Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program.

We present the details of a graphics processing unit (GPU) capable exchange correlation (XC) scheme integrated into the open source QUantum Interaction Computational Kernel (QUICK) program. Our implementation features an octree based numerical grid point partitioning scheme, GPU enabled grid pruning and basis and primitive function prescreening, and fully GPU capable XC energy and gradient algorithms. Benchmarking against the CPU version demonstrated that the GPU implementation is capable of delivering an impressive performance while retaining excellent accuracy.

Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?

FtmPT1 is a fungal indole prenyltransferase that affords Tryprostatin B from Brevianamide F and dimethylallyl pyrophosphate; however, when a single residue in the active site is mutated (Gly115Thr), a novel five-membered ring compound is obtained as the major product with Tryprostatin B as the minor product. Herein, we describe detailed studies of the catalysis of the Gly115Thr mutant of FtmPT1 with a focus on the observed regioselectivity of the reaction. We employ one- and two-dimensional potential of mean force simulations to explore the catalytic mechanism, along with molecular dynamics simulations exploring the reaction dynamics of the prenyl transfer reaction.

Acceleration of High Angular Momentum Electron Repulsion Integrals and Integral Derivatives on Graphics Processing Units.

We present an efficient implementation of ab initio self-consistent field (SCF) energy and gradient calculations that run on Compute Unified Device Architecture (CUDA) enabled graphical processing units (GPUs) using recurrence relations. We first discuss the machine-generated code that calculates the electron-repulsion integrals (ERIs) for different ERI types. Next we describe the porting of the SCF gradient calculation to GPUs, which results in an acceleration of the computation of the first-order derivative of the ERIs.

Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil.

The recognition and association of donepezil with acetylcholinesterase (AChE) has been extensively studied in the past several decades because of the former's use as a palliative treatment for mild Alzheimer disease. Herein we examine the conformational properties of donepezil and we re-examine the donepezil-AChE crystal structure using combined quantum mechanical/molecular mechanical (QM/MM) X-ray refinement tools. Donepezil's conformational energy surface was explored using the M06 suite of density functionals and with the MP2/complete basis set (CBS) method using the aug-cc-pVXZ (X = D and T) basis sets.

Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations.

Electron repulsion integral (ERI) calculation on graphical processing units (GPUs) can significantly accelerate quantum chemical calculations. Herein, the ab initio self-consistent-field (SCF) calculation is implemented on GPUs using recurrence relations, which is one of the fastest ERI evaluation algorithms currently available. A direct-SCF scheme to assemble the Fock matrix efficiently is presented, wherein ERIs are evaluated on-the-fly to avoid CPU-GPU data transfer, a well-known architectural bottleneck in GPU specific computation.

Catalytic mechanism of aromatic prenylation by NphB.

NphB is an aromatic prenyltransferase that catalyzes the attachment of a 10-carbon geranyl group to aromatic substrates. Importantly, NphB exhibits a rich substrate selectivity and product regioselectivity. A systematic computational study has been conducted in order to address several question associated with NphB-catalyzed geranylation.