Modeling Systems with π–π Interactions Using the Hartree–Fock Method with an Empirical Dispersion Correction

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Best practices for the maintenance and distribution of GAMESS are also discussed.

Computational Design of a Lantern Organic Framework

This study employed a computational quantum chemistry approach to design lantern organic framework (LOF) materials. Using the density functional theory method with the B3LYP-D3/6-31+G(d) level theory, novel lantern molecules ranging from two to eight bridges made of sp³ and sp carbon atoms to connect circulene bases that have phosphorous or silicon as anchor atoms were made. It was found that five-sp³-carbon and four-sp-carbon bridges are optimal candidates for constructing the lantern framework in the vertical direction. Although circulenes can be stacked vertically, their resulting HOMO-LUMO gaps remain relatively unchanged, indicating their potential applications as porous materials and for host-guest chemistry. The electrostatic potential surface maps reveal that LOF materials are relatively electrostatically neutral overall.

Open-Shell Variant of the London Dispersion-Corrected Hartree-Fock Method (HFLD) for the Quantification and Analysis of Noncovalent Interaction Energies

The London dispersion (LD)-corrected Hartree–Fock (HF) method (HFLD) is an ab initio approach for the quantification and analysis of noncovalent interactions (NCIs) in large systems that is based on the domain-based local pair natural orbital coupled-cluster (DLPNO-CC) theory. In the original HFLD paper, we discussed the implementation, accuracy, and efficiency of its closed-shell variant. Herein, an extension of this method to open-shell molecular systems is presented. Its accuracy is tested on challenging benchmark sets for NCIs, using CCSD(T) energies at the estimated complete basis set limit as reference. The HFLD scheme was found to be as accurate as the best-performing dispersion-corrected exchange-correlation functionals, while being nonempirical and equally efficient. In addition, it can be combined with the well-established local energy decomposition (LED) for the analysis of NCIs, thus yielding additional physical insights.

Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex

Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.

Benchmarking the Effective Fragment Potential Dispersion Correction on the S22 Test Set

The usual modeling of dispersion interactions in density functional theory (DFT) is often limited by the use of empirically fitted parameters. In this study, the accuracies of the popular empirical dispersion corrections and the first-principles derived effective fragment potential (EFP) dispersion correction are compared by computing the DFT-D and HF-D equilibria interaction energies and intermolecular distances of the S22 test set dimers. Functionals based on the local density approximation (LDA) and generalized gradient approximation (GGA), as well as hybrid functionals, are compared for the DFT-D calculations using coupled cluster CCSD(T) at the complete basis set (CBS) limit as the reference method. In general, the HF-D(EFP) method provides accurate equilibrium dimerization energies and intermolecular distances for hydrogen-bonded systems compared to the CCSD(T)/CBS reference data without using any empirical parameters. For dispersion-dominant and mixed systems, the structures and interaction energies obtained with the B3LYP-D(EFP) method are similar to or better than those obtained with the other DFT-D and HF-D methods. Overall, the first-principles derived -D(EFP) correction presents a robust alternative to the empirical -D corrections when used with the B3LYP functional for dispersion-dominant and mixed systems or with Hartree-Fock for hydrogen-bonded systems.

The INV24 test set: how well do quantum-chemical methods describe inversion and racemization barriers?

For years, there has been ongoing interest in experimentally and theoretically understanding inversion and racemization processes. However, to the best of our knowledge, there has been no computational study that systematically investigated how well low-level quantum-chemical methods predict inversion barriers. Herein, we provide an answer to this question and we present the INV24 benchmark set of 24 high-level, ab initio inversion barriers. INV24 covers inversion in triatomics, in pyramidal molecules, in one cyclic system, and in various helical and bowl-shaped compounds. Our results indicate that previously applied DFT approximations combined with small basis sets are not reliable enough and that at least a triple-ζ basis is needed for meaningful results. Moreover, we show that intramolecular London dispersion influences the barriers by 2 kcal/mol or more and that dispersion corrections should always be applied to DFT results. With our analysis of 34 DFT approximations, we can reproduce the well-known Jacob’s Ladder scheme with (meta-)generalized-gradient-approximation methods underestimating barriers and global-hybrid DFT functionals performing better. Range-separated hybrids or Minnesota-type hybrids are not particularly superior to more conventional methods, such as B3LYP-D3. The by far best results are achieved with dispersion-corrected double hybrids, which give results below the chemical accuracy target of 1 kcal/mol. They also outperform wave-function second-order perturbation theory approaches and we recommend using them whenever possible. Given that our systematic study of INV24 is the first of its kind, our findings have the potential to change common practice in this field and they will guide future investigations of inversion processes.

Silanol-Assisted Carbinolamine Formation in an Amine-Functionalized Mesoporous Silica Surface: Theoretical Investigation by Fragmentation Methods

The aldol reaction catalyzed by an amine-substituted mesoporous silica nanoparticle (amine-MSN) surface was investigated using a large molecular cluster model (Si392O958C6NH361) combined with the surface integrated molecular orbital/molecular mechanics (SIMOMM) and fragment molecular orbital (FMO) methods. Three distinct pathways for the carbinolamine formation, the first step of the amine-catalyzed aldol reaction, are proposed and investigated in order to elucidate the role of the silanol environment on the catalytic capability of the amine-MSN material. The computational study reveals that the most likely mechanism involves the silanol groups actively participating in the reaction, forming and breaking covalent bonds in the carbinolamine step. Therefore, the active participation of MSN silanol groups in the reaction mechanism leads to a significant reduction in the overall energy barrier for the carbinolamine formation. In addition, a comparison between the findings using a minimal cluster model and the Si392O958C6NH361 cluster suggests that the use of larger models is important when heterogeneous catalysis problems are the target.