Understanding non-covalent interactions in larger molecular complexes from first principles

in Journal of Chemical Physics (2019), 150

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non ... [more ▼]

Non-covalent interactions pervade all matter and play a fundamental role in layered materials, biological systems, and large molecular complexes. Despite this, our accumulated understanding of non-covalent interactions to date has been mainly developed in the tens-of-atoms molecular regime. This falls considerably short of the scales at which we would like to understand energy trends, structural properties, and temperature dependencies in materials where non-covalent interactions have an appreciable role. However, as more reference information is obtained beyond moderately sized molecular systems, our understanding is improving and we stand to gain pertinent insights by tackling more complex systems, such as supramolecular complexes, molecular crystals, and other soft materials. In addition, accurate reference information is needed to provide the drive for extending the predictive power of more efficient workhorse methods, such as density functional approximations that also approximate van der Waals dispersion interactions. In this perspective, we discuss the first-principles approaches that have been used to obtain reference interaction energies for beyond modestly sized molecular complexes. The methods include quantum Monte Carlo, symmetry-adapted perturbation theory, non-canonical coupled cluster theory, and approaches based on the random-phase approximation. By considering the approximations that underpin each method, the most accurate theoretical references for supramolecular complexes and molecular crystals to date are ascertained. With these, we also assess a handful of widely used exchange-correlation functionals in density functional theory. The discussion culminates in a framework for putting into perspective the accuracy of high-level wavefunction-based methods and identifying future challenges. [less ▲]

Stability of functionalized platform molecules on Au(111)

in Journal of Chemical Physics (2018), 149

Trioxatriangulenium (TOTA) platform molecules were functionalized with methyl, ethyl, ethynyl, propynyl, and hydrogen and sublimated onto Au(111) surfaces. Low-temperature scanning tunneling microscopy ... [more ▼]

Trioxatriangulenium (TOTA) platform molecules were functionalized with methyl, ethyl, ethynyl, propynyl, and hydrogen and sublimated onto Au(111) surfaces. Low-temperature scanning tunneling microscopy data reveal that >99% of ethyl-TOTA and methyl-TOTA remain intact, whereas 60% of H-TOTA and >99% of propynyl-TOTA and ethynyl-TOTA decompose. The observed tendency toward fragmentation on Au(111) is opposite to the sequence of gas-phase stabilities of the molecules. Although Au(111) is the noblest of all metal surfaces, the binding energies of the decomposition products to Au(111) destabilize the functionalized platforms by 2 to 3.9 eV (190–370 kJ/mol) and even render some of them unstable as revealed by density functional theory calculations. Van der Waals forces are important, as they drive the adsorption of the platform molecules. [less ▲]

Quantum tunneling of thermal protons through pristine graphene

in Journal of Chemical Physics (2018), 148(20), 204707

Engineering of atomically thin membranes for hydrogen isotope separation is an actual challenge which has a broad range of applications. Recent experiments [M. Lozada-Hidalgo et al., Science 351, 68 (2016 ... [more ▼]

Engineering of atomically thin membranes for hydrogen isotope separation is an actual challenge which has a broad range of applications. Recent experiments [M. Lozada-Hidalgo et al., Science 351, 68 (2016)] unambiguously demonstrate an order-of-magnitude difference in permeabilities of graphene-based membranes to protons and deuterons at ambient conditions, making such materials promising for novel separation technologies. Here we demonstrate that the permeability mechanism in such systems changes from quantum tunneling for protons to quasi-classical transport for heavier isotopes. Quantum nuclear effects exhibit large temperature and mass dependence, modifying the Arrhenius activation energy and Arrhenius prefactor for protons by more than 0.5 eV and by seven orders of magnitude correspondingly. Our findings not only shed light on the separation process for hydrogen isotope ions passing through pristine graphene but also offer new insights for controlling ion transport mechanisms in nanostructured separation membranes by manipulating the shape of the barrier and transport process conditions. [less ▲]

Perturbed path integrals in imaginary time: Efficiently modeling nuclear quantum effects in molecules and materials

in Journal of Chemical Physics (2018), 148(10), 102325

Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials ... [more ▼]

Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials. In this work, we extend our recently proposed perturbed path-integral (PPI) approach for modeling NQE in molecular systems [I. Poltavsky and A. Tkatchenko, Chem. Sci. 7, 1368 (2016)], which successfully combines the advantages of thermodynamic perturbation theory with path-integral molecular dynamics (PIMD), in a number of important directions. First, we demonstrate the accuracy, performance, and general applicability of the PPI approach to both molecules and extended (condensed-phase) materials. Second, we derive a series of estimators within the PPI approach to enable calculations of structural properties such as radial distribution functions (RDFs) that exhibit rapid convergence with respect to the number of beads in the PIMD simulation. Finally, we introduce an effective nuclear temperature formalism within the framework of the PPI approach and demonstrate that such effective temperatures can be an extremely useful tool in quantitatively estimating the “quantumness” associated with different degrees of freedom in the system as well as providing a reliable quantitative assessment of the convergence of PIMD simulations. Since the PPI approach only requires the use of standard second-order imaginary-time PIMD simulations, these developments enable one to include a treatment of NQE in equilibrium thermodynamic properties (such as energies, heat capacities, and RDFs) with the accuracy of higher-order methods but at a fraction of the computational cost, thereby enabling first-principles modeling that simultaneously accounts for the quantum mechanical nature of both electrons and nuclei in large-scale molecules and materials. [less ▲]

Conservation laws and work fluctuation relations in chemical reaction networks

in Journal of Chemical Physics (2018), 149(24),

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

in Journal of Chemical Physics (2017), 147

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 ... [more ▼]

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, and second order Møller-Plesset theory. These wavefunction based 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 ± 7 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. [less ▲]

Isotropic-nematic transition and cholesteric phases of helical Yukawa rods

in Journal of Chemical Physics (2016), 145(194904),

We present a Monte Carlo simulation study of helical Yukawa rods as a model for chiral liquid crystal mesogens.To simulate the cholesteric phase, we introduce a newsimulation method that uses softwalls ... [more ▼]

We present a Monte Carlo simulation study of helical Yukawa rods as a model for chiral liquid crystal mesogens.To simulate the cholesteric phase, we introduce a newsimulation method that uses softwalls and self-determined boundary conditions. We observe that the isotropic-nematic phase transition is shifted to lower volume fractions with decreasing salt concentration as well as with increasing internal pitch of the rods. For particular sets of interaction parameters, the sense of the cholesteric pitch inverts, i.e., depending on concentration, mesogens of a given handedness can produce cholesteric phases of both chiral senses. [less ▲]

Structure diagram of binary Lennard-Jones clusters

in Journal of Chemical Physics (2016), 145(024302),

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and ... [more ▼]

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory. lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures. [less ▲]

The early crystal nucleation process in hard spheres shows synchronised ordering and densification

in Journal of Chemical Physics (2016), 145

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the ... [more ▼]

We investigate the early part of the crystal nucleation process in the hard sphere fluid using data produced by computer simulation. We find that hexagonal order manifests continuously in the overcompressed liquid, beginning approximately one diffusion time before the appearance of the first “solid-like” particle of the nucleating cluster, and that a collective influx of particles towards the nucleation site occurs simultaneously to the ordering process: the density increases leading to nucleation are generated by the same individual particle displacements as the increases in order. We rule out the presence of qualitative differences in the early nucleation process between medium and low overcompressions and also provide evidence against any separation of translational and orientational order on the relevant lengthscales. [less ▲]

Glucans monomer-exchange dynamics as an open chemical network

in Journal of Chemical Physics (2015), 143

We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming ... [more ▼]

We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them. [less ▲]