scholarly journals Transferring structural knowledge across cognitive maps in humans and models

2019 ◽  
Author(s):  
Shirley Mark ◽  
Rani Moran ◽  
Thomas Parr ◽  
Steve Kennerley ◽  
Tim Behrens
Keyword(s):  
Computational Model ◽  
Cognitive Maps ◽  
Important Task ◽  
Basis Set ◽  
Structural Knowledge ◽  
Basis Sets ◽  
Structural Form ◽  
Structural Prior ◽  
Novel Environments

Relations between task elements often follow hidden underlying structural forms such as periodicities or hierarchies, whose inferences fosters performance. However, transferring structural knowledge to novel environments requires flexible representations that are generalizable over particularities of the current environment, such as its stimuli and size. We suggest that humans represent structural forms as abstract basis sets and that in novel tasks, the structural form is inferred and the relevant basis set is transferred. Using a computational model, we show that such representation allows inference of the underlying structural form, important task states, effective behavioural policies and the existence of unobserved state-trajectories. In two experiments, participants learned three abstract graphs during two successive days. We tested how structural knowledge acquired on Day-1 affected Day-2 performance. In line with our model, participants who had a correct structural prior were able to infer the existence of unobserved state-trajectories and appropriate behavioural policies.

scholarly journals Transferring structural knowledge across cognitive maps in humans and models

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Shirley Mark ◽  
Rani Moran ◽  
Thomas Parr ◽  
Steve W. Kennerley ◽  
Timothy E. J. Behrens
Keyword(s):  
Computational Model ◽  
Cognitive Maps ◽  
Important Task ◽  
Basis Set ◽  
Structural Knowledge ◽  
Basis Sets ◽  
Structural Form ◽  
Structural Prior ◽  
Novel Environments

Abstract Relations between task elements often follow hidden underlying structural forms such as periodicities or hierarchies, whose inferences fosters performance. However, transferring structural knowledge to novel environments requires flexible representations that are generalizable over particularities of the current environment, such as its stimuli and size. We suggest that humans represent structural forms as abstract basis sets and that in novel tasks, the structural form is inferred and the relevant basis set is transferred. Using a computational model, we show that such representation allows inference of the underlying structural form, important task states, effective behavioural policies and the existence of unobserved state-trajectories. In two experiments, participants learned three abstract graphs during two successive days. We tested how structural knowledge acquired on Day-1 affected Day-2 performance. In line with our model, participants who had a correct structural prior were able to infer the existence of unobserved state-trajectories and appropriate behavioural policies.

A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

2018 ◽  
Author(s):  
Danilo Carmona ◽  
David Contreras ◽  
Oscar A. Douglas-Gallardo ◽  
Stefan Vogt-Geisse ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Hydroxyl Radical ◽  
Ab Initio ◽  
Fenton Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dft Methods ◽  
Elementary Steps ◽  
Oxygen Oxygen ◽  
Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

DFT Benchmark Study of the O--O Bond Dissociation Energy in Peroxides Validated with High-Level Ab-Initio Calculations

2019 ◽  
Author(s):  
Danilo Carmona ◽  
Pablo Jaque ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Reference Value ◽  
Basis Set ◽  
Basis Sets ◽  
Mean Deviation ◽  
Bond Dissociation ◽  
Dissociation Energies ◽  
The Mean ◽  
Experimental Values ◽  
High Level ◽  
Almost All

<div><div><div><p>Peroxides play a central role in many chemical and biological pro- cesses such as the Fenton reaction. The relevance of these compounds lies in the low stability of the O–O bond which upon dissociation results in radical species able to initiate various chemical or biological processes. In this work, a set of 64 DFT functional-basis set combinations has been validated in terms of their capability to describe bond dissociation energies (BDE) for the O–O bond in a database of 14 ROOH peroxides for which experimental values ofBDE are available. Moreover, the electronic contributions to the BDE were obtained for four of the peroxides and the anion H2O2− at the CBS limit at CCSD(T) level with Dunning’s basis sets up to triple–ζ quality provid- ing a reference value for the hydrogen peroxide anion as a model. Almost all the functionals considered here yielded mean absolute deviations around 5.0 kcal mol−1. The smallest values were observed for the ωB97 family and the Minnesota M11 functional with a marked basis set dependence. Despite the mean deviation, order relations among BDE experimental values of peroxides were also considered. The ωB97 family was able to reproduce the relations correctly whereas other functionals presented a marked dependence on the chemical nature of the R group. Interestingly, M11 functional did not show a very good agreement with the established order despite its good performance in the mean error. The obtained results support the use of similar validation strategies for proper prediction of BDE or other molecular properties by DF Tmethods in subsequent related studies.</p></div></div></div>

Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

2019 ◽  
Author(s):  
Kamal Batra ◽  
Stefan Zahn ◽  
Thomas Heine
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Absolute Error ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Framework Materials ◽  
Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

AlN Nanotubes: A DFT Study of Al-27 and N-14 Electric Field Gradient Tensors

2007 ◽  
Vol 62 (12) ◽  
pp. 711-715 ◽  
Author(s):  
Ahmad Seif ◽  
Mahmoud Mirzaei ◽  
Mehran Aghaie ◽  
Asadollah Boshra
Keyword(s):  
Electric Field ◽  
Electric Field Gradient ◽  
Field Gradient ◽  
Density Functional ◽  
Quadrupole Coupling Constant ◽  
Basis Set ◽  
Basis Sets ◽  
B3lyp Method ◽  
Package Program ◽  
Nqr Parameters

Density functional theory (DFT) calculations were performed to calculate the electric field gradient (EFG) tensors at the sites of aliminium (27Al) and nitrogen (14N) nuclei in an 1 nm of length (6,0) single-walled aliminium nitride nanotube (AlNNT) in three forms of the tubes, i. e. hydrogencapped, aliminium-terminated and nitrogen-terminated as representatives of zigzag AlNNTs. At first, each form was optimized at the level of the Becke3,Lee-Yang-Parr (B3LYP) method, 6-311G∗∗ basis set. After, the EFG tensors were calculated at the level of the B3LYP method, 6-311++G∗∗ and individual gauge for localized orbitals (IGLO-II and IGLO-III) types of basis sets in each of the three optimized forms and were converted to experimentally measurable nuclear quadrupole resonance (NQR) parameters, i. e. quadrupole coupling constant (qcc) and asymmetry parameter (ηQ). The evaluated NQR parameters revealed that the considered model of AlNNT can be divided into four equivalent layers with similar electrostatic properties.With the exception of Al-1, all of the three other Al layers have almost the same properties, however, N layers show significant differences in the magnitudes of the NQR parameters in the length of the nanotube. Furthermore, the evaluated NQR parameters of Al-1 in the Al-terminated form and N-1 in the N-terminated form revealed the different roles of Al (base agent) and of N (acid agent) in AlNNT. All the calculations were carried out using the GAUSSIAN 98 package program.

scholarly journals The S66 Non-Covalent Interactions Benchmark Reconsidered Using Explicitly Correlated Methods Near the Basis Set Limit

2018 ◽  
Vol 71 (4) ◽  
pp. 238 ◽  
Author(s):  
Manoj K. Kesharwani ◽  
Amir Karton ◽  
Nitai Sylvetsky ◽  
Jan M. L. Martin
Keyword(s):  
Computational Cost ◽  
The Other ◽  
Basis Set ◽  
Basis Sets ◽  
Explicitly Correlated ◽  
Non Covalent Interactions ◽  
Explicitly Correlated Methods ◽  
The One ◽  
High Level ◽  
Covalent Interactions

The S66 benchmark for non-covalent interactions has been re-evaluated using explicitly correlated methods with basis sets near the one-particle basis set limit. It is found that post-MP2 ‘high-level corrections’ are treated adequately well using a combination of CCSD(F12*) with (aug-)cc-pVTZ-F12 basis sets on the one hand, and (T) extrapolated from conventional CCSD(T)/heavy-aug-cc-pV{D,T}Z on the other hand. Implications for earlier benchmarks on the larger S66×8 problem set in particular, and for accurate calculations on non-covalent interactions in general, are discussed. At a slight cost in accuracy, (T) can be considerably accelerated by using sano-V{D,T}Z+ basis sets, whereas half-counterpoise CCSD(F12*)(T)/cc-pVDZ-F12 offers the best compromise between accuracy and computational cost.

Net charges and valence AO's in the methylamines; the hydrogen basis set and the properties of nitrogen

1985 ◽  
Vol 63 (7) ◽  
pp. 1487-1491 ◽  
Author(s):  
Giuseppe Del Re ◽  
Sándor Fliszár ◽  
Michel Comeau ◽  
Claude Mijoule
Keyword(s):  
Basis Set ◽  
Basis Sets ◽  
Methyl Groups ◽  
Extended Form ◽  
Amine Nitrogen ◽  
Methyl Group ◽  
Net Charges ◽  
Extended Basis

Net charges and valence AO's for ammonia, methylamine, dimethylamine, and trimethylamine were calculated using extended basis sets. Superposition effects, evaluated by replacing Pople's standard 6-31G* basis by an extended form in which the basis of the ammonia H atoms and of the methyl groups of trimethylamine are retained in the treatment of each molecule, indicate that the quality of the treatment of amine nitrogen atoms is strongly dependent on the number of methyl groups. A new, augmented basis is proposed for the hydrogens, which appears to be reasonably well balanced: comparison with familiar (e.g., 6-31G*) calculations illustrates in what manner the treatment of nitrogen is worsened when even just one methyl group is replaced by hydrogen unless the impoverishment of the basis is suitably taken care of.

scholarly journals Theoretical Study of Solvent Effects on the Electronic and Thermodynamic Properties of Tetrathiafulvalene (TTF) Molecule Based on DFT

2021 ◽  
pp. 42-54
Author(s):  
Rabiu Nuhu Muhammad ◽  
N. M. Mahraz ◽  
A. S Gidado ◽  
A. Musa
Keyword(s):  
Thermodynamic Properties ◽  
Bond Length ◽  
Density Functional ◽  
Theoretical Study ◽  
Energy Gap ◽  
Basis Set ◽  
Basis Sets ◽  
Frontier Molecular Orbital ◽  
Orbital Energy ◽  
Chemical Hardness

Tetrathiafulvalene () is an organosulfur compound used in the production of molecular devices such as switches, sensors, nonlinear optical devices and rectifiers. In this work, a theoretical study on the effects of solvent on TTF molecule was investigated and reported based on Density Functional Theory (DFT) as implemented in Gaussian 03 package using B3LYP/6-31++G(d,p) basis set. Different solvents were introduced as a bridge to investigate their effects on the electronic structure. The HUMO, LUMO, energy gap, global chemical index, thermodynamic properties, NLO and DOS analysis of the TTF molecule in order to determine the reactivity and stability of the molecule were obtained. The results obtained showed that the solvents have effects on the electronic and non-linear-optical properties of the molecule. The optimized bond length revealed that the molecule has strong bond in gas phase with smallest bond length of about 1.0834Å than in the rest of the solvents. It was observed that the molecule is more stable in acetonitrile with HOMO-LUMO gap and chemical hardness of 3.6373eV and 1.8187eV respectively. This indicates that the energy gap and chemical hardness of TTF molecule increases with the increase in polarity and dielectric constant of the solvents. The computed results agreed with the results in the literature. The thermodynamics and NLO properties calculation also indicated that TTF molecule has highest value of specific heat capacity (Cv), total dipole moment () and first order hyperpolarizability () in acetonitrile, while acetone has the highest value of entropy and toluene has a slightly higher value of zero point vibrational energy (ZPVE) than the rest of the solvents. The results show that careful selection of the solvents and basis sets can tune the frontier molecular orbital energy gap of the molecule and can be used for molecular device applications.

scholarly journals Stable Occupancy of Hydrogen Molecules in Clathrate Hydrates and + THF Clathrate Hydrates Determined by Ab Initio Calculations

2010 ◽  
Vol 2010 ◽  
pp. 1-6 ◽  
Author(s):  
Prasad Yedlapalli ◽  
Sangyong Lee ◽  
Jae W. Lee
Keyword(s):  
Ab Initio ◽  
Binding Energies ◽  
Clathrate Hydrates ◽  
Basis Set ◽  
Large Cavity ◽  
Basis Sets ◽  
Pure Hydrogen ◽  
Point Energy ◽  
Small Cavity ◽  
Hydrogen Molecules

Structure II clathrate hydrates of pure hydrogen and binary hydrates of are studied using ab initio calculations to determine the stable occupancies of small cavities. Ab initio calculations are carried out for a double cavity consisting of one dodecahedron (small cavity) and one hexakaidecahedron (large cavity). These two cavities are attached to each other as in sII hydrates to form a double cavity. One or two molecules are placed in the small cavity and one THF (or 4 molecules) molecule is placed in the large cavity. We have determined the binding energies of the double cavities at the MP2 level using various basis sets (3-21G, 3-21G(2p), 3-21 G(2p), 6-31G, 6-31G(2p), and 6-31 G(2p)). Different basis sets yield different stable occupancies of the small cavity. The results from the highest basis set (6-31 G(2p) with zero point energy corrections) indicate that the single occupancy is slightly more favorable than the double occupancy in both the cases of pure hydrates and THF + double hydrates.

Sign in / Sign up

Export Citation Format

Share Document