Robert A. DiStasio

Current Status of the AMOEBA Polarizable Force Field

Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.

Long-range correlation energy calculated from coupled atomic response functions

An accurate determination of the electron correlation energy is an essential prerequisite for describing the structure, stability, and function in a wide variety of systems. Therefore, the development of efficient approaches for the calculation of the correlation energy (and hence the dispersion energy as well) is essential and such methods can be coupled with many density-functional approximations, local methods for the electron correlation energy, and even interatomic force fields. In this work, we build upon the previously developed many-body dispersion (MBD) framework, which is intimately linked to the random-phase approximation for the correlation energy. We separate the correlation energy into short-range contributions that are modeled by semi-local functionals and long-range contributions that are calculated by mapping the complex all-electron problem onto a set of atomic response functions coupled in the dipole approximation. We propose an effective range-separation of the coupling between the atomic response functions that extends the already broad applicability of the MBD method to non-metallic materials with highly anisotropic responses, such as layered nanostructures. Application to a variety of high-quality benchmark datasets illustrates the accuracy and applicability of the improved MBD approach, which offers the prospect of first-principles modeling of large structurally complex systems with an accurate description of the long-range correlation energy.

Advanced capabilities for materials modelling with Quantum ESPRESSO

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Collective many-body van der Waals interactions in molecular systems

Van der Waals (vdW) interactions are ubiquitous in molecules and condensed matter, and play a crucial role in determining the structure, stability, and function for a wide variety of systems. The accurate prediction of these interactions from first principles is a substantial challenge because they are inherently quantum mechanical phenomena that arise from correlations between many electrons within a given molecular system. We introduce an efficient method that accurately describes the nonadditive many-body vdW energy contributions arising from interactions that cannot be modeled by an effective pairwise approach, and demonstrate that such contributions can significantly exceed the energy of thermal fluctuations—a critical accuracy threshold highly coveted during molecular simulations—in the prediction of several relevant properties. Cases studied include the binding affinity of ellipticine, a DNA-intercalating anticancer agent, the relative energetics between the A- and B-conformations of DNA, and the thermodynamic stability among competing paracetamol molecular crystal polymorphs. Our findings suggest that inclusion of the many-body vdW energy is essential for achieving chemical accuracy and therefore must be accounted for in molecular simulations.

Report on the sixth blind test of organic crystal structure prediction methods

The results of the sixth blind test of organic crystal structure prediction methods are presented and discussed, highlighting progress for salts, hydrates and bulky flexible molecules, as well as on-going challenges.

Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

Polymorphs of molecular crystals are often very close in energy, yet they may possess very different physical and chemical properties. The understanding of polymorphism is therefore of great importance for a variety of applications, ranging from drug design to nonlinear optics and hydrogen storage. While the crystal structure prediction blind tests conducted by the Cambridge Crystallographic Data Centre have shown steady progress toward reliable structure prediction for molecular crystals, several challenges remain, including molecular salts, hydrates, and flexible molecules with several stable conformers. The ability to identify and rank all of the relevant polymorphs of a given molecular crystal hinges on an accurate description of their relative energetic stability. Hence, a first-principles quantum mechanical method that can attain the required accuracy of around 0.1–0.2 kcalmol 1 would clearly be an indispensable tool for polymorph prediction. In this work, we show that accounting for the nonadditive many-body dispersion (MBD) energy beyond the standard pairwise approximation is crucial for the correct qualitative and quantitative description of polymorphism in molecular crystals. We demonstrate this through three fundamental and stringent benchmark examples: glycine, oxalic acid, and tetrolic acid. These systems represent a broad class of molecular crystals, comprising hydrogenbonded (H-bonded) networks of amino acids and carboxylic acids. Among the first-principles methods, density functional theory (DFT) is the most widely used approach in the study of polymorphism in molecular crystals. However, most common exchange-correlation functionals (including hybrid functionals) are based on semi-local electron correlation, and thereby fail to capture the contribution of dispersion interactions to the stability of molecular crystals. These ubiquitous noncovalent interactions are quantum mechanical in nature and correspond to the multipole moments induced in response to instantaneous fluctuations in the electron density. To incorporate these long-range electron correlation effects within DFT, significant progress has been made by using the standard C6/R 6 pairwise additive expression for the dispersion energy. Indeed, DFT with pairwise dispersion terms can yield accurate results when the energy differences between molecular crystal polymorphs are sufficiently large. Notably, Neumann et al. have achieved the highest success rate in the last two blind tests using such methods. However, these pairwise dispersion approaches, even when used in conjunction with state-of-the-art functionals, are still unable to reach the level of accuracy required to describe polymorphism in many relevant molecular crystals, including glycine and oxalic acid. Recently, a novel and efficient method for describing the many-body dispersion (MBD) energy has been developed, building upon the Tkatchenko–Scheffler (TS) pairwise method. Within the TS approach, the effective dispersion coefficients (C6) are calculated from the DFTelectron density, hence the effect of the local environment of an atom in a molecule is accurately accounted for by construction. The MBD method presents a two-fold improvement over the TS approach by including: 1) the long-range electrodynamic screening through the self-consistent solution of the dipole– dipole electric-field coupling equations for the effective polarizability, and 2) the non-pairwise-additive many-body dispersion energy to infinite order through diagonalization of the Hamiltonian corresponding to a system of coupled fluctuating dipoles. The inclusion of the MBD energy in DFT leads to a significant improvement in the binding energies between organic molecules, and for the cohesion of the benzene and oligoacene molecular crystals. The MBD energy, like the TS energy, can be added to any DFT functional, requiring only the adjustment of a single rangeseparation parameter per functional. [*] N. Marom, J. R. Chelikowsky Center for Computational Materials Institute for Computational Engineering and Sciences The University of Texas at Austin Austin, TX 78712 (USA) E-mail: noa@ices.utexas.edu

Interatomic methods for the dispersion energy derived from the adiabatic connection fluctuation-dissipation theorem

Interatomic pairwise methods are currently among the most popular and accurate ways to include dispersion energy in density functional theory calculations. However, when applied to more than two atoms, these methods are still frequently perceived to be based on ad hoc assumptions, rather than a rigorous derivation from quantum mechanics. Starting from the adiabatic connection fluctuation-dissipation (ACFD) theorem, an exact expression for the electronic exchange-correlation energy, we demonstrate that the pairwise interatomic dispersion energy for an arbitrary collection of isotropic polarizable dipoles emerges from the second-order expansion of the ACFD formula upon invoking the random-phase approximation (RPA) or the full-potential approximation. Moreover, for a system of quantum harmonic oscillators coupled through a dipole-dipole potential, we prove the equivalence between the full interaction energy obtained from the Hamiltonian diagonalization and the ACFD-RPA correlation energy. This property makes the Hamiltonian diagonalization an efficient method for the calculation of the many-body dispersion energy. In addition, we show that the switching function used to damp the dispersion interaction at short distances arises from a short-range screened Coulomb potential, whose role is to account for the spatial spread of the individual atomic dipole moments. By using the ACFD formula, we gain a deeper understanding of the approximations made in the interatomic pairwise approaches, providing a powerful formalism for further development of accurate and efficient methods for the calculation of the dispersion energy.

A resolution-of-the-identity implementation of the local triatomics-in-molecules model for second-order Moller-Plesset perturbation theory with application to alanine tetrapeptide conformational energies

In this work, we incorporate the resolution-of-the-identity (RI) approximation into the theoretical framework of the local triatomics-in-molecules (TRIM) second-order Møller-Plesset (MP2) perturbation theory model. The resultant model, RI-TRIM MP2, emerges as a robust fourth-order methodology that extends the regime of practical MP2 calculations. With RI-TRIM MP2, correlation energy corrections can easily be obtained for systems that contain more than 125 heavy atoms with a computational timing cost less than those of the prerequisite self-consistent field procedure and popular density functional theory (DFT) alternatives. In this work, the chemical performance of RI-TRIM MP2 is numerically assessed against untruncated RI-MP2 and DFT (B3LYP) in determining the relative energies of 27 different alanine tetrapeptide conformations at the cc-pVXZ (X = D, T, and Q) levels and the results are T → Q extrapolated to the complete basis set limit. As the quality of the basis set employed increases, we report a significant reduction in the error introduced by the RI-TRIM approximation; at the cc-pVDZ level, the root mean-square (RMS) relative error was found as 0.192 kcal/mol and is decreased to an almost negligible 0.040 kcal/mol at the T → Q extrapolated complete basis set limit. Basis set dependence was investigated by computing the RMS (max) deviations from the extrapolated RI-MP2/cc-pV(TQ)Z data set found as 0.377 (0.944) kcal/mol (MP2/cc-pVTZ) and 0.250 (0.591) kcal/mol (TRIM MP2/cc-pVTZ). These deviations are chemically significant when compared against the conformer energy differences, suggesting that to obtain reliably converged relative conformational energies, computations must be done using the cc-pVTZ and cc-pVQZ basis sets followed by extrapolation to the cc-pV(TQ)Z limit. The findings reported herein also provide the first computational evidence demonstrating that the TRIM model approaches exactness as the one-particle basis approaches completeness.

Wavelike charge density fluctuations and van der Waals interactions at the nanoscale

Describing dispersion forces Dispersion or van der Waals interactions are attractive forces that arise from induced dipoles. They are not seen just in atoms and molecules but also in larger nanostructures and even macroscopic objects. Ambrosetti et al. created a qualitatively correct description of van der Waals interactions between polarizable nanostructures over a wide range of finite distances. This required delocalized electrons that have wavelike electron density fluctuations, unlike the more common approaches with dipoles fixed on atoms. Furthermore, the authors observed an enhancement in the nonlocality of the charge density response on the scale of 10 to 20 nm. Science, this issue p. 1171 The description of van der Waals interactions in nanostructures must include delocalized electron density fluctuations. Recent experiments on noncovalent interactions at the nanoscale have challenged the basic assumptions of commonly used particle- or fragment-based models for describing van der Waals (vdW) or dispersion forces. We demonstrate that a qualitatively correct description of the vdW interactions between polarizable nanostructures over a wide range of finite distances can only be attained by accounting for the wavelike nature of charge density fluctuations. By considering a diverse set of materials and biological systems with markedly different dimensionalities, topologies, and polarizabilities, we find a visible enhancement in the nonlocality of the charge density response in the range of 10 to 20 nanometers. These collective wavelike fluctuations are responsible for the emergence of nontrivial modifications of the power laws that govern noncovalent interactions at the nanoscale.

Local structure analysis in ab initio liquid water

Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps – a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.