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1.
J Chem Phys ; 152(24): 244116, 2020 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-32610969

RESUMO

The parameterization of torsional/dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields. Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms. To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values. However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses. In this paper, we propose a systematic and versatile workflow called TorsionDrive to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development. The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described. The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.

2.
J Chem Phys ; 152(18): 184108, 2020 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-32414239

RESUMO

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

3.
J Chem Inf Model ; 59(10): 4093-4099, 2019 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-31525920

RESUMO

Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/ ). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.

4.
J Chem Phys ; 151(4): 044114, 2019 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-31370516

RESUMO

We develop a stochastic resolution of identity representation to the second-order Matsubara Green's function (sRI-GF2) theory. Using a stochastic resolution of the Coulomb integrals, the second order Born self-energy in GF2 is decoupled and reduced to matrix products/contractions, which reduces the computational cost from O(N5) to O(N3) (with N being the number of atomic orbitals). The current approach can be viewed as an extension to our previous work on stochastic resolution of identity second order Møller-Plesset perturbation theory [T. Y. Takeshita et al., J. Chem. Theory Comput. 13, 4605 (2017)] and offers an alternative to previous stochastic GF2 formulations [D. Neuhauser et al., J. Chem. Theory Comput. 13, 5396 (2017)]. We show that sRI-GF2 recovers the deterministic GF2 results for small systems, is computationally faster than deterministic GF2 for N > 80, and is a practical approach to describe weak correlations in systems with 103 electrons and more.

5.
J Chem Theory Comput ; 15(8): 4386-4398, 2019 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-31283237

RESUMO

We introduce a free and open-source software package (PES-Learn) which largely automates the process of producing high-quality machine learning models of molecular potential energy surfaces (PESs). PES-Learn incorporates a generalized framework for producing grid points across a PES that is compatible with most electronic structure theory software. The newly generated or externally supplied PES data can then be used to train and optimize neural network or Gaussian process models in a completely automated fashion. Robust hyperparameter optimization schemes designed specifically for molecular PES applications are implemented to ensure that the best possible model for the data set is fit with high quality. The performance of PES-Learn toward fitting a few semiglobal PESs from the literature is evaluated. We also demonstrate the use of PES-Learn machine learning models in carrying out high-level vibrational configuration interaction computations on water and formaldehyde.

6.
J Chem Phys ; 149(18): 180901, 2018 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-30441927

RESUMO

The field of computational molecular sciences (CMSs) has made innumerable contributions to the understanding of the molecular phenomena that underlie and control chemical processes, which is manifested in a large number of community software projects and codes. The CMS community is now poised to take the next transformative steps of better training in modern software design and engineering methods and tools, increasing interoperability through more systematic adoption of agreed upon standards and accepted best-practices, overcoming unnecessary redundancy in software effort along with greater reproducibility, and increasing the deployment of new software onto hardware platforms from in-house clusters to mid-range computing systems through to modern supercomputers. This in turn will have future impact on the software that will be created to address grand challenge science that we illustrate here: the formulation of diverse catalysts, descriptions of long-range charge and excitation transfer, and development of structural ensembles for intrinsically disordered proteins.

7.
J Chem Phys ; 148(16): 164110, 2018 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-29716224

RESUMO

We present a symmetry-adapted perturbation theory (SAPT) for the interaction of two high-spin open-shell molecules (described by their restricted open-shell Hartree-Fock determinants) resulting in low-spin states of the complex. The previously available SAPT formalisms, except for some system-specific studies for few-electron complexes, were restricted to the high-spin state of the interacting system. Thus, the new approach provides, for the first time, a SAPT-based estimate of the splittings between different spin states of the complex. We have derived and implemented the lowest-order SAPT term responsible for these splittings, that is, the first-order exchange energy. We show that within the so-called S2 approximation commonly used in SAPT (neglecting effects that vanish as fourth or higher powers of intermolecular overlap integrals), the first-order exchange energies for all multiplets are linear combinations of two matrix elements: a diagonal exchange term that determines the spin-averaged effect and a spin-flip term responsible for the splittings between the states. The numerical factors in this linear combination are determined solely by the Clebsch-Gordan coefficients: accordingly, the S2 approximation implies a Heisenberg Hamiltonian picture with a single coupling strength parameter determining all the splittings. The new approach is cast into both molecular-orbital and atomic-orbital expressions: the latter enable an efficient density-fitted implementation. We test the newly developed formalism on several open-shell complexes ranging from diatomic systems (Li⋯H, Mn⋯Mn, …) to the phenalenyl dimer.

8.
J Chem Theory Comput ; 14(7): 3504-3511, 2018 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-29771539

RESUMO

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

9.
J Chem Phys ; 147(16): 161727, 2017 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-29096505

RESUMO

Accurate potential energy models are necessary for reliable atomistic simulations of chemical phenomena. In the realm of biomolecular modeling, large systems like proteins comprise very many noncovalent interactions (NCIs) that can contribute to the protein's stability and structure. This work presents two high-quality chemical databases of common fragment interactions in biomolecular systems as extracted from high-resolution Protein DataBank crystal structures: 3380 sidechain-sidechain interactions and 100 backbone-backbone interactions that inaugurate the BioFragment Database (BFDb). Absolute interaction energies are generated with a computationally tractable explicitly correlated coupled cluster with perturbative triples [CCSD(T)-F12] "silver standard" (0.05 kcal/mol average error) for NCI that demands only a fraction of the cost of the conventional "gold standard," CCSD(T) at the complete basis set limit. By sampling extensively from biological environments, BFDb spans the natural diversity of protein NCI motifs and orientations. In addition to supplying a thorough assessment for lower scaling force-field (2), semi-empirical (3), density functional (244), and wavefunction (45) methods (comprising >1M interaction energies), BFDb provides interactive tools for running and manipulating the resulting large datasets and offers a valuable resource for potential energy model development and validation.

10.
J Chem Theory Comput ; 13(7): 3185-3197, 2017 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-28489372

RESUMO

Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements.

11.
J Phys Chem Lett ; 7(12): 2197-203, 2016 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-27203625

RESUMO

Since the original fitting of Grimme's DFT-D3 damping parameters, the number and quality of benchmark interaction energies has increased significantly. Here, conventional benchmark sets, which focus on minimum-orientation radial curves at the expense of angular diversity, are augmented by new databases such as side chain-side chain interactions (SSI), which are composed of interactions gleaned from crystal data and contain no such minima-focused bias. Moreover, some existing databases such as S22×5 are extended to shorter intermolecular separations. This improved DFT-D3 training set provides a balanced description of distances, covers the entire range of interaction types, and at 1526 data points is far larger than the original training set of 130. The results are validated against a new collection of 6773 data points and demonstrate that the effect of refitting the damping parameters ranges from no change in accuracy (LC-ωPBE-D3) to an almost 2-fold decrease in average error (PBE-D3).

12.
Phys Chem Chem Phys ; 17(25): 16560-74, 2015 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-26055458

RESUMO

We assessed the performance of a large variety of modern density functional theory approaches for the adsorption of carbon dioxide on molecular models of pyridinic N-doped graphene. Specifically, we selected eight polyheterocyclic aromatic compounds ranging from pyridine and pyrazine to 1,6-diazacoronene and investigated their complexes with CO2 for a large range of intermolecular distances and including both in-plane and stacked orientations. The benchmark interaction energies were computed at the complete-basis-set limit MP2 level plus a CCSD(T) coupled-cluster correction in a moderate but carefully selected basis set. Using a set of 96 benchmark CCSD(T)-level interaction energies as a reference, we investigated the accuracy of DFT-based approaches as a function of the density functional, the dispersion correction, the basis set, and the counterpoise correction or lack thereof. While virtually all DFT variants exhibit some deterioration of accuracy for distances slightly shorter than the van der Waals minima, we were able to identify several schemes such as B2PLYP-D3 and M05-2X-D3 whose average errors on the entire benchmark data set are in the 5-10% range. The top DFT performers were subsequently used to investigate the energy profile for a carbon dioxide transition through model N-doped graphene pores. All investigated methods confirmed that the largest, N4H4 pore allows for a barrierless CO2 transition to the other side of a graphene sheet.

13.
J Phys Chem A ; 118(33): 6351-60, 2014 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-24476383

RESUMO

An accurate 2D ab initio potential energy surface of the He-C3 collisional system is calculated using the supermolecular coupled-cluster method with up to perturbative quadruple excitations, CCSDT(Q). This interaction potential is then incorporated in full close-coupling calculations of rotational excitation/de-excitation cross sections in He + C3 collisions for rotational levels j = 0, 2, ..., 10 and collision energies up to 1000 cm(-1). Corresponding rate coefficients are reported for temperature between 1 and 100 K. Results are found to be in excellent agreement with available theoretical data that were restricted to the temperature range of 5-15 K. Implications of the computed rate coefficients to astrophysical models of C3 and carbon clusters in interstellar and circumstellar environments are discussed.

14.
J Chem Theory Comput ; 10(8): 3140-50, 2014 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-26588285

RESUMO

We investigated the basis set convergence of high-order coupled-cluster interaction energy contributions for 21 small weakly bound complexes. By performing CCSDT(Q) calculations in at least the aug-cc-pVTZ basis set, and CCSDT calculations in at least aug-cc-pVQZ (aug-cc-pVTZ for one system), we found the convergence to be quite slow. In particular, the 6-31G*(0.25) and 6-31G**(0.25,0.15) bases advocated by Hobza et al. (J. Chem. Theory Comput. 2013, 9, 2151; ibid. 2013, 9, 3420) are unsuitable for the post-CCSD(T) effects, with average errors for the CCSDT(Q)-CCSD(T) interaction energy contribution of about 80% for 6-31G**(0.25,0.15) and 110% for 6-31G*(0.25). Upgrading the basis set to aug-cc-pVDZ reduces the average error to about 35% and extremely demanding CCSDT(Q)/aug-cc-pVTZ calculations are necessary for further improvement in accuracy. An error cancellation between basis set incompleteness effects at the CCSDT-CCSD(T) and CCSDT(Q)-CCSDT levels occurs for most (but not all) complexes, making it unproductive to carry out CCSDT calculations in a larger basis set than the more demanding CCSDT(Q) calculations. We also found that the frozen natural orbital approximation at the CCSDT and CCSDT(Q) levels works well only if the thresholds for discarding least occupied natural orbitals are very tight (significantly tighter than the thresholds recommended for molecular correlation energies in the original work of Rolik and Kállay, J. Chem. Phys. 2011, 134, 124111), making the performance gains quite limited. The interaction energy contributions through CCSDT(Q) are both a necessity and a bottleneck in the construction of top-accuracy interaction potentials and further improvements in the efficiency of high-order coupled-cluster calculations will be of great help.

15.
J Chem Phys ; 139(14): 144305, 2013 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-24116617

RESUMO

A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of (4)He-H2 and (3)He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture.

16.
J Chem Theory Comput ; 9(1): 370-89, 2013 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-26589040

RESUMO

Minimum energy structures and interaction energies are obtained for a series of polycyclic aromatic hydrocarbons (PAHs) interacting with a methane molecule. The PAHs include benzene, naphthalene, anthracene, phenanthrene, tetracene, pyrene, and coronene. Interaction energies are calculated using the highest level of theory and basis set available, that is, complete-basis-set extrapolated MP2 plus a conventional or explicitly correlated CCSD(T) correction in moderately sized basis sets. The results show that the singly coordinated minimum configuration observed earlier for benzene-methane is no longer the global minimum one for naphthalene and larger PAHs. Instead, triply coordinated geometries are lower in energy. The global minimum structures for methane interacting with extended systems like graphene sheets and carbon nanotubes are likely to be triply coordinated as well. A variety of novel dispersion-including DFT approaches are compared against the wave-function-based benchmark potential energy curves. The top performer, the B3LYP functional combined with the -D3 dispersion correction, is then employed to calculate interaction energies for methane interacting with hexabenzocoronene and circumcoronene in order to estimate the methane adsorption energy on graphite. The delicate balance between dispersion and exchange in PAH-methane interactions is elucidated using symmetry-adapted perturbation theory with a DFT description of monomers. The present study provides an important benchmark for the design and tuning of more approximate methods for an accurate description of hydrocarbon physisorption on carbon nanostructures.

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