Introducing the Automated Ligand Searcher.

The Automated Ligand Searcher (ALISE) is designed as an automated computational drug discovery tool. To approximate the binding free energy of ligands to a receptor, ALISE includes a three-stage workflow, with each stage involving an increasingly sophisticated computational method: molecular docking, molecular dynamics, and free energy perturbation, respectively. To narrow the number of potential ligands, poorly performing ligands are gradually segregated out. The performance and usability of ALISE are benchmarked for a case study containing known active ligands and decoys for the HIV protease. The example illustrates that ALISE filters the decoys successfully and demonstrates that the automation, comprehensiveness, and user-friendliness of the software make it a valuable tool for improved and faster drug development workflows.

Analytical approach to phonon calculations in the SCC-DFTB framework.

Detailed derivation of the analytical, reciprocal-space approach of Hessian calculation within the self-consistent-charge density-functional based tight-binding framework (SCC-DFTB) is presented. This approach provides an accurate and efficient way for obtaining the SCC-DFTB Hessian of periodic systems. Its superiority with respect to the traditional numerical force differentiation method is demonstrated for doped graphene, graphene nanoribbons, boron-nitride nanotubes, bulk zinc-oxide, and other systems.

Two-dimensional Cu2Si monolayer with planar hexacoordinate copper and silicon bonding.

Two-dimensional (2D) materials with planar hypercoordinate motifs are extremely rare due to the difficulty in stabilizing the planar hypercoordinate configurations in extended systems. Furthermore, such exotic motifs are often unstable. We predict a novel Cu2Si 2D monolayer featuring planar hexacoordinate copper and planar hexacoordinate silicon. This is a global minimum in 2D space which displays reduced dimensionality and rule-breaking chemical bonding. This system has been studied with density functional theory, including molecular dynamics simulations and electronic structure calculations. Bond order analysis and partitioning reveals 4c-2e σ bonds that stabilize the two-dimensional structure. We find that the system is quite stable during short annealing simulations up to 900 K, and predict that it is a nonmagnetic metal. This work opens up a new branch of hypercoordinate two-dimensional materials for study.

Revealing unusual chemical bonding in planar hyper-coordinate Ni2Ge and quasi-planar Ni2Si two-dimensional crystals.

We discover unusual chemical bonding in a novel planar hyper-coordinate Ni2Ge free-standing 2D monolayer, and also in a nearly planar slightly buckled Ni2Si monolayer. This unusual bonding is revealed by Solid State Adaptive Natural Density Partitioning analysis. This analysis shows that a new type of 2c-2e Ni-Si σ and 3c-2e Ni-Ge-Ni σ bonds stabilize these 2D crystals. This is completely different from any previously known 2D crystals. Both of these free-standing monolayers are global minima in two-dimensional space. Although their exotic structure has unprecedented chemical bonding, they show extraordinary stability as single layers. The stabilities of these frameworks are confirmed by phonon dispersion calculations and ab initio molecular dynamics calculations. For Ni2Si, the framework was maintained during short 10 ps molecular dynamics annealing up to 1500 K, while Ni2Ge survived 10 ps runs up to 900 K. Both systems are predicted to be non-magnetic and metallic. As these new 2D crystals contain hypercoordinated Group 14 atoms, they are examples of a new class of 2D crystals with unconventional chemical bonding and potentially exciting new properties. Interestingly, we find that the stabilities of Ni2Si and Ni2Ge are much higher than that of silicene and germanene. Thus, this work provides a novel way to stabilize 2D sheets of Group 14 elements.