相关论文: Mapping Enzymatic Catalysis using the Effective Fr…
The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by chorismate…
We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including…
We present a fast computational method to efficiently screen enzyme activity. In the presented method, the effect of mutations on the barrier height of an enzyme-catalysed reaction can be computed within 24 hours on roughly 10 processors.…
The development of quantum computing for molecular simulations is constrained by the limited number of qubits available on current Noisy Intermediate-Scale Quantum (NISQ) devices. The present work introduces the Virtual Orbital…
Herein, we present a new method to efficiently calculate electronically excited states in large molecular assemblies, consisting of hundreds of molecules. For this purpose, we combine the long-range corrected tight-binding…
We present a semi-empirical (PM6-based) computational method for systematically estimating the effect of all possible single mutants, within a certain radius of the active site, on the barrier height of an enzymatic reaction. The intent of…
The energy and analytic gradient are developed for FMO combined with the Hartree-Fock method augmented with three empirical corrections (HF-3c). The auxiliary basis set approach to FMO is extended to perform pair interaction energy…
We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudo-bond treatment of the…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
Photoemission orbital tomography (POT) from photoelectron momentum maps (PMMs) has enabled detailed analysis of the shape and energy of molecular orbitals in the adsorbed state. This study proposes a new POT method based on the PhaseLift.…
We propose an experimental procedure to cool fermionic atoms loaded into an optical lattice. The central idea is to spatially divide the system into entropy-rich and -poor regions by shaping the confining potential profile. Atoms in regions…
A massively parallel kinetic Monte Carlo (kMC) approach is proposed for simulating ionic migration in a crystal system by introducing the atomic fragmentation scheme (fragment kMC). The fragment kMC method achieved a reasonable parallel…
The elucidation of entropic contribution to enzyme catalysis has been debated over decades. The recent experimentally measured activation enthalpy and entropy, for chorismate rearrangement reaction in PchB brings up a hotly debated issue…
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine…
Once trained, machine-learned interatomic potentials (MLIPs) provide a fast and accurate way to study catalytic reaction pathways, but their performance strongly depends on the training set. Here, we compare nine MLIPs trained with…
H\"uckel molecular orbital (HMO) theory provides a semi-empirical treatment of the electronic structure in conjugated {\pi}-electronic systems. A scalable system-agnostic execution of HMO theory on a quantum computer is reported here based…
A scheme for computing charge-transfer matrix elements with the linear combination of fragment molecular orbitals and the 'nonempirically tuned range-separated' density functional is presented. It takes account of the self-consistent…
Fragment Molecular Orbital (FMO) calculations provide a framework to speed up quantum mechanical calculations and so can be used to explore structure-energy relationships in large and complex biomolecular systems. These calculations are…
Tracing the modifications of molecules in surface chemical reactions benefits from the possibility to image their orbitals. While delocalized frontier orbitals with {\pi}-character are imaged routinely with photoemission orbital tomography,…
Analytic first and second derivatives of the energy are developed for the fragment molecular orbital method interfaced with molecular mechanics in the electrostatic embedding scheme at the level of Hartree-Fock and density functional…