Atomic basis sets optimization using the generalized simulated annealing approach: New basis sets for the first row elements

Andrade, Miceal Dias de; Nascimento, Marco Antônio Chaer; Mundim, Kleber C.; Sobrinho, A. M. C.; Malbouisson, L. A. C.

doi:10.1002/qua.21666

Cited by 14 publications

(12 citation statements)

References 10 publications

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“…This possibility was tested in previous works,3, 4 where we investigated the permanent electrical dipole moment of some AH molecules, using the MRHFCI method and the standard STO‐6G bases and a new minimal basis CFG‐6G 6. In all cases, we have obtained electrical dipole moments close to the experimental results with a reduced number of configurations in the MRHF basis.…”

Section: Introductionmentioning

confidence: 59%

Quadrupole moment of the hydrogen fluoride using the multireference Hartree–Fock CI method

Malbouisson

Andrade

Sobrinho

2012

Int J of Quantum Chemistry

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In this work, the multireference Hartree-Fock configuration interaction method (MRHFCI) was applied to calculate the permanent electrical quadrupole moment of the hydrogen fluoride molecule, using the atomic bases STO-6G and CFG-6G. We have obtained MRHFCI functions, with energies comparable to the full CI ones, providing dipole and quadrupole moments in close agreement with the experimental values and with reduced MRHF basis, that is, with significant lower numbers of configurations.

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Section: Introductionmentioning

confidence: 59%

Quadrupole moment of the hydrogen fluoride using the multireference Hartree–Fock CI method

Malbouisson

Andrade

Sobrinho

2012

Int J of Quantum Chemistry

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“…The MRHFCI method was applied to calculate the permanent electrical dipole moment of some small molecules, LiH, BH, FH, CO and H 2 O and the quadrupole moment of the FH [3]- [5], using the standard STO-6G and a new minimal-6G bases [6]. For LiH molecule were performed MRHFCI calculations with the double-zeta (dz), triplezeta (tz) and polarized dz (dzp) bases.…”

Section: Previous Resultsmentioning

confidence: 99%

Quantum-Mechanical Information Content of Multiples Hartree-Fock Solutions. The Multi-Reference Hartree-Fock Configuration Interaction Method

Malbouisson

Sobrinho

Andrade³

2014

JMP

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The Hartree-Fock equation is non-linear and has, in principle, multiple solutions. The th ω HF extreme and its associated virtual spin-orbitals furnish an orthogonal base B ω of the full configuration interaction space. Although all B ω bases generate the same CI space, the corresponding configurations of each B ω base have distinct quantum-mechanical information contents. In previous works, we have introduced a multi-reference configuration interaction method, based on the multiple extremes of the Hartree-Fock problem. This method was applied to calculate the permanent electrical dipole and quadrupole moments of some small molecules using minimal and double, triple and polarized double-zeta bases. In all cases were possible, using a reduced number of configurations, to obtain dipole and quadrupole moments in close agreement with the experimental values and energies without compromising the energy of the state function. These results show the positive effect of the use of the multi-reference Hartree-Fock bases that allowed a better extraction of quantum mechanical information from the several B ω bases. But to extend these ideas for larger systems and atomic bases, it is necessary to develop criteria to build the multireference Hartree-Fock bases. In this project, we are beginning a study of the non-uniform distribution of quantum-mechanical information content of the B ω bases, searching identify the factors that allowed obtain the good results cited above.

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“…Different attempts were made to quantitatively compare GA and the different versions of simulated annealing, concluding that the Monte Carlo derived methods are more efficient for biomolecular studies [63]. In particular, GSA has been shown to be useful when applied to global optimization problems that involve long range interactions, such as in atomic parameterization [64], gravitational systems [65] and conformational optimization of small molecules and peptides [66–72]. GSA has been shown to be more efficient than CSA and FSA as the number of dimensions in the phase space increases [73].…”

Section: Simulated Annealingmentioning

confidence: 99%

Enhanced sampling techniques in molecular dynamics simulations of biological systems

Bernardi

Melo

Schulten

2015

Biochimica et Biophysica Acta (BBA) - General Subjects

641

495

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Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms.

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Atomic basis sets optimization using the generalized simulated annealing approach: New basis sets for the first row elements

Cited by 14 publications

References 10 publications

Quadrupole moment of the hydrogen fluoride using the multireference Hartree–Fock CI method

Quadrupole moment of the hydrogen fluoride using the multireference Hartree–Fock CI method

Quantum-Mechanical Information Content of Multiples Hartree-Fock Solutions. The Multi-Reference Hartree-Fock Configuration Interaction Method

Enhanced sampling techniques in molecular dynamics simulations of biological systems

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