Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance.

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable description of the underlying electronic structure in systems throughout biology, chemistry, physics, and materials science. However, the high computational cost associated with the evaluation of all required EXX quantities has limited the applicability of hybrid DFT in the treatment of large molecules and complex condensed-phase materials. To overcome this limitation, we describe a linear-scaling approach that utilizes a local representation of the occupied orbitals (e.g., maximally localized Wannier functions (MLWFs)) to exploit the sparsity in the real-space evaluation of the quantum mechanical exchange interaction in finite-gap systems. In this work, we present a detailed description of the theoretical and algorithmic advances required to perform MLWF-based ab initio molecular dynamics (AIMD) simulations of large-scale condensed-phase systems of interest at the hybrid DFT level. We focus our theoretical discussion on the integration of this approach into the framework of Car-Parrinello AIMD, and highlight the central role played by the MLWF-product potential (i.e., the solution of Poisson's equation for each corresponding MLWF-product density) in the evaluation of the EXX energy and wave function forces. We then provide a comprehensive description of the exx algorithm implemented in the open-source Quantum ESPRESSO program, which employs a hybrid MPI/OpenMP parallelization scheme to efficiently utilize the high-performance computing (HPC) resources available on current- and next-generation supercomputer architectures. This is followed by a critical assessment of the accuracy and parallel performance (e.g., strong and weak scaling) of this approach when AIMD simulations of liquid water are performed in the canonical (NVT) ensemble. With access to HPC resources, we demonstrate that exx enables hybrid DFT-based AIMD simulations of condensed-phase systems containing 500-1000 atoms (e.g., (H2O)256) with a wall time cost that is comparable to that of semilocal DFT. In doing so, exx takes us one step closer to routinely performing AIMD simulations of complex and large-scale condensed-phase systems for sufficiently long time scales at the hybrid DFT level of theory.

Reactivity and Transformation of Antimetastatic and Cytotoxic Rhodium(III)-Dimethyl Sulfoxide Complexes in Biological Fluids: An XAS Speciation Study.

Rhodium(III) anticancer drugs can exert preferential antimetastatic or cytotoxic activities, which are dependent on subtle structural changes. In order to delineate factors affecting the biotransformations and speciation, mer,cis-[RhCl3( S-dmso)2( O-dmso)] (A1) and mer,cis-[RhCl3( S-dmso)2(2N-indazole)] (A2) have been studied by X-ray absorption spectroscopy (XAS). Interactions of these complexes with saline buffer, cell culture media, serum proteins (albumin and apo-transferrin), native and chemically degraded collagen gels, and A549 cells have been studied using linear combination fitting (LCF) and 3D scatter plots of XAS data. Following initial aquation and hydrolysis reactions involving stepwise displacement of Cl- and S-/ O-dmso ligands, the Rh(III) complexes underwent further ligand substitution reactions with biological nucleophiles (e.g., amino acid residues of serum proteins). The reaction of A1 with chemically degraded collagen gel was postulated to be a key reason for its antimetastatic activity. Analyses of the XAS of Rh-treated bulk cells were consistent with structure-reactivity relationships in which the more reactive A1 was predominantly antimetastatic and the less reactive A2 was predominantly cytotoxic, showing relationships parallel to typical Ru(III) anticancer agents, i.e., NAMI-A ([ImH] trans-[RuCl4( S-dmso)( N-imidazole)2], ImH = imidazolium cation) and KP1019/NKP1339 (KP1019, [IndH] trans-[RuCl4(N-indazole)2], IndH = indazolium cation; NKP1339, sodium trans-[RuCl4(2N-indazole)2]), respectively.

On the geometric dependence of the molecular dipole polarizability in water: A benchmark study of higher-order electron correlation, basis set incompleteness error, core electron effects, and zero-point vibrational contributions.

In this work, we investigate how geometric changes influence the static dipole polarizability (α) of a water molecule by explicitly computing the corresponding dipole polarizability surface (DPS) across 3125 total (1625 symmetry-unique) geometries using linear response coupled cluster theory including single, double, and triple excitations (LR-CCSDT) and the doubly augmented triple-ζ basis set (d-aug-cc-pVTZ). Analytical formulae based on power series expansions of this ab initio surface are generated using linear least-squares analysis and provide highly accurate estimates of this quantity as a function of molecular geometry (i.e., bond and angle variations) in a computationally tractable manner. An additional database, which consists of 25 representative molecular geometries and incorporates a more thorough treatment of both basis sets and core electron effects, is provided as a current benchmark for this quantity and the corresponding leading-order C 6 dispersion coefficient. This database has been utilized to assess the importance of these effects as well as the relative accuracy that can be obtained using several quantum chemical methods and a library of density functional approximations. In addition to high-level electron correlation methods (like CCSD) and our analytical least-squares formulae, we find that the SCAN0, PBE0, MN15, and B97-2 hybrid functionals yield the most accurate descriptions of the molecular polarizability tensor in H2O. Using first-order perturbation theory, we compute the zero-point vibrational correction to α at the CCSDT/d-aug-cc-pVTZ level and find that this correction contributes approximately 3% to the isotropic (α iso) and nearly 50% to the anisotropic (α aniso) polarizability values. In doing so, we find that α iso = 9.8307 bohr3, which is in excellent agreement with the experimental value of 9.83 ± 0.02 bohr3 provided by Russell and Spackman. The DPS reported herein provides a benchmark-quality quantum mechanical estimate of this fundamental quantity of interest and should find extensive use in the development (and assessment) of next-generation force fields and machine-learning based approaches for modeling water in complex condensed-phase environments.

Unraveling substituent effects on the glass transition temperatures of biorenewable polyesters.

Converting biomass-based feedstocks into polymers not only reduces our reliance on fossil fuels, but also furnishes multiple opportunities to design biorenewable polymers with targeted properties and functionalities. Here we report a series of high glass transition temperature (Tg up to 184 °C) polyesters derived from sugar-based furan derivatives as well as a joint experimental and theoretical study of substituent effects on their thermal properties. Surprisingly, we find that polymers with moderate steric hindrance exhibit the highest Tg values. Through a detailed Ramachandran-type analysis of the rotational flexibility of the polymer backbone, we find that additional steric hindrance does not necessarily increase chain stiffness in these polyesters. We attribute this interesting structure-property relationship to a complex interplay between methyl-induced steric strain and the concerted rotations along the polymer backbone. We believe that our findings provide key insight into the relationship between structure and thermal properties across a range of synthetic polymers.

Exploiting Molecular Weight Distribution Shape to Tune Domain Spacing in Block Copolymer Thin Films.

We report a method for tuning the domain spacing ( Dsp) of self-assembled block copolymer thin films of poly(styrene- block-methyl methacrylate) (PS- b-PMMA) over a large range of lamellar periods. By modifying the molecular weight distribution (MWD) shape (including both the breadth and skew) of the PS block via temporal control of polymer chain initiation in anionic polymerization, we observe increases of up to 41% in Dsp for polymers with the same overall molecular weight ( Mn ≈ 125 kg mol-1) without significantly changing the overall morphology or chemical composition of the final material. In conjunction with our experimental efforts, we have utilized concepts from population statistics and least-squares analysis to develop a model for predicting Dsp based on the first three moments of the MWDs. This statistical model reproduces experimental Dsp values with high fidelity (with mean absolute errors of 1.2 nm or 1.8%) and provides novel physical insight into the individual and collective roles played by the MWD moments in determining this property of interest. This work demonstrates that both MWD breadth and skew have a profound influence over Dsp, thereby providing an experimental and conceptual platform for exploiting MWD shape as a simple and modular handle for fine-tuning Dsp in block copolymer thin films.

Different Ways of Hydrogen Bonding in Water - Why Does Warm Water Freeze Faster than Cold Water?

The properties of liquid water are intimately related to the H-bond network among the individual water molecules. Utilizing vibrational spectroscopy and modeling water with DFT-optimized water clusters (6-mers and 50-mers), 16 out of a possible 36 different types of H-bonds are identified and ordered according to their intrinsic strength. The strongest H-bonds are obtained as a result of a concerted push-pull effect of four peripheral water molecules, which polarize the electron density in a way that supports charge transfer and partial covalent character of the targeted H-bond. For water molecules with tetra- and pentacoordinated O atoms, H-bonding is often associated with a geometrically unfavorable positioning of the acceptor lone pair and donor σ*(OH) orbitals so that electrostatic rather than covalent interactions increasingly dominate H-bonding. There is a striking linear dependence between the intrinsic strength of H-bonding as measured by the local H-bond stretching force constant and the delocalization energy associated with charge transfer. Molecular dynamics simulations for 1000-mers reveal that with increasing temperature weak, preferentially electrostatic H-bonds are broken, whereas the number of strong H-bonds increases. An explanation for the question why warm water freezes faster than cold water is given on a molecular basis.

Vibrational Spectra of Molecular Crystals with the Generalized Energy-Based Fragmentation Approach.

The generalized energy-based fragmentation (GEBF) approach for molecular crystals with periodic boundary condition (PBC) (denoted as PBC-GEBF) is extended to allow vibrational spectra of molecular crystals to be easily computed at various theory levels. Within the PBC-GEBF approach, the vibrational frequencies of a molecular crystal can be directly evaluated from molecular quantum chemistry calculations on a series of nonperiodic molecular systems. With this approach, the vibrational spectra of molecular crystals can be calculated with much reduced computational costs at various theory levels, as compared to those required by the methods based on periodic electronic structure theory. By testing the performance of the PBC-GEBF method for two molecular crystals (CO2 and imidazole), we demonstrate that the PBC-GEBF approach can reproduce the results of the methods based on periodic electronic structure theory in predicting vibrational spectra of molecular crystals. We apply the PBC-GEBF method at second-order Møller-Plesset perturbation theory (PBC-GEBF-MP2 in short) to investigate the vibrational spectra of the urea and ammonia borane crystals. Our results show that the PBC-GEBF-MP2 method can provide quite accurate descriptions for the observed vibrational spectra of the two systems under study.