a thermal conductivity far surpassing existing hydrogel materials. Using the temperature-sensitive hydrogel PNIPAm and graphene molecules as base materials, this research utilized molecular dynamics simulations to graft graphene molecules onto PNIPAm molecules in different ways, resulting in the temperature-sensitive hydrogel material PNIPAm-g-graphene. Non-equilibrium molecular dynamics (NEMD) was employed to calculate the thermal conductivity of this material under different temperature conditions. The results indicate that the thermal conductivity of PNIPAm-g-graphene can reach up to 1.95474 W/m K (graphene grafted at  CH₃ functional group, temperature at 280 K). Compared to the thermal conductivity of PNIPAm under the same conditions (0.45 W/m K), the increase in thermal conductivity is significant, demonstrating excellent thermal conductivity compared to PNIPAm. Subsequently, this study analyzed the underlying mechanisms of different thermal conductivities in materials obtained by grafting graphene molecules at different points using the method of overlap in Phonon Density of States Curves (PDOS) from the perspective of interfacial thermal conduction. Finally, through computational fluid dynamics (CFD) simulations, this study investigates the chip's adaptive cooling performance with PNIPAm-g-graphene material. The results show that, compared to traditional temperature-sensitive hydrogels, PNIPAm-g-graphene can achieve efficient adaptive cooling of chip hotspots before the cooling fluid temperature reaches its LCST value. This finding is significant for the field of chip cooling. The study proposes a new method for rapid, adaptive cooling of chip hotspots and explores its feasibility from the perspectives of molecular dynamics and CFD simulation. It holds importance in the thermal management of electronic devices and the rapid adaptive cooling of electronic chips.