Advancing Non-Atom-Centered Basis Methods for More Accurate Interaction Energies: Benchmarks and Large-Scale Applications.

Recent advances in local electron correlation approaches have enabled the relatively routine access to CCSD(T) [that is, coupled cluster (CC) with single, double, and perturbative triple excitations] computations for molecules of a hundred or more atoms. Here, approaching their complete basis set (CBS) limit becomes more challenging due to extensive basis set superposition errors, often necessitating the use of large atomic orbital (AO) basis sets with diffuse functions. Here, we study a potential remedy in the form of non-atom-centered or floating orbitals (FOs).

State-of-the-art local correlation methods enable affordable gold standard quantum chemistry for up to hundreds of atoms.

In this feature, we review the current capabilities of local electron correlation methods up to the coupled cluster model with single, double, and perturbative triple excitations [CCSD(T)], which is a gold standard in quantum chemistry. The main computational aspects of the local method types are assessed from the perspective of applications, but the focus is kept on how to achieve chemical accuracy (, <1 kcal mol uncertainty), as well as on the broad scope of chemical problems made accessible. The performance of state-of-the-art methods is also compared, including the most employed DLPNO and, in particular, our local natural orbital (LNO) CCSD(T) approach.

Basis-Set Limit CCSD(T) Energies for Large Molecules with Local Natural Orbitals and Reduced-Scaling Basis-Set Corrections.

The calculation of density-based basis-set correction (DBBSC), which remedies the basis-set incompleteness (BSI) error of the correlation energy, is combined with local approximations. Aiming at large-scale applications, the procedure is implemented in our efficient local natural orbital-based coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme. To this end, the range-separation function, which characterizes the one-electron BSI in space, is decomposed into the sum of contributions from individual localized molecular orbitals (LMOs).

Development of analytic gradients for the Huzinaga quantum embedding method and its applications to large-scale hybrid and double hybrid DFT forces.

The theory of analytic gradients is presented for the projector-based density functional theory (DFT) embedding approach utilizing the Huzinaga-equation. The advantages of the Huzinaga-equation-based formulation are demonstrated. In particular, it is shown that the projector employed does not appear in the Lagrangian, and the potential risk of numerical problems is avoided at the evaluation of the gradients.

Polarizable AMOEBA Model for Simulating Mg·Protein·Nucleotide Complexes.

Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent cations to catalytic sites. However, modeling divalent cations in MM simulations has been challenging.

Many-Body Methods for Surface Chemistry Come of Age: Achieving Consensus with Experiments.

The adsorption energy of a molecule onto the surface of a material underpins a wide array of applications, spanning heterogeneous catalysis, gas storage, and many more. It is the key quantity where experimental measurements and theoretical calculations meet, with agreement being necessary for reliable predictions of chemical reaction rates and mechanisms. The prototypical molecule-surface system is CO adsorbed on MgO, but despite intense scrutiny from theory and experiment, there is still no consensus on its adsorption energy.

Linear-Scaling Local Natural Orbital CCSD(T) Approach for Open-Shell Systems: Algorithms, Benchmarks, and Large-Scale Applications.

The extension of the highly optimized local natural orbital (LNO) coupled cluster (CC) with single-, double-, and perturbative triple excitations [LNO-CCSD(T)] method is presented for high-spin open-shell molecules based on restricted open-shell references. The techniques enabling the outstanding efficiency of the closed-shell LNO-CCSD(T) variant are adopted, including the iteration- and redundancy-free second-order Møller-Plesset and (T) formulations as well as the integral-direct, memory- and disk use-economic, and OpenMP-parallel algorithms. For large molecules, the efficiency of our open-shell LNO-CCSD(T) method approaches that of its closed-shell parent method due to the application of restricted orbital sets for demanding integral transformations and a novel approximation for higher-order long-range spin-polarization effects.

Basis Set Limit CCSD(T) Energies for Extended Molecules via a Reduced-Cost Explicitly Correlated Approach.

Several approximations are introduced and tested to reduce the computational expenses of the explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)] method for both closed and open-shell species. First, the well-established frozen natural orbital (FNO) technique is adapted to explicitly correlated CC approaches. Second, our natural auxiliary function (NAF) scheme is employed to reduce the size of the auxiliary basis required for the density fitting approximation regularly used in explicitly correlated calculations.

Stability of Carbocyclic Phosphinyl Radicals: Effect of Ring Size, Delocalization, and Sterics.

In this computational study, we report on the stability of cyclic phosphinyl radicals with an aim for a systematical assessment of stabilization effects. The radical stabilization energies (RSEs) were calculated using isodesmic reactions for a large number of carbocyclic radicals possessing different ring sizes and grades of unsaturation. In general, the RSE values range from -1.

Size-consistent explicitly correlated triple excitation correction.

A new approach is proposed to reduce the basis set incompleteness error of the triple excitation correction in explicitly correlated coupled-cluster singles and doubles with perturbative triples calculations. Our method is similar to the intuitive triples correction approach of Knizia et al. [J.

Methyl-Induced Polarization Destabilizes the Noncovalent Interactions of N-Methylated Lysines.

Lysine methylation can modify noncovalent interactions by altering lysine's hydrophobicity as well as its electronic structure. Although the ramifications of the former are documented, the effects of the latter remain largely unknown. Understanding the electronic structure is important for determining how biological methylation modulates protein-protein binding, and the impact of artificial methylation experiments in which methylated lysines are used as spectroscopic probes and protein crystallization facilitators.

Linear-Scaling Open-Shell MP2 Approach: Algorithm, Benchmarks, and Large-Scale Applications.

A linear-scaling local second-order Møller-Plesset (MP2) method is presented for high-spin open-shell molecules based on restricted open-shell (RO) reference functions. The open-shell local MP2 (LMP2) approach inherits the iteration- and redundancy-free formulation and the completely integral-direct, OpenMP-parallel, and memory and disk use economic algorithms of our closed-shell LMP2 implementation. By utilizing restricted local molecular orbitals for the demanding integral transformation step and by introducing a novel long-range spin-polarization approximation, the computational cost of RO-LMP2 approaches that of closed-shell LMP2.

Accurate Reduced-Cost CCSD(T) Energies: Parallel Implementation, Benchmarks, and Large-Scale Applications.

The accurate and systematically improvable frozen natural orbital (FNO) and natural auxiliary function (NAF) cost-reducing approaches are combined with our recent coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] implementations. Both of the closed- and open-shell FNO-CCSD(T) codes benefit from OpenMP parallelism, completely or partially integral-direct density-fitting algorithms, checkpointing, and hand-optimized, memory- and operation count effective implementations exploiting all permutational symmetries. The closed-shell CCSD(T) code requires negligible disk I/O and network bandwidth, is MPI/OpenMP parallel, and exhibits outstanding peak performance utilization of 50-70% up to hundreds of cores.

Transferable interactions of Li and Mg ions in polarizable models.

Therapeutic implications of Li, in many cases, stem from its ability to inhibit certain Mg-dependent enzymes, where it interacts with or substitutes for Mg. The underlying details of its action are, however, unknown. Molecular simulations can provide insights, but their reliability depends on how well they describe relative interactions of Li and Mg with water and other biochemical groups.

Improved description of ligand polarization enhances transferability of ion-ligand interactions.

The reliability of molecular mechanics (MM) simulations in describing biomolecular ion-driven processes depends on their ability to accurately model interactions of ions simultaneously with water and other biochemical groups. In these models, ion descriptors are calibrated against reference data on ion-water interactions, and it is then assumed that these descriptors will also satisfactorily describe interactions of ions with other biochemical ligands. The comparison against the experiment and high-level quantum mechanical data show that this transferability assumption can break down severely.

The MRCC program system: Accurate quantum chemistry from water to proteins.

MRCC is a package of ab initio and density functional quantum chemistry programs for accurate electronic structure calculations. The suite has efficient implementations of both low- and high-level correlation methods, such as second-order Møller-Plesset (MP2), random-phase approximation (RPA), second-order algebraic-diagrammatic construction [ADC(2)], coupled-cluster (CC), configuration interaction (CI), and related techniques. It has a state-of-the-art CC singles and doubles with perturbative triples [CCSD(T)] code, and its specialties, the arbitrary-order iterative and perturbative CC methods developed by automated programming tools, enable achieving convergence with regard to the level of correlation.

Integral-Direct and Parallel Implementation of the CCSD(T) Method: Algorithmic Developments and Large-Scale Applications.

A completely integral-direct, disk I/O, and network traffic economic coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] implementation has been developed relying on the density-fitting approximation. By fully exploiting the permutational symmetry, the presented algorithm is highly operation count and memory-efficient. Our measurements demonstrate excellent strong scaling achieved via hybrid MPI/OpenMP parallelization and a highly competitive, 60-70% utilization of the theoretical peak performance on up to hundreds of cores.

Reduced-Scaling Correlation Methods for the Excited States of Large Molecules: Implementation and Benchmarks for the Second-Order Algebraic-Diagrammatic Construction Approach.

A framework for reduced-scaling implementation of excited-state correlation methods is presented. An algorithm is introduced to construct excitation-specific local domains, which include all important molecular orbitals for the excitation as well as for electron correlation. The orbital space dimensions of the resulting compact domains are further decreased utilizing our reduced-cost techniques developed previously [.

Approaching the Basis Set Limit of CCSD(T) Energies for Large Molecules with Local Natural Orbital Coupled-Cluster Methods.

Recent optimization efforts and extensive benchmark applications are presented illustrating the accuracy and efficiency of the linear-scaling local natural orbital (LNO) coupled-cluster single-, double-, and perturbative triple-excitations [CCSD(T)] method. A composite threshold combination hierarchy (Loose, Normal, Tight, etc.) is introduced, which enables black box convergence tests and is useful to estimate the accuracy of the LNO-CCSD(T) energies with respect to CCSD(T).

Dual Basis Set Approach for Density Functional and Wave Function Embedding Schemes.

A dual basis (DB) approach is proposed which is suitable for the reduction of the computational expenses of the Hartree-Fock, Kohn-Sham, and wave function-based correlation methods. The approach is closely related to the DB approximation of Head-Gordon and co-workers [ J. Chem.

Optimization of the Linear-Scaling Local Natural Orbital CCSD(T) Method: Improved Algorithm and Benchmark Applications.

An optimized implementation of the local natural orbital (LNO) coupled-cluster (CC) with single-, double-, and perturbative triple excitations [LNO-CCSD(T)] method is presented. The integral-direct, in-core, highly efficient domain construction technique of our local second-order Møller-Plesset (LMP2) scheme is extended to the CC level. The resulting scheme, which is also suitable for general-order LNO-CC calculations, inherits the beneficial properties of the LMP2 approach, such as the asymptotically linear-scaling operation count, the asymptotically constant data storage requirement, and the completely independent domain calculations.

Stereocontrol in Diphenylprolinol Silyl Ether Catalyzed Michael Additions: Steric Shielding or Curtin-Hammett Scenario?

The enantioselectivity of amine-catalyzed reactions of aldehydes with electrophiles is often explained by simple steric arguments emphasizing the role of the bulky group of the catalyst that prevents the approach of the electrophile from the more hindered side. This standard steric shielding model has recently been challenged by the discovery of stable downstream intermediates, which appear to be involved in the rate-determining step of the catalytic cycle. The alternative model, referred to as the Curtin-Hammett scenario of stereocontrol, assumes that the enantioselectivity is related to the stability and reactivity of downstream intermediates.

Optimization of the linear-scaling local natural orbital CCSD(T) method: Redundancy-free triples correction using Laplace transform.

An improved algorithm is presented for the evaluation of the (T) correction as a part of our local natural orbital (LNO) coupled-cluster singles and doubles with perturbative triples [LNO-CCSD(T)] scheme [Z. Rolik et al., J.

Reduced-cost linear-response CC2 method based on natural orbitals and natural auxiliary functions.

A reduced-cost density fitting (DF) linear-response second-order coupled-cluster (CC2) method has been developed for the evaluation of excitation energies. The method is based on the simultaneous truncation of the molecular orbital (MO) basis and the auxiliary basis set used for the DF approximation. For the reduction of the size of the MO basis, state-specific natural orbitals (NOs) are constructed for each excited state using the average of the second-order Møller-Plesset (MP2) and the corresponding configuration interaction singles with perturbative doubles [CIS(D)] density matrices.