# Showing papers in "Journal of Chemical Physics in 2012"

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TL;DR: This perspective reviews some recent progress and ongoing challenges in density functional theory.

Abstract: Density functional theory (DFT) is an incredible success story. The low computational cost, combined with useful (but not yet chemical) accuracy, has made DFT a standard technique in most branches of chemistry and materials science. Electronic structure problems in a dazzling variety of fields are currently being tackled. However, DFT has many limitations in its present form: too many approximations, failures for strongly correlated systems, too slow for liquids, etc. This perspective reviews some recent progress and ongoing challenges.

1,303 citations

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TL;DR: The last decade has seen a surge of enthusiasm in the DFT community to tackle this problem and in so-doing to extend the applicability of DFT-based methods, and some of the promising schemes to emerge in recent years are discussed.

Abstract: Electron dispersion forces play a crucial role in determining the structure and properties of biomolecules, molecular crystals, and many other systems. However, an accurate description of dispersion is highly challenging, with the most widely used electronic structure technique, density functional theory (DFT), failing to describe them with standard approximations. Therefore, applications of DFT to systems where dispersion is important have traditionally been of questionable accuracy. However, the last decade has seen a surge of enthusiasm in the DFT community to tackle this problem and in so-doing to extend the applicability of DFT-based methods. Here we discuss, classify, and evaluate some of the promising schemes to emerge in recent years. A brief perspective on the outstanding issues that remain to be resolved and some directions for future research are also provided.

930 citations

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TL;DR: A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid-solid transformations involving both atomic and unit-cell degrees of freedom and it is demonstrated that the method is robust for mechanisms dominated either by atomic motion or by unit- cell deformation.

Abstract: A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid–solid transformations involving both atomic and unit-cell degrees of freedom. We combine atomic and cell degrees of freedom into a unified description of the crystal structure so that calculated reaction paths are insensitive to the choice of periodic cell. For the rock-salt to wurtzite transition in CdSe, we demonstrate that the method is robust for mechanisms dominated either by atomic motion or by unit-cell deformation; notably, the lowest-energy transition mechanism found by our G-SSNEB changes with cell size from a concerted transformation of the cell coordinates in small cells to a nucleation event in large cells. The method is efficient and can be applied to systems in which the force and stress tensor are calculated using density functional theory.

687 citations

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Yale University

^{1}TL;DR: This Perspective examines the most significant theoretical and computational obstacles to achieving nonadiabatic dynamics realism, and suggests some possible strategies that may prove fruitful.

Abstract: Nonadiabatic dynamics—nuclear motion evolving on multiple potential energy surfaces—has captivated the interest of chemists for decades. Exciting advances in experimentation and theory have combined to greatly enhance our understanding of the rates and pathways of nonadiabatic chemical transformations. Nevertheless, there is a growing urgency for further development of theories that are practical and yet capable of reliable predictions, driven by fields such as solar energy, interstellar and atmospheric chemistry, photochemistry, vision, single molecule electronics, radiation damage, and many more. This Perspective examines the most significant theoretical and computational obstacles to achieving this goal, and suggests some possible strategies that may prove fruitful.

524 citations

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TL;DR: A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented, and an atom pair-wise potential corrects for the inter- and intra- molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations.

Abstract: A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza’s S66×8 set of non-covalently bound complexes (528 data points). The method’s target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%‐30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen’s ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanineglycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFTD3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCPcorrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza’s S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author’s website. © 2012 American Institute of Physics .[ http://dx.doi.org/10.1063/1.3700154]

503 citations

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TL;DR: A methodology for the rigorous nonperturbative derivation of magnetic pseudospin Hamiltonians of mononuclear complexes and fragments based on ab initio calculations of their electronic structure is described and working expressions are derived for the pseudospIn Zeeman and zero-field splitting Hamiltonian corresponding to arbitrary pseudospins.

Abstract: A methodology for the rigorous nonperturbative derivation of magnetic pseudospin Hamiltonians of mononuclear complexes and fragments based on ab initio calculations of their electronic structure is described. It is supposed that the spin-orbit coupling and other relativistic effects are already taken fully into account at the stage of quantum chemistry calculations of complexes. The methodology is based on the establishment of the correspondence between the ab initio wave functions of the chosen manifold of multielectronic states and the pseudospin eigenfunctions, which allows to define the pseudospin Hamiltonians in the unique way. Working expressions are derived for the pseudospin Zeeman and zero-field splitting Hamiltonian corresponding to arbitrary pseudospins. The proposed calculation methodology, already implemented in the SINGLE_ANISO module of the MOLCAS-7.6 quantum chemistry package, is applied for a first-principles evaluation of pseudospin Hamiltonians of several complexes exhibiting weak, moderate, and very strong spin-orbit coupling effects.

502 citations

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TL;DR: The connections between amorphous structure, high frequency motions, molecular motion, structural relaxation, stability against crystallization, and material properties, and the interpretation of supercooled liquid and glass properties in terms of the potential energy landscape is explored.

Abstract: Supercooled liquids and glasses are important for current and developing technologies. Here we provide perspective on recent progress in this field. The interpretation of supercooled liquid and glass properties in terms of the potential energy landscape is discussed. We explore the connections between amorphous structure, high frequency motions, molecular motion, structural relaxation, stability against crystallization, and material properties. Recent developments that may lead to new materials or new applications of existing materials are described.

476 citations

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TL;DR: An alternative method of simulating fermions with qubits, first proposed by Bravyi and Kitaev, is developed that reduces the simulation cost to O(log n) qubit operations for one fermionic operation and demonstrates the superior efficiency of the Bravyi-Kitaev method for all quantum computations of electronic structure.

Abstract: Quantum simulation is an important application of future quantum computers with applications in quantum chemistry, condensed matter, and beyond. Quantum simulation of fermionic systems presents a specific challenge. The Jordan-Wigner transformation allows for representation of a fermionic operator by O(n) qubit operations. Here, we develop an alternative method of simulating fermions with qubits, first proposed by Bravyi and Kitaev [Ann. Phys. 298, 210 (2002); e-print arXiv:quant-ph/0003137v2], that reduces the simulation cost to O(log n) qubit operations for one fermionic operation. We apply this new Bravyi-Kitaev transformation to the task of simulating quantum chemical Hamiltonians, and give a detailed example for the simplest possible case of molecular hydrogen in a minimal basis. We show that the quantum circuit for simulating a single Trotter time step of the Bravyi-Kitaev derived Hamiltonian for H(2) requires fewer gate applications than the equivalent circuit derived from the Jordan-Wigner transformation. Since the scaling of the Bravyi-Kitaev method is asymptotically better than the Jordan-Wigner method, this result for molecular hydrogen in a minimal basis demonstrates the superior efficiency of the Bravyi-Kitaev method for all quantum computations of electronic structure.

452 citations

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TL;DR: Decoherence provides physical justification of surface hopping, obviating the need for ad hoc surface hopping rules and providing an improvement over the most popular surface hopping technique.

Abstract: A simple surface hopping method for nonadiabatic molecular dynamics is developed. The method derives from a stochastic modeling of the time-dependent Schrodinger and master equations for open systems and accounts simultaneously for quantum mechanical branching in the otherwise classical (nuclear) degrees of freedom and loss of coherence within the quantum (electronic) subsystem due to coupling to nuclei. Electronic dynamics in the Hilbert space takes the form of a unitary evolution, intermittent with stochastic decoherence events that are manifested as a localization toward (adiabatic) basis states. Classical particles evolve along a single potential energy surface and can switch surfaces only at the decoherence events. Thus, decoherence provides physical justification of surface hopping, obviating the need for ad hoc surface hopping rules. The method is tested with model problems, showing good agreement with the exact quantum mechanical results and providing an improvement over the most popular surface hopping technique. The method is implemented within real-time time-dependent density functional theory formulated in the Kohn-Sham representation and is applied to carbon nanotubes and graphene nanoribbons. The calculated time scales of non-radiative quenching of luminescence in these systems agree with the experimental data and earlier calculations.

437 citations

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Jilin University

^{1}TL;DR: It is found that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency.

Abstract: We have developed an efficient method for cluster structure prediction based on the generalization of particle swarm optimization (PSO). A local version of PSO algorithm was implemented to utilize a fine exploration of potential energy surface for a given non-periodic system. We have specifically devised a technique of so-called bond characterization matrix (BCM) to allow the proper measure on the structural similarity. The BCM technique was then employed to eliminate similar structures and define the desirable local search spaces. We find that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency. We have incorporated Metropolis criterion into our method to further enhance the structural evolution towards low-energy regimes of potential energy surfaces. Our method has been extensively benchmarked on Lennard-Jones clusters with different sizes up to 150 atoms and applied into prediction of new structures of medium-sized Lin (n = 20, 40, 58) clusters. High search efficiency was achieved, demonstrating the reliability of the current methodology and its promise as a major method on cluster structure prediction.

430 citations

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TL;DR: The self-consistent continuum solvation model provides a very effective and compact fit of computational and experimental data, whereby the static dielectric constant of the solvent and one parameter allow to fit the electrostatic energy provided by the polarizable continuum model with a mean absolute error of 0.3 kcal/mol on a set of 240 neutral solutes.

Abstract: The solvation model proposed by Fattebert and Gygi [J. Comput. Chem. 23, 662 (2002)] and Scherlis et al. [J. Chem. Phys. 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. We first recast the problem in terms of induced polarization charges that act as a direct mapping of the self-consistent continuum dielectric; this allows to define a functional form for the dielectric that is well behaved both in the high-density region of the nuclear charges and in the low-density region where the electronic wavefunctions decay into the solvent. Second, we outline an iterative procedure to solve the Poisson equation for the quantum fragment embedded in the solvent that does not require multigrid algorithms, is trivially parallel, and can be applied to any Bravais crystallographic system. Last, we capture some of the non-electrostatic or cavitation terms via a combined use of the quantum volume and quantum surface [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)] of the solute. The resulting self-consistent continuum solvation model provides a very effective and compact fit of computational and experimental data, whereby the static dielectric constant of the solvent and one parameter allow to fit the electrostatic energy provided by the polarizable continuum model with a mean absolute error of 0.3 kcal/mol on a set of 240 neutral solutes. Two parameters allow to fit experimental solvation energies on the same set with a mean absolute error of 1.3 kcal/mol. A detailed analysis of these results, broken down along different classes of chemical compounds, shows that several classes of organic compounds display very high accuracy, with solvation energies in error of 0.3-0.4 kcal/mol, whereby larger discrepancies are mostly limited to self-dissociating species and strong hydrogen-bond-forming compounds.

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TL;DR: The recently implemented exchange-hole dipole moment (XDM) model is compared with other approaches in the literature to find that XDM roughly doubles the accuracy of DFT-D2 and non-local functionals in computed lattice energies while, at the same time, predicting cell geometries within less than 2% of the experimental result on average.

Abstract: A benchmark for non-covalent interactions in solids (C21) based on the experimental sublimation enthalpies and geometries of 21 molecular crystals is presented. Thermal and zero-point effects are carefully accounted for and reference lattice energies and thermal pressures are provided, which allow dispersion-corrected density functionals to be assessed in a straightforward way. Other thermal corrections to the sublimation enthalpy (the 2RT term) are reexamined. We compare the recently implemented exchange-hole dipole moment (XDM) model with other approaches in the literature to find that XDM roughly doubles the accuracy of DFT-D2 and non-local functionals in computed lattice energies (4.8 kJ/mol mean absolute error) while, at the same time, predicting cell geometries within less than 2% of the experimental result on average. The XDM model of dispersion interactions is confirmed as a very promising approach in solid-state applications.

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TL;DR: A general formulation to compute anharmonic vibrational averages and transition properties at the second-order of perturbation theory is derived from the Rayleigh-Schrödinger development and can be easily adapted to various properties.

Abstract: A general formulation to compute anharmonic vibrational averages and transition properties at the second-order of perturbation theory is derived from the Rayleigh-Schrodinger development. This approach is intended to be applicable to any property expanded as a Taylor series up to the third order with respect to normal coordinates or their associated momenta. The equations are straightforward to implement and can be easily adapted to various properties, as illustrated for the case of electric and magnetic dipole moments. From those, infrared and vibrational circular dichroism spectra can be readily obtained. This fully automatic procedure has been applied to several chiral molecules of small-to-medium sizes and compared to the standard double harmonic approximation and to experimental data.

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TL;DR: The global-hybrid version of the Perdew-Burke-Ernzerhoff GGA density functional (PBE0) is found to offer the best overall performance with a mean absolute error (MAE) of 0.28 eV, while the local density approximation functional (SVWN) outperformed all non-GH GGAs tested.

Abstract: The performance of 24 density functionals, including 14 meta-generalized gradient approximation (mGGA) functionals, is assessed for the calculation of vertical excitation energies against an experimental benchmark set comprising 14 small- to medium-sized compounds with 101 total excited states. The experimental benchmark set consists of singlet, triplet, valence, and Rydberg excited states. The global-hybrid (GH) version of the Perdew-Burke-Ernzerhoff GGA density functional (PBE0) is found to offer the best overall performance with a mean absolute error (MAE) of 0.28 eV. The GH-mGGA Minnesota 2006 density functional with 54% Hartree-Fock exchange (M06-2X) gives a lower MAE of 0.26 eV, but this functional encounters some convergence problems in the ground state. The local density approximation functional consisting of the Slater exchange and Volk-Wilk-Nusair correlation functional (SVWN) outperformed all non-GH GGAs tested. The best pure density functional performance is obtained with the local version of the Minnesota 2006 mGGA density functional (M06-L) with an MAE of 0.41 eV.

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Jilin University

^{1}TL;DR: A structure prediction method for layered materials based on two-dimensional (2D) particle swarm optimization algorithm is developed and a new family of mono-layered boron nitride structures with different chemical compositions is predicted.

Abstract: A structure prediction method for layered materials based on two-dimensional (2D) particle swarm optimization algorithm is developed. The relaxation of atoms in the perpendicular direction within a given range is allowed. Additional techniques including structural similarity determination, symmetry constraint enforcement, and discretization of structure constructions based on space gridding are implemented and demonstrated to significantly improve the global structural search efficiency. Our method is successful in predicting the structures of known 2D materials, including single layer and multi-layer graphene, 2D boron nitride (BN) compounds, and some quasi-2D group 6 metals(VIB) chalcogenides. Furthermore, by use of this method, we predict a new family of mono-layered boron nitride structures with different chemical compositions. The first-principles electronic structure calculations reveal that the band gap of these N-rich BN systems can be tuned from 5.40 eV to 2.20 eV by adjusting the composition.

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TL;DR: The grid inhomogeneous solvation theory (GIST) as mentioned in this paper discretizes the equations of inhomogenous solvation theories onto a three-dimensional grid situated in the region of interest around a solute molecule or complex.

Abstract: The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a three-dimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit[7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.

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TL;DR: A new model for analyzing the photophysics of polymer aggregates is introduced taking into account exciton motion along a polymer chain and across polymer chains, and the predictions neatly account for the H-like dominance exhibited by the PL from spin-cast films and the J- like dominance exhibited from highly ordered P3HT nanofibers self-assembled in toluene.

Abstract: A new model for analyzing the photophysics of polymer aggregates is introduced taking into account exciton motion along a polymer chain and across polymer chains. Excitonic coupling and vibronic coupling are treated on equal footing using a Holstein-based Hamiltonian represented in a multi-particle basis set. In the HJ-aggregate model the competition between intrachain (through-bond) coupling leading to Wannier-Mott excitons, and interchain (through-space) coupling leading to Frenkel excitons, is studied in detail for two model dimers: one composed of red-phase polydiacetylene (PDA) chains and the other composed of regioregular P3HT chains. The resulting photophysical properties are shown to depend critically on the relative magnitudes of the intrachain and interchain exciton bandwidths. Dominant intraband (interband) coupling favors a photophysical response resembling J-aggregates (H-aggregates). In PDA dimers, where intrachain coupling prevails, the absorption spectrum is dominated by the 0-0 peak, as is characteristic of J-aggregates. The photoluminescence (PL) spectrum displays hybrid character: the ratio of the main (0-0) band to the first vibronic sideband intensities is initially zero at T = 0 K due to the forbidden nature of the 0-0 transition, but then increases with temperature in a manner characteristic of H-aggregates, peaking when kT ≈ ΔE, where ΔE is the interchain splitting. Further increases in temperature result in a decline of the PL ratio, as in a J-aggregate. This remarkable H to J transition is also predicted for the temperature dependence of the radiative decay rate, k(rad). The maximum (peak) rate scales as, k(rad) (max)∼(W(intra)/W(inter))(1/2), where W(intra) (W(inter)) is the intrachain (interchain) exciton bandwidth. Hence, when W(intra) is sufficiently larger than W(inter) the dimer displays thermally activated superradiance. In P3HT the intrachain coupling is far weaker than in PDA making the intrachain and interchain couplings comparable in the crystalline phase. Although the absorption spectral line shape is still well-accounted for by the conventional H-aggregate model, the photoluminescence is more sensitive, with H or J behavior tunable by changes in morphology. Long range intrachain order which coincides with weaker interchain interactions induces J-aggregate behavior, while short range intrachain order and the resulting stronger interchain coupling induces H-aggregate behavior. Our predictions neatly account for the H-like dominance exhibited by the PL from spin-cast films and the J-like dominance exhibited by the PL from highly ordered P3HT nanofibers self-assembled in toluene.

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TL;DR: In this paper, the spin-adapted density matrix renormalization group (DMRG) algorithm was extended to quantum chemical Hamiltonians, which involves using a quasi-density matrix, to ensure that the renormalized DMRG states are eigenfunctions of S^2, and the Wigner-Eckart theorem to reduce overall storage and computational costs.

Abstract: We extend the spin-adapted density matrix renormalization group (DMRG) algorithm of McCulloch and Gulacsi [Europhys. Lett. 57, 852 (2002)]10.1209/epl/i2002-00393-0 to quantum chemical Hamiltonians. This involves using a quasi-density matrix, to ensure that the renormalized DMRG states are eigenfunctions of S^2, and the Wigner-Eckart theorem, to reduce overall storage and computational costs. We argue that the spin-adapted DMRG algorithm is most advantageous for low spin states. Consequently, we also implement a singlet-embedding strategy due to Tatsuaki [Phys. Rev. E 61, 3199 (2000)]10.1103/PhysRevE.61.3199 where we target high spin states as a component of a larger fictitious singlet system. Finally, we present an efficient algorithm to calculate one- and two-body reduced density matrices from the spin-adapted wavefunctions. We evaluate our developments with benchmark calculations on transition metal system active space models. These include the Fe_2S_2, [Fe_2S_2(SCH_3)_4]^(2−), and Cr_2 systems. In the case of Fe_2S_2, the spin-ladder spacing is on the microHartree scale, and here we show that we can target such very closely spaced states. In [Fe_2S_2(SCH_3)_4]^(2−), we calculate particle and spin correlation functions, to examine the role of sulfur bridging orbitals in the electronic structure. In Cr_2 we demonstrate that spin-adaptation with the Wigner-Eckart theorem and using singlet embedding can yield up to an order of magnitude increase in computational efficiency. Overall, these calculations demonstrate the potential of using spin-adaptation to extend the range of DMRG calculations in complex transition metal problems.

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TL;DR: Ouldridge et al. as mentioned in this paper introduced a sequence-dependent parametrization for a coarse-grained DNA model, which introduces sequencedependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes.

Abstract: We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software.

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TL;DR: This new approximation reduces the 4th-order ERI tensor to a product of five matrices, simultaneously reducing the storage requirement as well as increasing the flexibility to regroup terms and reduce scaling behavior.

Abstract: Many approximations have been developed to help deal with the O(N4) growth of the electron repulsion integral (ERI) tensor, where N is the number of one-electron basis functions used to represent the electronic wavefunction. Of these, the density fitting (DF) approximation is currently the most widely used despite the fact that it is often incapable of altering the underlying scaling of computational effort with respect to molecular size. We present a method for exploiting sparsity in three-center overlap integrals through tensor decomposition to obtain a low-rank approximation to density fitting (tensor hypercontraction density fitting or THC-DF). This new approximation reduces the 4th-order ERI tensor to a product of five matrices, simultaneously reducing the storage requirement as well as increasing the flexibility to regroup terms and reduce scaling behavior. As an example, we demonstrate such a scaling reduction for second- and third-order perturbation theory (MP2 and MP3), showing that both can be c...

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TL;DR: Some broadly- known and some less broadly-known consequences of Einstein's special relativity in quantum chemistry are discussed, and a brief outline of the theoretical methods currently in use are provided, along with a discussion of recent developments and selected applications.

Abstract: This perspective article discusses some broadly-known and some less broadly-known consequences of Einstein's special relativity in quantum chemistry, and provides a brief outline of the theoretical methods currently in use, along with a discussion of recent developments and selected applications. The treatment of the electron correlation problem in relativistic quantum chemistry methods, and expanding the reach of the available relativistic methods to calculate all kinds of energy derivative properties, in particular spectroscopic and magnetic properties, requires on-going efforts.

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TL;DR: In this article, the adiabatic, relativistic, and quantum electrodynamics (QED) contributions to the pair potential of helium were computed, fitted separately, and applied, together with the nonrelativistic Born-Oppenheimer (BO) potential, in calculations of thermophysical properties of helium and of the helium dimer.

Abstract: The adiabatic, relativistic, and quantum electrodynamics (QED) contributions to the pair potential of helium were computed, fitted separately, and applied, together with the nonrelativistic Born-Oppenheimer (BO) potential, in calculations of thermophysical properties of helium and of the properties of the helium dimer. An analysis of the convergence patterns of the calculations with increasing basis set sizes allowed us to estimate the uncertainties of the total interaction energy to be below 50 ppm for interatomic separations R smaller than 4 bohrs and for the distance R = 5.6 bohrs. For other separations, the relative uncertainties are up to an order of magnitude larger (and obviously still larger near R = 4.8 bohrs where the potential crosses zero) and are dominated by the uncertainties of the nonrelativistic BO component. These estimates also include the contributions from the neglected relativistic and QED terms proportional to the fourth and higher powers of the fine-structure constant α. To obtain such high accuracy, it was necessary to employ explicitly correlated Gaussian expansions containing up to 2400 terms for smaller R (all R in the case of a QED component) and optimized orbital bases up to the cardinal number X = 7 for larger R. Near-exact asymptotic constants were used to describe the large-R behavior of all components. The fitted potential, exhibiting the minimum of −10.996 ± 0.004 K at R = 5.608 0 ± 0.000 1 bohr, was used to determine properties of the very weakly bound 4He2 dimer and thermophysical properties of gaseous helium. It is shown that the Casimir-Polder retardation effect, increasing the dimer size by about 2 A relative to the nonrelativistic BO value, is almost completely accounted for by the inclusion of the Breit-interaction and the Araki-Sucher contributions to the potential, of the order α2 and α3, respectively. The remaining retardation effect, of the order of α4 and higher, is practically negligible for the bound state, but is important for the thermophysical properties of helium. Such properties computed from our potential have uncertainties that are generally significantly smaller (sometimes by nearly two orders of magnitude) than those of the most accurate measurements and can be used to establish new metrology standards based on properties of low-density helium.

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TL;DR: The W1-F12 theoretical values for benzene, naphthalene, and anthracene are in very good to reasonable agreement with experiment, and the accepted experimental value for naphthacene cannot be reconciled with those for the lower acenes: it is suggested that Δ(f)H(298)(∘)[naphthACene(g)] = 74.25 ± 1 kcal/mol is a more realistic estimate.

Abstract: In an attempt to extend the applicability of the W1 and W2 ab initio computational thermochemistry methods, we propose explicitly correlated versions thereof, denoted W1-F12 and W2-F12. In W2-F12, we can “save” one cardinal number (viz., angular momentum) in the basis set sequences without loss in accuracy; in W1-F12, we can do so for first-row compounds but not for second-row compounds. At a root mean square deviation (RMSD) = 0.19 kcal/mol for the first-row molecules in the W4-11 benchmark dataset, W1-F12 is in fact superior to ordinary W1 theory. For the entire W4-11 set, W2-F12 yields a RMSD = 0.20 kcal/mol, comparable to 0.19 kcal/mol from ordinary W2 theory. The extended applicability ranges of W1-F12 and W2-F12 are not just due to the lower computational cost but also to greatly reduced memory and especially storage requirements. They are illustrated through applications to nucleic acids and to polyacenes (with up to four rings), for which the following revised gas-phase heats of formation are foun...

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Rice University

^{1}TL;DR: In this article, the authors derive and implement a "variation after projection" PHF theory, which can be applied to both collinear and non-collinear spin cases, and can be used in conjunction with deliberate symmetry breaking and restoration of other molecular symmetries like complex conjugation and point group.

Abstract: Projected Hartree–Fock (PHF) theory has a long history in quantum chemistry. PHF is here understood as the variational determination of an N-electron broken symmetry Slater determinant that minimizes the energy of a projected state with the correct quantum numbers. The method was actively pursued for several decades but seems to have been abandoned. We here derive and implement a “variation after projection” PHF theory using techniques different from those previously employed in quantum chemistry. Our PHF methodology has modest mean-field computational cost, yields relatively simple expressions, can be applied to both collinear and non-collinear spin cases, and can be used in conjunction with deliberate symmetry breaking and restoration of other molecular symmetries like complex conjugation and point group. We present several benchmark applications to dissociation curves and singlet-triplet energy splittings, showing that the resulting PHF wavefunctions are of high quality multireference character. We also provide numerical evidence that in the thermodynamic limit, the energy in PHF is not lower than that of broken-symmetry HF, a simple consequence of the lack of size consistency and extensivity of PHF.

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ETH Zurich

^{1}TL;DR: A highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters and efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures.

Abstract: We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore, adaptive surrogate models are proposed in order to reduce the computational cost associated with the large number of MD model runs. The effectiveness and computational efficiency of the proposed Bayesian framework is demonstrated in MD simulations of liquid and gaseous argon.

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TL;DR: It is argued that, in the presence of strong coupling between electronic excitations and quantized vibrations, a concrete and important advantage of quantum coherent dynamics is precisely to tune resonances that promote fast and effective energy distribution.

Abstract: The influence of fast vibrations on energy transfer and conversion in natural molecular aggregates is an issue of central interest. This article shows the important role of high-energy quantized vibrations and their non-equilibrium dynamics for energy transfer in photosynthetic systems with highly localized excitonic states. We consider the cryptophyte antennae protein phycoerythrin 545 and show that coupling to quantized vibrations, which are quasi-resonant with excitonic transitions is fundamental for biological function as it generates non-cascaded transport with rapid and wider spatial distribution of excitation energy. Our work also indicates that the non-equilibrium dynamics of such vibrations can manifest itself in ultrafast beating of both excitonic populations and coherences at room temperature, with time scales in agreement with those reported in experiments. Moreover, we show that mechanisms supporting coherent excitonic dynamics assist coupling to selected modes that channel energy to preferential sites in the complex. We therefore argue that, in the presence of strong coupling between electronic excitations and quantized vibrations, a concrete and important advantage of quantum coherent dynamics is precisely to tune resonances that promote fast and effective energy distribution.

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TL;DR: The exchange-hole dipole moment model of dispersion interactions of Becke and Johnson is implemented for calculations in solids using the pseudopotentials/plane-waves approach and retains the simplicity and efficiency of semilocal functionals while accurately treating dispersion interaction via a semiempirical asymptotic expansion.

Abstract: The exchange-hole dipole moment model of dispersion interactions of Becke and Johnson [J. Chem. Phys. 127 154108 (2007)] is implemented for calculations in solids using the pseudopotentials/plane-waves approach. The resulting functional retains the simplicity and efficiency of semilocal functionals while accurately treating dispersion interactions via a semiempirical asymptotic expansion. The dispersion coefficients are calculated completely ab initio using local quantities alone (density, gradient, Laplacian, and kinetic energy density). The two empirical parameters in the damping function are calculated by fit to a 65-molecule training set recalculated under periodic boundary conditions. Calculations in simple solids offer good results with minimal computational cost compared to electronic relaxation.

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TL;DR: The usefulness of the exact TDPES in interpreting coupled electron-nuclear dynamics is discussed in this article, where the authors show how features of its structure indicate the mechanism of dissociation.

Abstract: the usefulness of the exact TDPES in interpreting coupled electron-nuclear dynamics: we show how features of its structure indicate the mechanism of dissociation. We compare the exact TDPES with potential energy surfaces from the time-dependent Hartree-approach, and also compare traditional Ehrenfest dynamics with Ehrenfest dynamics on the exact TDPES. © 2012 American Institute of Physics .[ http://dx.doi.org/10.1063/1.4745836]

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TL;DR: Analytical results based on the Landau-Zener theory of adiabatic transitions, as well as numerical quantum mechanical calculations, provide insight into the dependence of cross effect DNP on various experimental parameters, including MAS frequency, microwave field strength, spin relaxation rates, hyperfine and electron-electron dipole coupling strengths, and the nature of the biradical dopants.

Abstract: We present theoretical calculations of dynamic nuclear polarization (DNP) due to the cross effect in nuclear magnetic resonance under magic-angle spinning (MAS). Using a three-spin model (two electrons and one nucleus), cross effect DNP with MAS for electron spins with a large g-anisotropy can be seen as a series of spin transitions at avoided crossings of the energy levels, with varying degrees of adiabaticity. If the electron spin-lattice relaxation time T1e is large relative to the MAS rotation period, the cross effect can happen as two separate events: (i) partial saturation of one electron spin by the applied microwaves as one electron spin resonance (ESR) frequency crosses the microwave frequency and (ii) flip of all three spins, when the difference of the two ESR frequencies crosses the nuclear frequency, which transfers polarization to the nuclear spin if the two electron spins have different polarizations. In addition, adiabatic level crossings at which the two ESR frequencies become equal serve to maintain non-uniform saturation across the ESR line. We present analytical results based on the Landau-Zener theory of adiabatic transitions, as well as numerical quantum mechanical calculations for the evolution of the time-dependent three-spin system. These calculations provide insight into the dependence of cross effect DNP on various experimental parameters, including MAS frequency, microwave field strength, spin relaxation rates, hyperfine and electron-electron dipole coupling strengths, and the nature of the biradical dopants.

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TL;DR: An implementation of the spin-flip (SF) variant of time-dependent density functional theory (TD-DFT) within the Tamm-Dancoff approximation and non-collinear (NC) formalism for local, generalized gradient approximation, hybrid, and range-separated functionals is reported.

Abstract: We report an implementation of the spin-flip (SF) variant of time-dependent density functional theory (TD-DFT) within the Tamm-Dancoff approximation and non-collinear (NC) formalism for local, generalized gradient approximation, hybrid, and range-separated functionals. The performance of different functionals is evaluated by extensive benchmark calculations of energy gaps in a variety of diradicals and open-shell atoms. The benchmark set consists of 41 energy gaps. A consistently good performance is observed for the Perdew-Burke-Ernzerhof (PBE) family, in particular PBE0 and PBE50, which yield mean average deviations of 0.126 and 0.090 eV, respectively. In most cases, the performance of original (collinear) SF-TDDFT with 50-50 functional is also satisfactory (as compared to non-collinear variants), except for the same-center diradicals where both collinear and non-collinear SF variants that use LYP or B97 exhibit large errors. The accuracy of NC-SF-TDDFT and collinear SF-TDDFT with 50-50 and BHHLYP is very similar. Using PBE50 within collinear formalism does not improve the accuracy.