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Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant. [ABSTRACT FROM AUTHOR]

In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties. [ABSTRACT FROM AUTHOR]

Geopolymers, synthesized through alkaline activation of aluminosilicates, have emerged as a sustainable alternative for traditional ordinary Portland cement. In spite of the satisfactory mechanical performance and sustainability-related benefits, the large scale acceptance of geopolymers in the construction industry is still limited due to poor understanding of the composition-property relationships. Molecular simulation is a powerful tool to develop such relationships, provided that the adopted molecular structure represents the experimental data effectively. Toward this end, this paper presents a new molecular structure of sodium aluminosilicate hydrate geopolymer gels, inspired from the traditional calcium silicate hydrates gel. In contrast to the existing model—where water is uniformly distributed in the structure—we present a layered-but-disordered structure. This new structure incorporates water in the interlayer space of the aluminosilicate network. The structural features of the new proposed molecular structure are evaluated in terms of both short- and medium-range order features such as pair distribution functions, bond angle distributions, and structure factor. The structural features of the newly proposed molecular structure with interlayer water show better correlation with the experimental observations as compared to the existing traditional structure signifying an increased plausibility of the proposed structure. The proposed structure can be adopted as a starting point toward the realistic multiscale simulation-based design and development of geopolymers. [ABSTRACT FROM AUTHOR]

Advances in experimental methodology aligned with technological developments, such as 3rd generation light sources, X-ray Free Electron Lasers, and High Harmonic Generation, have led to a paradigm shift in the capability of X-ray spectroscopy to deliver high temporal and spectral resolution on an extremely broad range of samples in a wide array of different environments. Importantly, the complex nature and high information content of this class of techniques mean that detailed theoretical studies are often essential to provide a firm link between the spectroscopic observables and the underlying molecular structure and dynamics. In this paper, we present approaches for simulating dynamical processes in X-ray spectroscopy based upon on-the-fly quantum dynamics with a Gaussian basis set. We show that it is possible to provide a fully quantum description of X-ray spectra without the need of precomputing highly multidimensional potential energy surfaces. It is applied to study two different dynamical situations, namely, the core-hole lifetime dynamics of the water monomer and the dissociation of C F 4 + recently studied using pump-probe X-ray spectroscopy. Our results compare favourably to previous experiments, while reducing the computational effort, providing the scope to apply them to larger systems. [ABSTRACT FROM AUTHOR]

In this paper, the molecular dynamics of a series of ester derivatives of ibuprofen (IBU), in which the hydrogen atom from the hydroxyl group was substituted by the methyl, isopropyl, hexyl, and benzyl moieties, has been investigated using Broadband dielectric (BD), Nuclear magnetic resonance (NMR), and Raman spectroscopies. We found that except for benzyl IBU (Ben-IBU), an additional process (slow mode, SM) appears in dielectric spectra in all examined compounds. It is worth noting that this relaxation process was observed for the first time in non-modified IBU (a Debye relaxation). According to suggestions by Affouard and Correia [J. Phys. Chem. B. 114, 11397 (2010)] as well as further studies by Adrjanowicz et al. [J. Chem. Phys. 139, 111103 (2013)] on Met-IBU, it was attributed to synperiplanar–antiperiplanar conformational changes within the molecule. Herein, we have shown that with an increasing molecular weight of the substituent, the relaxation times of the SM become longer and its activation energy significantly increases. Moreover, this new relaxation mode was found to be broader than a simple Debye relaxation in Iso-IBU and Hex-IBU. Additional complementary NMR studies indicated that either there is a significant slowdown of the rotation around the O=C—O—R moiety or this kind of movement is completely suppressed in the case of Ben-IBU. Therefore, the SM is not observed in the dielectric loss spectra of this compound. Finally, we carried out isothermal experiments on the samples which have a different thermal history. Interestingly, it turned out that the relaxation times of the structural processes are slightly shorter with respect to those obtained from temperature dependent measurements. This effect was the most prominent in the case of Hex-IBU, while for Ben-IBU, it was not observed at all. Additional time-dependent measurements revealed the ongoing equilibration manifested by the continuous shift of the structural process, until it finally reached its equilibrium position. Further Raman investigations showed that this effect may be related to the rotational/conformational equilibration of the long hexyl chains. Our results are the first ones demonstrating that the structural process is sensitive to the conformational equilibration occurring in the specific highly viscous systems. [ABSTRACT FROM AUTHOR]

Photo-induced electron detachment spectroscopy of anionic boron clusters, B4- and B5-, is theoretically investigated by performing electronic structure calculations and nuclear dynamics simulations. While the electronic potential energy surfaces (X1Ag, ã3B2u, b3B1u, Ã1B2u, c3B2g, and B1B2g of neutral B4 and X2B2, Ã2A1, B2B2, C2A1, D2B1, and E2A1 of neutral B5) and their coupling surfaces are constructed in this paper, the details of the nuclear dynamics on these electronic states are presented in Paper II. Electronic structure calculations are carried out at the complete active space self-consistent field - multi-reference configuration interaction level of theory employing the correlation consistent polarized valance triple zeta basis set. Using the calculated electronic structure data suitable vibronic Hamiltonians are constructed utilizing a diabatic electronic basis and displacement coordinates of the normal vibrational modes. The theoretical results are discussed in relation to those recorded in recent experiments. [ABSTRACT FROM AUTHOR]

In the present paper, we report a molecular dynamics simulation of two-dimensional Lennard-Jones system with a simple square start configuration. Mean square displacement was computed showing interesting dependence on high pressure conditions in short time scale, corresponding to an abrupt restructurization. This paper is the first to report the qualitative and quantitative details of this phenomenon. [ABSTRACT FROM AUTHOR]

Over the last number of years several simulation methods have been introduced to study rare events such as nucleation. In this paper we examine the crystal nucleation rate of hard spheres using three such numerical techniques: molecular dynamics, forward flux sampling, and a Bennett-Chandler-type theory where the nucleation barrier is determined using umbrella sampling simulations. The resulting nucleation rates are compared with the experimental rates of Harland and van Megen [Phys. Rev. E 55, 3054 (1997)], Sinn et al. [Prog. Colloid Polym. Sci. 118, 266 (2001)], Schätzel and Ackerson [Phys. Rev. E 48, 3766 (1993)], and the predicted rates for monodisperse and 5% polydisperse hard spheres of Auer and Frenkel [Nature 409, 1020 (2001)]. When the rates are examined in units of the long-time diffusion coefficient, we find agreement between all the theoretically predicted nucleation rates, however, the experimental results display a markedly different behavior for low supersaturation. Additionally, we examined the precritical nuclei arising in the molecular dynamics, forward flux sampling, and umbrella sampling simulations. The structure of the nuclei appears independent of the simulation method, and in all cases, the nuclei contains on average significantly more face-centered-cubic ordered particles than hexagonal-close-packed ordered particles. [ABSTRACT FROM AUTHOR]

Various structural and dynamical properties of a network are encoded in the eigenvalues of walk matrix describing random walks on the network. In this paper, we study the spectra of walk matrix of the Koch network, which displays the prominent scale-free and small-world features. Utilizing the particular architecture of the network, we obtain all the eigenvalues and their corresponding multiplicities. Based on the link between the eigenvalues of walk matrix and random target access time defined as the expected time for a walker going from an arbitrary node to another one selected randomly according to the steady-state distribution, we then derive an explicit solution to the random target access time for random walks on the Koch network. Finally, we corroborate our computation for the eigenvalues by enumerating spanning trees in the Koch network, using the connection governing eigenvalues and spanning trees, where a spanning tree of a network is a subgraph of the network, that is, a tree containing all the nodes. [ABSTRACT FROM AUTHOR]

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7Tc) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs. [ABSTRACT FROM AUTHOR]

We report on a further investigation of a new method that can be used to address vibrational dynamics and propagation of stress waves in liquids. The method is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the atomic level stress correlation functions. This decomposition, as was demonstrated previously for a model liquid studied in molecular dynamics simulations, reveals the presence of stress waves propagating over large distances and a structure that resembles the pair density function. In this paper, by performing the Fourier transforms of the atomic level stress correlation functions, we elucidate how the lifetimes of the stress waves and the ranges of their propagation depend on their frequency, wavevector, and temperature. These results relate frequency and wavevector dependence of the generalized viscosity to the character of propagation of the shear stress waves. In particular, the results suggest that an increase in the value of the frequency dependent viscosity at low frequencies with decrease of temperature is related to the increase in the ranges of propagation of the stress waves of the corresponding low frequencies. We found that the ranges of propagation of the shear stress waves of frequencies less than half of the Einstein frequency extend well beyond the nearest neighbor shell even above the melting temperature. The results also show that the crossover from quasilocalized to propagating behavior occurs at frequencies usually associated with the Boson peak. [ABSTRACT FROM AUTHOR]

In a previous paper [I. Napari, J. Julin, and H. Vehkamäki, J. Chem. Phys. 131, 244511 (2009)] we compared sizes of critical and equilibrium clusters in Lennard-Jones vapors using various geometrical clusters definitions. In particular, we found that the critical and equilibrium clusters were of the same size if each constituent atom in the cluster was required to have at least five neighboring atoms (ten Wolde-Frenkel cluster) but the critical clusters were much larger if only one neighboring atom was sufficient to fulfill the cluster definition (Stillinger cluster). The conclusion was that the critical clusters at high vapor densities have more ramified structure than the corresponding equilibrium clusters. In this study we have performed new molecular dynamics simulations to enlighten this matter. It is found that the surprising conclusion of the earlier work can be traced to the mean first passage time method which was used to obtain critical cluster sizes from simulations. When a certain sized Stillinger cluster first appears in the simulation, the cluster tends to have a more ramified structure than Stillinger clusters of that size observed later in the simulation. However, for the latter clusters the ratio of Stillinger and ten Wolde-Frenkel sizes in the vapor is the same as in the equilibrium simulations, implying similar structure of critical and equilibrium clusters. [ABSTRACT FROM AUTHOR]

In this paper, we propose coarse-grained single-site (CGSS), wall-CO2, and CO2-CO2 interaction potential models to study the structure of carbon dioxide under confinement. The CGSS potentials are used in an empirical potential based quasi-continuum theory, EQT, to compute the center-of-mass density and potential profiles of CO2 confined inside different size graphite slit pores. Results obtained from EQT are compared with those obtained from all-atom molecular dynamics (AA-MD) simulations, and are found to be in good agreement with each other. Though these CGSS interaction potentials are primarily developed and parameterized for EQT, they are also used to perform coarse-grained molecular dynamics (CG-MD) simulations. The results obtained from CG-MD simulations are also found to be in reasonable agreement with AA-MD simulation results. [ABSTRACT FROM AUTHOR]

Reduced-dimensionality, coarse-grained models are commonly employed to describe the structure and dynamics of large molecular systems. In those models, the dynamics is often described by Langevin equations of motion with phenomenological parameters. This paper presents a rigorous coarse-graining method for the dynamics of linear systems. In this method, as usual, the conformational space of the original atomistic system is divided into master and slave degrees of freedom. Under the assumption that the characteristic timescales of the masters are slower than those of the slaves, the method results in Langevin-type equations of motion governed by an effective potential of mean force. In addition, coarse-graining introduces hydrodynamic-like coupling among the masters as well as non-trivial inertial effects. Application of our method to the long-timescale part of the relaxation spectra of proteins shows that such dynamic coupling is essential for reproducing their relaxation rates and modes. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were conducted to investigate the structural properties of melts of nonconcatenated ring polymers and compared to melts of linear polymers. The longest rings were composed of N = 1600 monomers per chain which corresponds to roughly 57 entanglement lengths for comparable linear polymers. For the rings, the radius of gyration squared, g2>, was found to scale as N4/5 for an intermediate regime and N2/3 for the larger rings indicating an overall conformation of a crumpled globule. However, almost all beads of the rings are 'surface beads' interacting with beads of other rings, a result also in agreement with a primitive path analysis performed in the next paper [J. D. Halverson, W. Lee, G. S. Grest, A. Y. Grosberg, and K. Kremer, J. Chem. Phys. 134, 204905 (2011)]. Details of the internal conformational properties of the ring and linear polymers as well as their packing are analyzed and compared to current theoretical models. [ABSTRACT FROM AUTHOR]

Dynamic and structural properties of biological polymers are important to their function but it is difficult to obtain information on molecular flexibility at an atomic level. This paper describes how a normal mode analysis can be used to describe the equilibrium and nonequilibrium properties of complex polymer systems such as DNA in solution. A weak coupling between the chain deformation and the local chain orientation simplifies the calculations. A crossover in the normal mode behavior is proposed with a transition from straight rod bend modes to longitudinal oscillations of a coil conformation as a function of the stiffness and the degree of polymerization. [ABSTRACT FROM AUTHOR]

The hydrogen storage system LiH + NH3 ↔ LiNH2 + H2 is one of the most promising hydrogen storage systems, where the reaction yield can be increased by replacing Li in LiH with other alkali metals (Na or K) in order of Li < Na < K. In this paper, we have studied the alkali metal M (M = Li, Na, K) dependence of the reactivity of MH with NH3 by calculating the potential barrier of the H2 desorption process from the reaction of an M2H2 cluster with an NH3 molecule based on the ab initio structure optimization method. We have shown that the height of the potential barrier becomes lower in order of Li, Na, and K, where the difference of the potential barrier in Li and Na is relatively smaller than that in Na and K, and this tendency is consistent with the recent experimental results. We have also shown that the H-H distance of the H2 dimer at the transition state takes larger distance and the change of the potential energy around the transition state becomes softer in order of Li, Na, and K. There are almost no M dependence in the charge of the H atom in NH3 before the reaction, while that of the H atom in M2H2 takes larger negative value in order of Li, Na, and K. We have also performed molecular dynamics simulations on the M2H2-NH3 system and succeeded to reproduce the H2 desorption from the reaction of Na2H2 with NH3. [ABSTRACT FROM AUTHOR]

In this paper, we construct an effective model for the dynamics of an excluded-volume chain under confinement by extending the formalism of Rouse modes. We make specific predictions about the behavior of the modes for a single polymer confined to a tube. The results are tested against Monte Carlo simulations using the bond-fluctuation algorithm which uses a lattice representation of the polymer chain with excluded-volume effects. [ABSTRACT FROM AUTHOR]

We present in this paper a thermodynamic analysis of benzene properties under shock conditions as given by molecular dynamics (MD) simulations. Reactive MD simulations of benzene predict a decomposition threshold corresponding to the flection point on the experimental Hugoniot curve. A polymerlike carbonated structure is observed for pressures above this threshold, but the calculated Hugoniot curve is in disagreement with the experimental one at high pressure. On the contrary, a system consisting of a diamond cluster in hydrogen gas leads to a correct prediction of the pressure on the Hugoniot curves. The central question is then linked to the kinetics of the transition between the polymerlike structure and the diamond cluster. [ABSTRACT FROM AUTHOR]

The vast majority of molecular dynamics simulations are based on nonpolarizable force fields with fixed partial charges for all atoms. The traditional way to obtain these charges are quantum-mechanical calculations performed prior to simulation. Unfortunately, the set of the partial charges heavily relies on the method and the basis set used. Therefore, investigations of the influence of charge variation on simulation data are necessary in order to validate various charge sets. This paper elucidates the consequences of different charge sets on the structure and dynamics of the ionic liquid: 1-ethyl-3-methyl-imidazolium dicyanoamide. The structural features seem to be more or less independent of the partial charge set pointing to a dominance of shape force as modeled by Lennard–Jones parameters. This can be seen in the radial distribution and orientational correlation functions. The role of electrostatic forces comes in when studying dynamical properties. Here, significant deviations between different charge sets can be observed. Overall, dynamics seems to be governed by viscosity. In fact, all dynamical parameters presented in this work can be converted from one charge set to another by viscosity scaling. [ABSTRACT FROM AUTHOR]

In this paper, we analyze the melting behavior of zirconium nanowire using the results of a series of molecular dynamics simulations. Our calculation employs a well-fitted, tight-binding many-body potential for zirconium atoms. The melting point of the nanowire is predicted by the root-mean-square displacements for inner and outer shells. Our simulations predict two melting behaviors: one is the inner melting and the other is the outer melting. Our results reveal that the melting of nanowire starts from the inner shell atoms. The melting point of zirconium nanowire is lower than the bulk value (2125 K). Moreover, the melting point of the inner shell is lower than that of the outer shell. A coexistence of crystal and liquid units is observed in the melting process of nanowire. An investigation of local clusters is carried out to further analyze the melting mechanism of the nanowire. The presence of the local clusters 1331, 1321, 1211, etc. is an indication of disordered structures. The pair and angular correlation functions are also presented for the analysis of the melting behavior. It is not only the diffusion of single atom but the diffusion of clusters result in the occurrence of the melting. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

SchNetPack is a versatile neural network toolbox that addresses both the requirements of method development and the application of atomistic machine learning. Version 2.0 comes with an improved data pipeline, modules for equivariant neural networks, and a PyTorch implementation of molecular dynamics. An optional integration with PyTorch Lightning and the Hydra configuration framework powers a flexible command-line interface. This makes SchNetPack 2.0 easily extendable with a custom code and ready for complex training tasks, such as the generation of 3D molecular structures. [ABSTRACT FROM AUTHOR]

In this paper, the structure of CO2 clusters made of less than a hundred of molecules is studied by means of electron diffraction experiments and molecular dynamics simulations. According to previous works, CO2 clusters are expected to undergo a transition in this size range, from an icosahedral structure to the bulk cubic structure. Electron diffraction patterns have been recorded from clusters produced in a free jet expansion of gaseous CO2. These patterns provide evidence of a structural change occurring in clusters made of a few tens of molecules. (CO2)N models, with 13

Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra. [ABSTRACT FROM AUTHOR]

In standard molecular junctions, a molecular structure is placed between and connected to metal leads. Understanding how mechanical tuning in such molecular junctions can change heat conductance has interesting applications in nanoscale energy transport. In this work, we use nonequilibrium molecular dynamics simulations to address the effect of stretching on the phononic contribution to the heat conduction of molecular junctions consisting of single long-chain alkanes and various metal leads, such as Ag, Au, Cu, Ni, and Pt. The thermal conductance of such junctions is found to be much smaller than the intrinsic thermal conductance of the polymer and significantly depends on the nature of metal leads as expressed by the metal–molecule coupling and metal vibrational density of states. This behavior is expected and reflects the mismatch of phonon spectra at the metal molecule interfaces. As a function of stretching, we find a behavior similar to what was observed earlier [M. Dinpajooh and A. Nitzan, J. Chem. Phys. 153, 164903 (2020)] for pure polymeric structures. At relatively short electrode distances, where the polyethylene chains are compressed, it is found that the thermal conductances of the molecular junctions remain almost constant as one stretches the polymer chains. At critical electrode distances, the thermal conductances start to increase, reaching the values of the fully extended molecular junctions. Similar behaviors are observed for junctions in which several long-chain alkanes are sandwiched between various metal leads. These findings indicate that this behavior under stretching is an intrinsic property of the polymer chain and not significantly associated with the interfacial structures. [ABSTRACT FROM AUTHOR]

How is the orientation of molecular liquids ordered on cooling? What are the basic structures of molecular glasses, e.g., close to the crystalline structure or some special structures such as icosahedral cluster? These are long-standing questions in liquid and glass physics. We have constructed a novel cryostat to prepare simple molecular glasses by vapor deposition and performed in situ synchrotron radiation x-ray diffraction experiments. The glassy state of a simple molecule CS2, which cannot be vitrified by normal liquid quenching, was successfully prepared with this instrument, and its diffraction data were collected in a wide Q-range of 0.16–25.7 Å−1 with a high-energy diffractometer at BL04B2, SPring-8. The diffraction data of liquid CS2 were also recorded in a wide temperature range of 160–300 K. These diffraction data were analyzed with molecular dynamics simulations and reverse Monte Carlo modelings to investigate orientational correlation. From the obtained 3D structure models, the orientational correlation between neighboring CS2 molecules was investigated quantitatively as a function of temperature. At room temperature, the parallel and T-shaped arrangements are preferred for the nearest neighbor correlation. On cooling, these arrangements are developed gradually, and its rate became prominent below the melting temperature (162 K). In the glassy state, the slipped-parallel arrangement is dominant as well as the T-shaped arrangement. Both arrangements appear in the CS2 crystal, indicating that the structure of glassy CS2 is close to that of crystalline CS2. [ABSTRACT FROM AUTHOR]

This special issue presents a series of papers that highlight a new and evolving view of water's molecular role in biological structure and dynamics. Increasingly water is appreciated for playing an active role in biological function rather than just serving as a spectator. The areas represented include molecular interfaces with water, biological self-assembly, conformational changes by macromolecules, and chemical reactivity [ABSTRACT FROM AUTHOR]

We report molecular dynamics simulations of nanotubes imbibing decane at an oil/vapor interface at 300 K. We find that the smallest (7,7) nanotubes imbibe extremely rapidly (<=800 m/s), with the imbibition speed slowing as the tube’s radius increases. The density profiles of the imbibing fluid in the pores are analyzed as a function of time. We find that the imbibing liquid is well described by the advection-diffusion equation and present expressions for the density profiles (in x and t) of the imbibing fluid as a function of the adsorption energy and surface friction of the pore. In addition we have analyzed the molecular structure of the imbibed fluid in nanotubes and describe how molecular conformations change with nanotube radius and position in the pore. We are therefore able to provide a complete description of the imbibition of a wetting fluid, decane, for a wide range of nanopores. [ABSTRACT FROM AUTHOR]

The theory and first implementation of a vibrational coupled cluster (VCC) method for calculations of the vibrational structure of molecules is presented. Different methods for introducing approximate VCC methods are discussed including truncation according to a maximum number of simultaneous mode excitations as well as an interaction space order concept is introduced. The theory is tested on calculation of anharmonic frequencies for a three-mode model system and a formaldehyde quartic force field. The VCC method is compared to vibrational self-consistent-field, vibrational Møller–Plesset perturbation theory, and vibrational configuration interaction (VCI). A VCC calculation typically gives higher accuracy than a corresponding VCI calculation with the same number of parameters and the same formal operation count.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Understanding the response of the surface of metallic solids to external electric field sources is crucial to characterize electrode–electrolyte interfaces. Continuum electrostatics offer a simple description of the induced charge density at the electrode surface. However, such a simple description does not take into account features related to the atomic structure of the solid and to the molecular nature of the solvent and of the dissolved ions. In order to illustrate such effects and assess the ability of continuum electrostatics to describe the induced charge distribution, we investigate the behavior of a gold electrode interacting with sodium or chloride ions fixed at various positions, in a vacuum or in water, using all-atom constant-potential classical molecular dynamics simulations. Our analysis highlights important similarities between the two approaches, especially under vacuum conditions and when the ion is sufficiently far from the surface, as well as some limitations of the continuum description, namely, neglecting the charges induced by the adsorbed solvent molecules and the screening effect of the solvent when the ion is close to the surface. While the detailed features of the charge distribution are system-specific, we expect some of our generic conclusions on the induced charge density to hold for other ions, solvents, and electrode surfaces. Beyond this particular case, the present study also illustrates the relevance of such molecular simulations to serve as a reference for the design of improved implicit solvent models of electrode–electrolyte interfaces. [ABSTRACT FROM AUTHOR]

Herein, we examined the effect of finite size and wettability on the structural dynamics and the molecular arrangement of the propylene carbonate derivative, (S)-(−)-4-methoxymethyl-1,3-dioxolan-2-one (assigned as s-methoxy-PC), incorporated into alumina and silica porous templates of pore diameters d = 4 nm–10 nm using Raman and broadband dielectric spectroscopy, differential scanning calorimetry, and x-ray diffraction. It was demonstrated that only subtle changes in the molecular organization and short-range order of confined s-methoxy-PC molecules were detected. Yet, a significant deviation of the structural dynamics and depression of the glass transition temperatures, Tg, was found for all confined samples with respect to the bulk material. Interestingly, these changes correlate with neither the finite size effects nor the interfacial energy but seem to vary with wettability, generally. Nevertheless, for s-methoxy-PC infiltrated into native (more hydrophilic) and modified (more hydrophobic) silica templates of the same nanochannel size (d = 4 nm), a change in the dynamics and Tg was negligible despite a significant variation in wettability. These results indicated that although wettability might be a suitable variable to predict alteration of the structural dynamics and depression of the glass transition temperature, other factors, i.e., surface roughness and the density packing, might also have a strong contribution to the observed confinement effects. [ABSTRACT FROM AUTHOR]

We present in detail and validate an effective Monte Carlo approach for the calculation of the nuclear vibrational densities via integration of molecular eigenfunctions that we have preliminary employed to calculate the densities of the ground and the excited OH stretch vibrational states in the protonated glycine molecule [Aieta et al., Nat Commun 11, 4348 (2020)]. Here, we first validate and discuss in detail the features of the method on a benchmark water molecule. Then, we apply it to calculate on-the-fly the ab initio anharmonic nuclear densities in the correspondence of the fundamental transitions of NH and CH stretches in protonated glycine. We show how we can gain both qualitative and quantitative physical insight by inspection of different one-nucleus densities and assign a character to spectroscopic absorption peaks using the expansion of vibrational states in terms of harmonic basis functions. The visualization of the nuclear vibrations in a purely quantum picture allows us to observe and quantify the effects of anharmonicity on the molecular structure, also to exploit the effect of IR excitations on specific bonds or functional groups, beyond the harmonic approximation. We also calculate the quantum probability distribution of bond lengths, angles, and dihedrals of the molecule. Notably, we observe how in the case of one type of fundamental NH stretching, the typical harmonic nodal pattern is absent in the anharmonic distribution. [ABSTRACT FROM AUTHOR]

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post–Hartree–Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension. [ABSTRACT FROM AUTHOR]

Transition states are fundamental to understanding the reaction dynamics qualitatively in chemical physics. To date various methods of first principle location of the transition states have been developed. In the absence of the knowledge of the final structure, the softest-mode following method climbs up to a transition state without calculating the Hessian matrix. One weakness of this kind of approaches is that the number of rotations to determine the softest mode is usually unpredictable. In this paper, we propose a locally optimal search direction finding algorithm, namely LOR, which is an extension of the traditional conjugate gradient method without additional calculations of the forces. We also show that the translation of forces improves the numerical stability. Experiments for the Baker test system show that the proposed algorithm is much faster than the original dimer conjugate gradient method. [ABSTRACT FROM AUTHOR]

The trapping process in polymer systems constitutes a fundamental mechanism for various other dynamical processes taking place in these systems. In this paper, we study the trapping problem in two representative polymer networks, Cayley trees and Vicsek fractals, which separately model dendrimers and regular hyperbranched polymers. Our goal is to explore the impact of trap location on the efficiency of trapping in these two important polymer systems, with the efficiency being measured by the average trapping time (ATT) that is the average of source-to-trap mean first-passage time over every staring point in the whole networks. For Cayley trees, we derive an exact analytic formula for the ATT to an arbitrary trap node, based on which we further obtain the explicit expression of ATT for the case that the trap is uniformly distributed. For Vicsek fractals, we provide the closed-form solution for ATT to a peripheral node farthest from the central node, as well as the numerical solutions for the case when the trap is placed on other nodes. Moreover, we derive the exact formula for the ATT corresponding to the trapping problem when the trap has a uniform distribution over all nodes. Our results show that the influence of trap location on the trapping efficiency is completely different for the two polymer networks. In Cayley trees, the leading scaling of ATT increases with the shortest distance between the trap and the central node, implying that trap's position has an essential impact on the trapping efficiency; while in Vicsek fractals, the effect of location of the trap is negligible, since the dominant behavior of ATT is identical, respective of the location where the trap is placed. We also present that for all cases of trapping problems being studied, the trapping process is more efficient in Cayley trees than in Vicsek fractals. We demonstrate that all differences related to trapping in the two polymer systems are rooted in their underlying topological structures. [ABSTRACT FROM AUTHOR]

From a specific definition of the roto-translational (external) and intramolecular (internal) coordinates, a constrained dynamics algorithm is derived for removing the roto-translational motions during molecular dynamics simulations, within the leap-frog integration scheme. In the paper the theoretical basis of this new method and its statistical mechanical consistency are reported, together with two applications. © 2000 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A broad variety of liquids conform to density scaling: relaxation times can be expressed as a function of the ratio of temperature to density, the latter raised to a material constant γ. For atomic liquids interacting only through simple pair potentials, the exponent γ is very nearly equal to n/3, where n is the steepness of the intermolecular potential, while for molecular liquids having rigid bonds and built using the same interatomic potential, γ > n/3. We find that for this class of molecular liquids, γ = n/δ, where the parameter δ relates the intermolecular distance to the density along an isomorph (the line of approximately constant dynamics and structure). δ depends only on the molecular structure and not the interatomic potential. [ABSTRACT FROM AUTHOR]

Carbonate-based lithium-ion electrolytes are of great importance due to their close relationship with the resulting battery efficiency and safety. Modifying the organic electrolyte has been paramount for achieving more efficient and safer lithium-ion batteries. However, the molecular picture of the electrolyte is still under scrutiny. Lately, ultrafast infrared spectroscopic studies have investigated the solvation structure and dynamics of the lithium ion (Li+) in both linear and cyclic carbonates. However, theoretical studies describing the molecular arrangements and transformation occurring in such time scales are scarce. In this study, ab initio molecular dynamics simulations were used to obtain the molecular structure and dynamics of the Li+ solvation shell in cyclic and linear carbonates. The theoretical results showed that molecular arrangement of the carbonates directly coordinating Li+ is not significantly altered by the carbonate chemical nature. However, the cyclic and linear carbonates showed significant different pictures of the overall solvation shell due to the intercalation phenomenon observed for cyclic carbonates, which significantly alters the motions of coordinated solvent. In addition, the intercalation appears to affect the propensity of ion pair formation and/or solvent exchange. Finally, the dynamics of the geometrical changes of the carbonates solvating Li+ is found to occur with characteristic times of tenths of picoseconds, while ion pair and solvent chemical exchange appear to happen in time scales which are at least an order of magnitude larger. Our study provides a comprehensive picture of the structure and dynamics of the molecular components in different carbonate-based lithium-ion electrolytes occurring in picosecond time scales. [ABSTRACT FROM AUTHOR]

Classical molecular dynamics simulations at the interfaces of two (meth)acrylate polymers, poly(2-methoxyethylacrylate) (PMEA) and poly(methyl methacrylate) (PMMA), upon contact with water are performed to elucidate interfacial molecular structures from the interface-specific nonlinear spectroscopic point of view. PMEA has methoxy oxygen in the side chain, while PMMA does not have it, and its impacts on the interfacial structure are particularly focused on. The force fields of PMEA and PMMA used in the classical simulation are modeled so as to reproduce the radial distribution functions and the vibrational density of states calculated by ab initio molecular dynamics simulations, where a stronger hydrogen-bonding interaction between water and methoxy oxygen of PMEA than the conventional molecular modeling predicts is found. The imaginary part of the second order nonlinear susceptibility is theoretically calculated for these two interfaces, showing a definite difference between them. The origin of the spectral difference is discussed on the basis of the decomposition analysis of the spectra and the interfacial molecular structures. [ABSTRACT FROM AUTHOR]

Molecular search phenomena are observed in a variety of chemical and biological systems. During the search, the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic modes. To understand the mechanisms of molecular search with alternating dynamics, we investigate the search dynamics with stochastic transitions between two conformations in a one-dimensional discrete-state stochastic model. It is explicitly analyzed using the first-passage time probability method to obtain a full dynamic description of the search process. A general dynamic phase diagram is developed. It is found that there are several dynamic regimes in the molecular search with conformational transitions, and they are determined by the relative values of the relevant length scales in the system. Theoretical predictions are fully supported by Monte Carlo computer simulations. [ABSTRACT FROM AUTHOR]

We present simulations of the force-extension curves of strong polyelectrolytes with varying intrinsic stiffness as well as specifically treating hyaluronic acid, a polyelectrolyte of intermediate stiffness. Whereas fully flexible polyelectrolytes show a high-force regime where extension increases nearly logarithmically with force, we find that the addition of even a small amount of stiffness alters the short-range structure and removes this logarithmic elastic regime. This further confirms that the logarithmic regime is a consequence of the short-ranged "wrinkles" in the flexible chain. As the stiffness increases, the force-extension curves tend toward and reach the wormlike chain behavior. Using the screened Coulomb potential and a simple bead-spring model, the simulations are able to reproduce the hyaluronic acid experimental force-extension curves for salt concentrations ranging from 1 to 500 mM. Furthermore, the simulation data can be scaled to a universal curve like the experimental data. The scaling analysis is consistent with the interpretation that, in the low-salt limit, the hyaluronic acid chain stiffness scales with salt with an exponent of −0.7, rather than either of the two main theoretical predictions of −0.5 and −1. Furthermore, given the conditions of the simulation, we conclude that this exponent value is not due to counterion condensation effects, as had previously been suggested. [ABSTRACT FROM AUTHOR]

The structural and dynamic properties of water molecules in a uniformly charged nanopore have been studied using the method of classical molecular dynamics simulation. When confined in an uncharged nanopore with an appropriate radius, water molecules are aligned along the nanopore axis and form a single-file structure with the dipole vectors pointing toward the same end of the nanopore. We demonstrate here that when the nanopore is uniformly charged, the water molecules in the nanopore pack more tightly and the water molecules near the two ends of the nanopore are no longer aligned along the nanopore axis but tend to be aligned perpendicularly to the nanopore axis. The water dipole vectors do not point toward the same nanopore end. When the nanopore is positively charged, the water molecules in the nanopore align with their oxygen atoms pointing to the center of the nanopore. The central water molecule forms an L-defect. However for a negatively charged nanopore, the water molecules in the nanopore take up the opposite orientation. A D-defect is formed at the center of the nanopore. Furthermore, the water molecules in the negatively charged nanopore with moderate atomic partial charges diffuse and transport more quickly than the water molecules in an uncharged nanopore. [ABSTRACT FROM AUTHOR]

Equimolar mixtures of glymes and organic lithium salts are known to produce solvate ionic liquids, in which the stability of the [Li(glyme)]+ complex plays an important role in determining the ionic dynamics. Since these mixtures have attractive physicochemical properties for application as electrolytes, it is important to understand the dependence of the stability of the [Li(glyme)]+ complex on the ion dynamics. A series of microsecond molecular dynamics simulations has been conducted to investigate the dynamic properties of these solvate ionic liquids. Successful solvate ionic liquids with high stability of the [Li(glyme)]+ complex have been shown to have enhanced ion dynamics. Li-glyme pair exchange rarely occurs: its characteristic time is longer than that of ion diffusion by one or two orders of magnitude. Li-glyme pair exchange most likely occurs through cluster formation involving multiple [Li(glyme)]+ pairs. In this process, multiple exchanges likely take place in a concerted manner without the production of energetically unfavorable free glyme or free Li+ ions. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics. [ABSTRACT FROM AUTHOR]

We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics simulations reveal a clear formation of S-DNA when the B-DNAis stretched along the 3′ directions of the opposite strands (OS3) and is characterized by the changes in the number of H-bonds, entropy, and free energy. Stretching along the 5′ directions of the opposite strands (OS5) leads to force induced melting form of theDNA. Interestingly, stretching along the opposite ends of the same strand leads to a coexistence of both the S- and melted M-DNA structures. We also do the structural characterization of the S-DNA by calculating various helical parameters. We find that the S-DNA has a twist of ~10° which corresponds to a helical repeat length of ~36 base pairs in close agreement with the previous experimental results. Moreover, we find that the free energy barrier between the canonical and overstretched states of DNA is higher for the same termini pulling protocol in comparison to all other protocols considered in this work. Overall, our observations not only reconcile with the available experimental results qualitatively but also enhance the understanding of different overstretched DNA structures. [ABSTRACT FROM AUTHOR]

The equation of state and the structure of liquid carbon are studied by molecular simulation. Both classical and quantum molecular dynamics (QMD) are used to calculate the equation of state and the distribution of chemical bonds at 6000 K in the pressure range 1-25 GPa. Our calculations and results of other authors show that liquid carbon has a fairly low density on the order of 1.2-1.35 g/cm³ at pressures about 1 GPa. Owing to the coordination number analysis, this fact can be attributed to the high content of sp¹-bonded atoms (more than 50% according to our ab initio computations). Six empirical potentials have been tested in order to describe the density dependence of pressure and structure at 6000 K. As a result, only one potential, ReaxFF/lg, was able to reproduce the QMD simulations for both the equation of state and the fraction of sp¹, sp², sp³-bonded atoms. [ABSTRACT FROM AUTHOR]

Hybrid simulations, in which a part of the system is treated with atomistic resolution and the remainder is represented on a coarse-grained level, allow for fast sampling while using the accuracy of atomistic force fields. We apply a hybrid scheme to study the mechanical unfolding and refolding of a molecular complex using force probe molecular dynamics (FPMD) simulations. The degrees of freedom of the solvent molecules are treated in a coarse-grained manner while atomistic resolution is retained for the solute. The coupling between the solvent and the solute is provided using virtual sites. We test two different common coarse-graining procedures, the iterative Boltzmann inversion method and the force matching procedure, and find that both methodologies give similar results. The results of the FPMD simulations are compared to all-atom simulations of the same system and we find that differences between these simulations and the ones using the hybrid scheme are in a similar range as the differences obtained when using different atomistic force fields. Thus, a hybrid scheme yields qualitatively correct results in the strong non-equilibrium situation the system is experiencing in FPMD simulations. [ABSTRACT FROM AUTHOR]

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm-1 for every local proton configuration, with the region 2000-2600 cm-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O...H+...O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H5O+2 moiety. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulation studies were performed to investigate the structural and dynamic properties of liquid carbon disulfide (CS2) from ambient to elevated pressure conditions. The results obtained have revealed structural changes at high pressures, which are related to the more dense packing of the molecules inside the first solvation shell. The calculated neutron and X-ray structure factors have been compared with available experimental diffraction data, also revealing the pressure effects on the short-range structure of the liquid. The pressure effects on the translational, reorientational, and residence dynamics are very strong, revealing a significant slowing down when going from ambient pressure to 1.2 GPa. The translational dynamics of the linear CS2 molecules have been found to be more anisotropic at elevated pressures, where cage effects and librational motions are reflected on the shape of the calculated time correlation functions and their corresponding spectral densities. [ABSTRACT FROM AUTHOR]

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na+, K+, and Cl- ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions. [ABSTRACT FROM AUTHOR]