Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis

Given the piecewise approach to modeling intermolecular interactions for force fields, they can be difficult to parameterize since they are fit to data like total energies that only indirectly connect to their separable functional forms. Furthermore, by neglecting certain types of molecular interactions such as charge penetration and charge transfer, most classical force fields must rely on, but do not always demonstrate, how cancellation of errors occurs among the remaining molecular interactions accounted for such as exchange repulsion, electrostatics, and polarization. In this work we present the first generation of the (many-body) MB-UCB force field that explicitly accounts for the decomposed molecular interactions commensurate with a variational energy decomposition analysis, including charge transfer, with force field design choices that reduce the computational expense of the MB-UCB potential while remaining accurate. We optimize parameters using only single water molecule and water cluster data up through pentamers, with no fitting to condensed phase data, and we demonstrate that high accuracy is maintained when the force field is subsequently validated against conformational energies of larger water cluster data sets, radial distribution functions of the liquid phase, and the temperature dependence of thermodynamic and transport water properties. We conclude that MB-UCB is comparable in performance to MB-Pol, but is less expensive and more transferable by eliminating the need to represent short-ranged interactions through large parameter fits to high order polynomials

Understanding brønsted-acid catalyzed monomolecular reactions of Alkanes in Zeolite Pores by combining insights from experiment and theory

Acidic zeolites are effective catalysts for the cracking of large hydrocarbon molecules into lower molecular weight products required for transportation fuels. However, the ways in which the zeolite structure affects the catalytic activity at BrOnsted protons are not fully understood. One way to characterize the influence of the zeolite structure on the catalysis is to study alkane cracking and dehydrogenation at very low conversion, conditions for which the kinetics are well defined. To understand the effects of zeolite structure on the measured rate coefficient (k(app)), it is necessary to identify the equilibrium constant for adsorption into the reactant state (Kads-H+) and the intrinsic rate coefficient of the reaction (k(int)) at reaction temperatures, since k(app) is proportional to the product of Kads-H+ and k(int). We show that Kads-H+ cannot be calculated from experimental adsorption data collected near ambient temperature, but can, however, be estimated accurately from configurational-bias Monte Carlo (CBMC) simulations. Using monomolecular cracking and dehydrogenation of C-3-C-6 alkanes as an example, we review recent efforts aimed at elucidating the influence of the acid site location and the zeolite framework structure on the observed values of k(app) and its components, Kads-H+ and k(int)

Inelastic transport theory from first-principles: methodology and applications for nanoscale devices

We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TranSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green's function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in [Frederiksen et al., Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.Comment: 24 pages, 17 figure

Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

Structure optimization in an off-lattice protein model

We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the pruned-enriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off lattice models. For 2 dimensions we found states with lower energy than previously proposed putative ground states, for all chain lengths $\ge 13$. This indicates that PERM has the potential to produce native states also for more realistic protein models. For $d=3$, where no published ground states exist, we present some putative lowest energy states for future comparison with other methods.Comment: 4 pages, 2 figure

Entanglement Measures for Single- and Multi-Reference Correlation Effects

Electron correlation effects are essential for an accurate ab initio description of molecules. A quantitative a priori knowledge of the single- or multi-reference nature of electronic structures as well as of the dominant contributions to the correlation energy can facilitate the decision regarding the optimum quantum chemical method of choice. We propose concepts from quantum information theory as orbital entanglement measures that allow us to evaluate the single- and multi-reference character of any molecular structure in a given orbital basis set. By studying these measures we can detect possible artifacts of small active spaces.Comment: 14 pages, 4 figure

Liquid State Anomalies for the Stell-Hemmer Core-Softened Potential

We study the Stell-Hemmer potential using both analytic (exact $1d$ and approximate $2d$) solutions and numerical $2d$ simulations. We observe in the liquid phase an anomalous decrease in specific volume and isothermal compressibility upon heating, and an anomalous increase in the diffusion coefficient with pressure. We relate the anomalies to the existence of two different local structures in the liquid phase. Our results are consistent with the possibility of a low temperature/high pressure liquid-liquid phase transition.Comment: 4 pages in one gzipped ps file including 11 figures; One RevTex and 11 gzipped eps figure

Ab initio coupled-cluster and configuration interaction calculations for 16-O using V_UCOM

Using the ground-state energy of 16-O obtained with the realistic V_UCOM interaction as a test case, we present a comprehensive comparison of different configuration interaction (CI) and coupled-cluster (CC) methods, analyzing the intrinsic advantages and limitations of each of the approaches. In particular, we use the importance-truncated (IT) CI and no-core shell model (NCSM) schemes with up to 4-particle-4-hole (4p4h) excitations as well as the size extensive CC methods with a complete treatment of one- and two-body clusters (CCSD) and a non-iterative treatment of connected three-body clusters via the completely renormalized correction to the CCSD energy defining the CR-CC(2,3) approach. We discuss the impact of the center-of-mass contaminations, the choice of the single-particle basis, and size-extensivity on the resulting energies. When the IT-CI and IT-NCSM methods include the 4p4h excitations and when the CC calculations include the 1p1h, 2p2h, and 3p3h clusters, as in the CR-CC(2,3) approach, we observe an excellent agreement among the different methodologies. This shows that despite their individual limitations, the IT-CI, IT-NCSM, and CC methods can provide precise and consistent ab initio nuclear structure predictions. Furthermore, the IT-CI, IT-NCSM, and CC ground-state energy values obtained with 16-O are in good agreement with the experimental value, proving that the V_UCOM two-body interaction allows for a realistic description of binding energies for heavier nuclei and that all of the methods used in this study account for most of the relevant particle correlation effects.Comment: 20 pages, 4 figures, 1 table (v2: extended version in response to referees' comments