arXiv subjects

Mariana Rossi

Publications and source records attributed to Mariana Rossi.

66 records · Page 4Linked to original sources

arXiv2018

i-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations

Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born-Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.

physics.chem-ph↗

arXiv2018

All-Electron, Real-Space Perturbation Theory for Homogeneous Electric Fields: Theory, Implementation, and Application within DFT

Within density-functional theory, perturbation theory~(PT) is the state-of-the-art formalism for assessing the response to homogeneous electric fields and the associated material properties, e.g., polarizabilities, dielectric constants, and Raman intensities. Here we derive a real-space formulation of PT and present an implementation within the all-electron, numeric atom-centered orbitals electronic structure code FHI-aims that allows for massively-parallel calculations. As demonstrated by extensive validation, this allows the rapid computation of accurate response properties of molecules and solids. As an application showcase, we present harmonic and anharmonic Raman spectra, the latter obtained by combining hundreds of thousands of PT calculations with \textit{ab initio} molecular dynamics. By using the PBE exchange-correlation functional with many-body van der Waals corrections, we obtain spectra in good agreement with experiment especially with respect to lineshapes for the isolated paracetamol molecule and two polymorphs of the paracetamol crystal.

cond-mat.mtrl-sci↗

arXiv2017

Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature

Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQE) influence properties of these systems. In this work, we explore the impact of NQE on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account conformational entropy and anharmonicities at finite temperatures. We propose that when when adsorption is weak and NQE on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We calculate the contribution of NQE to the free energies, including anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared to harmonic estimates. We also find that the dissociation has a negligible contribution from tunneling, but is dominated by ZPE, which can enhance the rate by three orders of magnitude. Finally we highlight how both temperature and NQE indirectly impact dipoles and the redistribution of electron density, causing work function to changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in work function provides a possible approach to determine experimentally the most stable configurations of water oligomers on the stepped surfaces.

physics.chem-ph↗

arXiv2017

Properties of the water to boron nitride interaction: from zero to two dimensions with benchmark accuracy

Molecular adsorption on surfaces plays an important part in catalysis, corrosion, desalination, and various other processes that are relevant to industry and in nature. As a complement to experiments, accurate adsorption energies can be obtained using various sophisticated electronic structure methods that can now be applied to periodic systems. The adsorption energy of water on boron nitride substrates, going from zero to 2-dimensional periodicity, is particularly interesting as it calls for an accurate treatment of polarizable electrostatics and dispersion interactions, as well as posing a practical challenge to experiments and electronic structure methods. Here, we present reference adsorption energies, static polarizabilities, and dynamic polarizabilities, for water on BN substrates of varying size and dimension. Adsorption energies are computed with coupled cluster theory, fixed-node quantum Monte Carlo (FNQMC), the random phase approximation (RPA), and second order Møller-Plesset (MP2) theory. These explicitly correlated methods are found to agree in molecular as well as periodic systems. The best estimate of the water/h-BN adsorption energy is $-107\pm7$ meV from FNQMC. In addition, the water adsorption energy on the BN substrates could be expected to grow monotonically with the size of the substrate due to increased dispersion interactions but interestingly, this is not the case here. This peculiar finding is explained using the static polarizabilities and molecular dispersion coefficients of the systems, as computed from time-dependent density functional theory (DFT). Dynamic as well as static polarizabilities are found to be highly anisotropic in these systems. In addition, the many-body dispersion method in DFT emerges as a particularly useful estimation of finite size effects for other expensive, many-body wavefunction based methods.

cond-mat.mtrl-sci↗

arXiv2017

Fine Tuning Classical and Quantum Molecular Dynamics using a Generalized Langevin Equation

Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level of control can be achieved for the dynamical properties computed from thermostatted trajectories. By developing quantitative measures of the disturbance induced by the GLE to the Hamiltonian dynamics of a harmonic oscillator, we show that these analytical results accurately predict the behavior of strongly anharmonic systems. We also show that it is possible to correct, to a significant extent, the effects of the GLE term onto the corresponding microcanonical dynamics, which puts on more solid grounds the use of non-equilibrium Langevin dynamics to approximate quantum nuclear effects and could help improve the prediction of dynamical quantities from techniques that use a Langevin term to stabilize dynamics. Finally we address the use of thermostats in the context of approximate path-integral-based models of quantum nuclear dynamics. We demonstrate that a custom-tailored GLE can alleviate some of the artifacts associated with these techniques, improving the quality of results for the modelling of vibrational dynamics of molecules, liquids and solids.

physics.chem-ph↗

arXiv2016

Stability of Complex Biomolecular Structures: Vander Waals, Hydrogen Bond Cooperativity, and Nuclear Quantum Effects

Biomolecules are complex systems stabilized by a delicate balance of weak interactions, making it important to assess all energetic contributions in an accurate manner. However, it is a priori unclear which contributions make more of an impact. Here, we examine stacked polyglutamine (polyQ) strands, a peptide repeat often found in amyloid aggregates. We investigate the role of hydrogen bond (HB) cooperativity, van der Waals (vdW) dispersion interactions, and quantum contributions to free energies, including anharmonicities through density functional theory and ab initio path integral simulations. Of these various factors, we find that the largest impact on structural stabilization comes from vdW interactions. HB cooperativity is the second largest contribution as the size of the stacked chain grows. Competing nuclear quantum effects make the net quantum contribution small but very sensitive to anharmonicities, vdW, and the number of HBs. Our results suggest that a reliable treatment of these systems can only be attained by considering all of these components.

physics.chem-ph↗

arXiv2016

Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general.

physics.chem-ph↗

arXiv2016

Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

Molecular crystals often exist in multiple competing polymorphs, showing significantly different physico-chemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form: A real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

cond-mat.mtrl-sci↗

arXiv2014

On the Consistency of Approximate Quantum Dynamics Simulation Methods for Vibrational Spectra in the Condensed Phase

Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these limitations can be traced down to two approaches: methods that treat a small subset of the degrees of freedom with rigorous quantum mechanics, considering the rest of the system as a static or classical environment, and methods that treat the whole system quantum mechanically, but using approximate dynamics. Here we perform a systematic comparison between these two philosophies for the description of quantum effects in vibrational spectroscopy, taking the Embedded Local Monomer (LMon) model and a mixed quantum-classical (MQC) model as representatives of the first family of methods, and centroid molecular dynamics (CMD) and thermostatted ring polymer molecular dynamics (TRPMD) as examples of the latter. We use as benchmarks D$_2$O doped with HOD and pure H$_2$O at three distinct thermodynamic state points (ice Ih at 150K, and the liquid at 300K and 600K), modeled with the simple q-TIP4P/F potential energy and dipole moment surfaces. With few exceptions the different techniques yield IR absorption frequencies that are consistent with one another within a few tens of cm$^{-1}$. Comparison with classical molecular dynamics demonstrates the importance of nuclear quantum effects up to the highest temperature, and a detailed discussion of the discrepancies between the various methods let us draw some (circumstantial) conclusions about the impact of the very different approximations that underlie them. Such cross validation between radically different approaches could indicate a way forward to further improve the state of the art in simulations of condensed-phase quantum dynamics.

physics.chem-ph↗

arXiv2014

How to remove the spurious resonances from ring polymer molecular dynamics

Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual differences, practical implementations of these methods differ in just two respects: the choice of the Parrinello-Rahman mass matrix and whether or not a thermostat is applied to the internal modes of the ring polymer during the dynamics. Here we explore a method which is halfway between the two approximations: we keep the path integral bead masses equal to the physical particle masses but attach a Langevin thermostat to the internal modes of the ring polymer during the dynamics. We justify this by showing analytically that the inclusion of an internal mode thermostat does not affect any of the desirable features of RPMD: thermostatted RPMD (TRPMD) is equally valid with respect to everything that has actually been proven about the method as RPMD itself. In particular, because of the choice of bead masses, the resulting method is still optimum in the short-time limit, and the transition state approximation to its reaction rate theory remains closely related to the semiclassical instanton approximation in the deep quantum tunneling regime. In effect, there is a continuous family of methods with these properties, parameterised by the strength of the Langevin friction. Here we explore numerically how the approximation to quantum dynamics depends on this friction, with a particular emphasis on vibrational spectroscopy. We find that a broad range of frictions approaching optimal damping give similar results, and that these results are immune to both the resonance problem of RPMD and the curvature problem of CMD.

physics.chem-ph↗

arXiv2012

Impact of vibrational entropy on the stability of unsolvated peptide helices with increasing length

Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address a part of this question in a bottom-up approach. We show how intrinsic helical structure is stabilized with length and temperature for a series of experimentally well studied unsolvated alanine based polypeptides, Ac-Alan-LysH+. By exploring extensively the conformational space of these molecules, we find that helices emerge as the preferred structure in the length range n=4-8 not just due to enthalpic factors (hydrogen bonds and their cooperativity, van der Waals dispersion interactions, electrostatics), but importantly also by a vibrational entropic stabilization over competing conformers at room temperature. The stabilization is shown to be due to softer low-frequency vibrational modes in helical conformers than in more compact ones. This observation is corroborated by including anharmonic effects explicitly through \emph{ab initio} molecular dynamics, and generalized by testing different terminations and considering larger helical peptide models.

physics.chem-ph↗

arXiv2007

Theoretical study of N-complexes in carbon nanotubes

We have made a systematic theoretical study to determine which are the most stable structures for substitutional nitrogen defects in carbon nanotubes, by making total energy calculations via DFT. These calculations were made for a (5,5) and a (8,0) nanotube to check the influence of chirality and for a graphene sheet, to check the limit of infinite diameter. In all these systems, we found that either substitutional nitrogen or structures containing two vacancies surrounded by four pyridine-like rings have the lowest formation energy, depending on the value of the nitrogen chemical potential. These defects have lower formation energies in nanotubes than in the graphene sheet.

cond-mat.other↗