PatCID: an open-access dataset of chemical structures in patent documents.

The automatic analysis of patent publications has potential to accelerate research across various domains, including drug discovery and material science. Within patent documents, crucial information often resides in visual depictions of molecule structures. PatCID (Patent-extracted Chemical-structure Images database for Discovery) allows to access such information at scale.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations.

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems.

Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide.

For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state over extended states and the paired helix bundle in the assembly of two helices. The energetic contributions of attractive protein-solvent interactions are separated into quasi-chemical components consisting of a short-range part arising from interactions with solvent in the first hydration shell and the remaining long-range part that is well described by a Gaussian. In the helix-coil transition, short-range attractive protein-solvent interactions outweigh hydrophobic hydration and favor the extended coil states.

Semiempirical Molecular Dynamics (SEMD) I: Midpoint-Based Parallel Sparse Matrix-Matrix Multiplication Algorithm for Matrices with Decay.

In this paper, we present a novel, highly efficient, and massively parallel implementation of the sparse matrix-matrix multiplication algorithm inspired by the midpoint method that is suitable for matrices with decay. Compared with the state of the art in sparse matrix-matrix multiplications, the new algorithm heavily exploits data locality, yielding better performance and scalability, approaching a perfect linear scaling up to a process box size equal to a characteristic length that is intrinsic to the matrices. Moreover, the method is able to scale linearly with system size reaching constant time with proportional resources, also regarding memory consumption.

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model.

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain.

Solvation free energy of the peptide group: its model dependence and implications for the additive-transfer free-energy model of protein stability.

The group-additive decomposition of the unfolding free energy of a protein in an osmolyte solution relative to that in water poses a fundamental paradox: whereas the decomposition describes the experimental results rather well, theory suggests that a group-additive decomposition of free energies is, in general, not valid. In a step toward resolving this paradox, here we study the peptide-group transfer free energy. We calculate the vacuum-to-solvent (solvation) free energies of (Gly)n and cyclic diglycine (cGG) and analyze the data according to experimental protocol.

Regularizing Binding Energy Distributions and the Hydration Free Energy of Protein Cytochrome C from All-Atom Simulations.

By introducing an external field to temper short-range protein water interactions, we regularize the statistical problem of calculating the hydration free energy, μ(ex), of the protein cytochrome C using the potential distribution theorem. Using this approach, we calculate the nonelectrostatic (dispersion) and electrostatic contributions to μ(ex). The nonelectrostatic contribution interpreted within an accessible surface area approach leads to a surface energy parameter that is about twice the value based on the hydration of small alkanes: at the size scale of the protein, hydrophobic hydration is more stronger relative to small alkanes.

Communication: regularizing binding energy distributions and thermodynamics of hydration: theory and application to water modeled with classical and ab initio simulations.

The high-energy tail of the distribution of solute-solvent interaction energies is poorly characterized for condensed systems, but this tail region is of principal interest in determining the excess free energy of the solute. We introduce external fields centered on the solute to modulate the short-range repulsive interaction between the solute and solvent. This regularizes the binding energy distribution and makes it easy to calculate the free energy of the solute with the field.

Communication: Thermodynamics of water modeled using ab initio simulations.

We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. Assuming classical statistical mechanical simulations at 350 K model the liquid at 298 K, the calculated free energy is found in fair agreement with experiments, but the excess internal energy and hence also the excess entropy are not. The utility of thermodynamic characterization in understanding the role of high temperatures to mimic nuclear quantum effects and in evaluating ab initio simulations is noted.

Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals.

In the free energy of hydration of a solute, the chemical contribution is given by the free energy required to expel water molecules from the coordination sphere and the packing contribution is given by the free energy required to create the solute-free coordination sphere (the observation volume) in bulk water. With the simple point charge/extended (SPC/E) water model as a reference, we examine the chemical and packing contributions in the free energy of water simulated using different electron density functionals. The density is fixed at a value corresponding to that for SPC/E water at a pressure of 1 bar.

Magnetic linear response properties calculations with the Gaussian and augmented-plane-wave method.

We introduce a method for the all-electron calculation of the NMR chemical shifts and the EPR g tensor using the Gaussian and augmented-plane-wave method. The presented approach is based on the generalized density functional perturbation theory. The method is validated by comparison with other theoretical methods for a selection of small molecules.

Extended Lagrangian Born-Oppenheimer molecular dynamics with dissipation.

Stability and dissipation in the propagation of the electronic degrees of freedom in time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [Niklasson et al., Phys. Rev.

Direct energy functional minimization under orthogonality constraints.

The direct energy functional minimization problem in electronic structure theory, where the single-particle orbitals are optimized under the constraint of orthogonality, is explored. We present an orbital transformation based on an efficient expansion of the inverse factorization of the overlap matrix that keeps orbitals orthonormal. The orbital transformation maps the orthogonality constrained energy functional to an approximate unconstrained functional, which is correct to some order in a neighborhood of an orthogonal but approximate solution.

A smooth script-l1-norm sparseness function for orbital based linear scaling total energy minimization.

A smooth [script-l](1)-norm based function to obtain a sparse representation of the orbital coefficients is introduced. This sparseness function is further parametrized with respect to unitary transformations among the occupied orbitals. Thus the function can be straightforwardly included in an optimization scheme or used on the fly during self-consistent field iterations to induce or maintain the sparsity of the orbital coefficients.

Linear scaling density matrix perturbation theory for basis-set-dependent quantum response calculations: an orthogonal formulation.

Linear scaling density matrix perturbation theory [A. M. N.

Parallel algorithm for the computation of the Hartree-Fock exchange matrix: gas phase and periodic parallel ONX.

In this paper we present an efficient parallelization of the ONX algorithm for linear computation of the Hartree-Fock exchange matrix [J. Chem. Phys.

Energy gradients with respect to atomic positions and cell parameters for the Kohn-Sham density-functional theory at the Gamma point.

The application of theoretical methods based on density-functional theory is known to provide atomic and cell parameters in very good agreement with experimental values. Recently, construction of the exact Hartree-Fock exchange gradients with respect to atomic positions and cell parameters within the Gamma-point approximation has been introduced. In this article, the formalism is extended to the evaluation of analytical Gamma-point density-functional atomic and cell gradients.

Exchange energy gradients with respect to atomic positions and cell parameters within the Hartree-Fock Gamma-point approximation.

Recently, linear scaling construction of the periodic exact Hartree-Fock exchange matrix within the Gamma-point approximation has been introduced [J. Chem. Phys.

Nonorthogonal density-matrix perturbation theory.

Recursive density-matrix perturbation theory [A.M.N.

Higher-order response in O(N) by perturbed projection.

Perturbed projection for linear scaling solution of the coupled-perturbed self-consistent-field equations [V. Weber, A.M.

Linear scaling computation of the Fock matrix. VIII. Periodic boundaries for exact exchange at the Gamma point.

A translationally invariant formulation of the Hartree-Fock (HF) Gamma-point approximation is presented. This formulation is achieved through introduction of the minimum image convention (MIC) at the level of primitive two-electron integrals, and implemented in a periodic version of the ONX algorithm [E. Schwegler, M.

Ab initio linear scaling response theory: electric polarizability by perturbed projection.

A linear scaling method for calculation of the static ab initio response within self-consistent field theory is developed and applied to the calculation of the static electric polarizability. The method is based on the density matrix perturbation theory [Phys. Rev.

One-pot rhodium(i)-catalyzed hydroboration of alkenes: radical conjugate addition.

B-Alkylcatecholboranes, prepared by rhodium(I)-catalyzed hydroboration of alkenes, are suitable radical precursors for conjugate addition to activated olefins. This procedure proved to be particularly useful for the control of the regio- and chemoselectivity of such tandem processes. Enantioselective hydroboration has also been successfully coupled with radical chain reaction in a one-pot process.