Nature Methods, Год журнала: 2024, Номер 21(3), С. 372 - 376
Опубликована: Фев. 27, 2024
Collaborations between researchers and companies can progress swimmingly teams quickly validate findings mature methods. All too often, things can't advance the 'Valley of Death' looms. New ways to collaborate, underpinned by computational muscle, help.
Язык: Английский
The Journal of Chemical Physics, Год журнала: 2024, Номер 160(11)
Опубликована: Март 21, 2024
Conformer–rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Phys. 22, 7169 (2020)] as driver calculations at extended tight-binding level (xTB), it offers a variety molecular- metadynamics simulations, geometry optimization, structure analysis capabilities. Implemented algorithms include procedures conformational sampling, explicit solvation studies, calculation absolute entropy, identification protonation deprotonation sites. Calculations are set up to run concurrently, providing single-node parallelization. CREST designed require minimal user input comes with implementation GFNn-xTB Hamiltonians GFN-FF force-field. Furthermore, interfaces any quantum chemistry force-field software can easily be created. In this article, we present recent developments code show selection applications most important features program. An novelty refactored backend, which provides significant speed-up small or medium-sized drug molecules allows more sophisticated setups, example, mechanics/molecular mechanics minimum energy crossing point calculations.
Язык: Английский
Процитировано
108
Faraday Discussions, Год журнала: 2024, Номер unknown
Опубликована: Янв. 1, 2024
In this contribution, the challenges associated with long-term development of general-purpose quantum chemical software packages are discussed and illustrated example ORCA package.
Язык: Английский
Процитировано
10
Chemical Communications, Год журнала: 2024, Номер 60(24), С. 3240 - 3258
Опубликована: Янв. 1, 2024
This article gives a perspective on the progress of AI tools in computational chemistry through lens author's decade-long contributions put wider context trends this rapidly expanding field. over last decade is tremendous: while ago we had glimpse what was to come many proof-of-concept studies, now witness emergence AI-based that are mature enough make faster and more accurate simulations increasingly routine. Such turn allow us validate even revise experimental results, deepen our understanding physicochemical processes nature, design better materials, devices, drugs. The rapid introduction powerful rise unique challenges opportunities discussed too.
Язык: Английский
Процитировано
7
The Journal of Chemical Physics, Год журнала: 2023, Номер 159(18)
Опубликована: Ноя. 10, 2023
The traditional foundation of science lies on the cornerstones theory and experiment. Theory is used to explain experiment, which in turn guides development theory. Since advent computers computational algorithms, computation has risen as third cornerstone science, joining experiment an equal footing. Computation become essential part modern amending by enabling accurate comparison complicated theories sophisticated experiments, well guiding triage both design targets experiments novel methods. Like relies continued investment infrastructure: it requires hardware (the physical computer calculation run) software source code programs that performs wanted simulations). In this Perspective, I discuss present-day challenges side chemistry, arise from fast-paced programming models, hardware. argue many these could be solved with reusable open libraries, are a public good, enhance reproducibility accelerate availability state-of-the-art methods improved software.
Язык: Английский
Процитировано
15
Journal of Chemical Theory and Computation, Год журнала: 2024, Номер 20(21), С. 9464 - 9477
Опубликована: Окт. 30, 2024
The
Язык: Английский
Процитировано
6
The Journal of Physical Chemistry C, Год журнала: 2024, Номер 128(19), С. 7987 - 7998
Опубликована: Май 2, 2024
Data-driven catalyst design is a promising approach for addressing the challenges in identifying suitable catalysts synthetic transformations. Models with descriptor calculations relying solely on precatalyst structure are potentially generalizable but may overlook catalyst–substrate interactions. This study explores substrate-specific interactions context of Rh-catalyzed asymmetric hydrogenation to elucidate impact substrate inclusion and descriptors derived from it. We compare complex methyl 2-acetamidoacrylate as model generic involving placeholder substrate, norbornadiene, across 11 Rh-based bidentate bisphosphine ligands. For these systems, full conformer ensemble analysis reveals an intriguing finding: rigid induces conformational freedom ligand. flexibility gives rise more diverse landscape, showing previously overlooked aspect dynamics. Electronic variations particularly highlight differences between structures. suggests that precatalyst-like models lack crucial insights into catalyst. speculate such be general phenomenon can influence development predictive computational TM-based catalysis.
Язык: Английский
Процитировано
4
The Journal of Chemical Physics, Год журнала: 2024, Номер 161(3)
Опубликована: Июль 15, 2024
PyDFT-QMMM is a Python-based package for performing hybrid quantum mechanics/molecular mechanics (QM/MM) simulations at the density functional level of theory. The program designed to treat short-range and long-range interactions through user-specified combinations electrostatic mechanical embedding procedures within periodic simulation domains, providing necessary interfaces external chemistry molecular dynamics software. To enable direct electrostatics in systems, we have derived implemented force terms our previously described QM/MM/PME approach [Pederson McDaniel, J. Chem. Phys. 156, 174105 (2022)]. Communication with software packages Psi4 OpenMM facilitated Python application programming (APIs). core library contains basic utilities running QM/MM simulations, plug-in entry-points are provided users implement custom energy/force calculation integration routines, an extensible architecture. user interacts primarily its API, allowing complex workflow development scripting, example, interfacing PLUMED free energy simulations. We provide benchmarks forces conservation alternative approaches. further demonstrate simple example use case water solute solvent system, which radial distribution functions computed from 100 ps simulations; this highlight how solvation structure sensitive different basis-set choices due under- or over-polarization QM molecule’s electron density.
Язык: Английский
Процитировано
3
The Journal of Chemical Physics, Год журнала: 2024, Номер 161(8)
Опубликована: Авг. 22, 2024
A portable and performant graphics processing unit (GPU)-accelerated library for electron repulsion integral (ERI) evaluation, named LibERI, has been developed implemented via directive-based (e.g., OpenMP OpenACC) standard language parallelism Fortran DO CONCURRENT). Offloaded ERIs consist of integrals over low high contraction s, p, d functions using the rotated-axis Rys quadrature methods. GPU codes are factorized based on previous developments [Pham et al., J. Chem. Theory Comput. 19(8), 2213-2221 (2023)] with two layers screening quartet presorting. In this work, density is moved to enhance computational efficacy large molecular systems. The L-shells in Pople basis set also separated into pure S P shells increase ERI homogeneity reduce atomic operations memory footprint. LibERI compatible any quantum chemistry drivers supporting MolSSI Driver Interface. Benchmark calculations interfaced GAMESS software package were carried out various architectures results show that performance comparable other state-of-the-art GPU-accelerated TeraChem GMSHPC) and, some cases, outperforms conventionally CUDA kernels QUICK) while fully maintaining portability.
Язык: Английский
Процитировано
3
The Journal of Chemical Physics, Год журнала: 2025, Номер 162(3)
Опубликована: Янв. 17, 2025
We present pyVPT2, a program to perform second-order vibrational perturbation theory (VPT2) computations obtain anharmonic frequencies. This is written in Python and can utilize any of the several quantum chemistry programs that have been interfaced QCEngine project Molecular Sciences Software Institute (MolSSI). The requisite single point energy, gradient, or Hessian be automatically performed distributed-parallel fashion by optionally using MolSSI’s QCFractal software. With VPT2 frequencies now computed lack their own capabilities.
Язык: Английский
Процитировано
0
The Journal of Physical Chemistry A, Год журнала: 2025, Номер unknown
Опубликована: Фев. 28, 2025
AtomDB is a free and open-source Python library for accessing manipulating neutral charged atomic species their promolecular properties. It serves as computational toolset, operating on an accompanying "extended periodic table" database, with experimental data covering wide range of charges multiplicities. includes facilities computing promolecules: local properties, constructed from the corresponding densities, scalar computed both taking into account whether properties are extensive or intensive. designed to be easy use, extend, maintain: it follows best practices modern software development, including comprehensive documentation, testing, continuous integration/delivery protocols, package management. This article official release note library.
Язык: Английский
Процитировано
0