A simple basis set approach to solute electronic structure and free energy in solution

1993 ◽  
Vol 97 (9) ◽  
pp. 1723-1728 ◽  
Author(s):  
Hyung J. Kim ◽  
Roberto Bianco ◽  
Bradley J. Gertner ◽  
James T. Hynes
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Basis Set ◽  
Simple Basis

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

Disordering of MgAl2O4 spinel from first principles

2000 ◽  
Vol 64 (2) ◽  
pp. 311-317 ◽  
Author(s):  
M. C. Warren ◽  
M. T. Dove ◽  
S. A. T. Redfern
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
First Principles ◽  
Large Scale ◽  
Experimental Measurements ◽  
Zero Temperature ◽  
Macroscopic Models ◽  
Tetrahedral Sites ◽  
Degree Of Order ◽  
Good Agreement

AbstractAt high temperature, MgAl2O4 spinel is stabilized by disorder of Mg and Al between octahedral and tetrahedral sites. This behaviour has been measured up to 1700 K in recent neutron experiments, but the extrapolation of subsequently fitted thermodynamic models is not reliable. First principles simulation of the electronic structure of such minerals can in principle accurately predict disorder, but would require unfeasibly large computing resources. We have instead parameterized on-site and short-ranged cluster potentials using a small number of electronic structure simulations at zero temperature. These potentials were then used in large-scale statistical simulations at finite temperatures to predict disordering thermodynamics beyond the range of experimental measurements. Within the temperature range of the experiment, good agreement is obtained for the degree of order. The entropy and free energy are calculated and compared to those from macroscopic models.

scholarly journals Uncertainty quantification for quantum chemical models of complex reaction networks

2016 ◽  
Vol 195 ◽  
pp. 497-520 ◽  
Author(s):  
Jonny Proppe ◽  
Tamara Husch ◽  
Gregor N. Simm ◽  
Markus Reiher
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
State Space ◽  
Time Scales ◽  
Reaction Network ◽  
Reaction Networks ◽  
Multiple Time Scales ◽  
Complex Reaction ◽  
Discrete State ◽  
Continuous State

For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.

scholarly journals Thermodynamic Parameters of PbTe Crystals: DFT-Calculations

2015 ◽  
Vol 16 (1) ◽  
pp. 28-33
Author(s):  
D. M. Freik ◽  
B. P. Volochanska ◽  
T. O. Parashchuk
Keyword(s):  
Density Functional Theory ◽  
Free Energy ◽  
Electronic Structure ◽  
Thermodynamic Parameters ◽  
Quantum Chemical ◽  
Density Functional ◽  
Cubic Phase ◽  
Functional Theory ◽  
Temperature Dependences ◽  
Analytical Expressions

Based on the analysis of the crystal NaCl type and electronic structure of cubic phase CdS crystals the cluster models have been built for calculation of the geometric and thermodynamic parameters. According to density functional theory (DFT) and using the hybrid valence base set B3LYP the temperature dependence of the energy ΔE and the enthalpy ΔH of formation, Gibbs free energy ΔG, entropy ΔS, specific heat at constant volume CV and pressure CP of the crystals have been found. The analytical expressions of the temperature dependences of presented thermodynamic parameters which was approximated from the quantum- chemical calculations data and with using mathematical package Maple 14 have been received.

scholarly journals r2SCAN-3c: An Efficient “Swiss Army Knife” Composite Electronic-Structure Method

2020 ◽  
Author(s):  
Stefan Grimme ◽  
Andreas Hansen ◽  
Sebastian Ehlert ◽  
Jan-Michael Mewes
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Chemical Space ◽  
Noncovalent Interactions ◽  
New Method ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Benchmark Database ◽  
The Cost ◽  
Conformational Energies

The recently proposed second revision of the SCAN meta-GGA density-functional approximation (DFA) {Furness et al., J. Phys. Chem. Lett. 2020, 11, 8208-8215, termed r<sup>2</sup>SCAN} is used to construct an efficient composite electronic-structure method termed r<sup>2</sup>SCAN-3c, expanding the "3c'' series (hybrid: HSE/PBEh-3c, GGA: B97-3c, HF: HF-3c) to themGGA level. To this end, the unaltered r<sup>2</sup>SCAN functional is combined with a tailor-made <br>triple-zeta Gaussian AO-basis as well as with refitted D4 and gCP corrections for London-dispersion and basis-set superposition error. The performance of the new method is evaluated for the GMTKN55 thermochemical database covering large parts of chemical space with about 1500 <br>data points, as well as additional benchmarks for noncovalent interactions, organometallic reactions, lattice energies of organic molecules and ices, as well as for the adsorption on polar salt and non-polar coinage-metal surfaces. These comprehensive tests reveal a spectacular performance and robustness of r<sup>2</sup>SCAN-3c for reaction energies and noncovalent interactions in molecular and periodic systems, as well as outstanding conformational energies, and consistent structures. At just one tenth of the cost, r<sup>2</sup>SCAN-3c provides one of the best results of all semi-local DFT/QZ methods ever tested for the GMTKN55 benchmark database. Specifically for reaction and conformational energies as well as for noncovalent interactions, the new method outperforms hybrid-DFT/QZ approaches, compared to which the computational savings are even larger (factor 100-1000).<br>In relation to other "3c'' methods, r<sup>2</sup>SCAN-3c by far surpasses the accuracy of its predecessor B97-3c at only about twice the cost. The perhaps most relevant remaining systematic deviation of r<sup>2</sup>SCAN-3c is due to self-interaction-error, owing to its mGGA nature. However, SIE is notably reduced compared to other (m)GGAs, as is demonstrated for several examples. After all, this remarkably efficient and robust method is chosen as our new group default, replacing previous low-level DFT and partially even expensive high-level methods in most standard applications for systems with up to several hundreds of atoms.<br><br>

scholarly journals r2SCAN-3c: An Efficient “Swiss Army Knife” Composite Electronic-Structure Method

2020 ◽  
Author(s):  
Stefan Grimme ◽  
Andreas Hansen ◽  
Sebastian Ehlert ◽  
Jan-Michael Mewes
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Chemical Space ◽  
Noncovalent Interactions ◽  
New Method ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Benchmark Database ◽  
The Cost ◽  
Conformational Energies

The recently proposed second revision of the SCAN meta-GGA density-functional approximation (DFA) {Furness et al., J. Phys. Chem. Lett. 2020, 11, 8208-8215, termed r<sup>2</sup>SCAN} is used to construct an efficient composite electronic-structure method termed r<sup>2</sup>SCAN-3c, expanding the "3c'' series (hybrid: HSE/PBEh-3c, GGA: B97-3c, HF: HF-3c) to themGGA level. To this end, the unaltered r<sup>2</sup>SCAN functional is combined with a tailor-made <br>triple-zeta Gaussian AO-basis as well as with refitted D4 and gCP corrections for London-dispersion and basis-set superposition error. The performance of the new method is evaluated for the GMTKN55 thermochemical database covering large parts of chemical space with about 1500 <br>data points, as well as additional benchmarks for noncovalent interactions, organometallic reactions, lattice energies of organic molecules and ices, as well as for the adsorption on polar salt and non-polar coinage-metal surfaces. These comprehensive tests reveal a spectacular performance and robustness of r<sup>2</sup>SCAN-3c for reaction energies and noncovalent interactions in molecular and periodic systems, as well as outstanding conformational energies, and consistent structures. At just one tenth of the cost, r<sup>2</sup>SCAN-3c provides one of the best results of all semi-local DFT/QZ methods ever tested for the GMTKN55 benchmark database. Specifically for reaction and conformational energies as well as for noncovalent interactions, the new method outperforms hybrid-DFT/QZ approaches, compared to which the computational savings are even larger (factor 100-1000).<br>In relation to other "3c'' methods, r<sup>2</sup>SCAN-3c by far surpasses the accuracy of its predecessor B97-3c at only about twice the cost. The perhaps most relevant remaining systematic deviation of r<sup>2</sup>SCAN-3c is due to self-interaction-error, owing to its mGGA nature. However, SIE is notably reduced compared to other (m)GGAs, as is demonstrated for several examples. After all, this remarkably efficient and robust method is chosen as our new group default, replacing previous low-level DFT and partially even expensive high-level methods in most standard applications for systems with up to several hundreds of atoms.<br><br>

scholarly journals Accuracy and Reliability in the Simulation of Vibrational Spectra: A Comprehensive Benchmark of Energies and Intensities Issuing From Generalized Vibrational Perturbation Theory to Second Order (GVPT2)

2021 ◽  
Vol 8 ◽  
Author(s):  
Qin Yang ◽  
Marco Mendolicchio ◽  
Vincenzo Barone ◽  
Julien Bloino
Keyword(s):  
Perturbation Theory ◽  
Electronic Structure ◽  
Density Functional ◽  
Computational Cost ◽  
Theoretical Data ◽  
Infrared Region ◽  
Second Order ◽  
Basis Set ◽  
Molecular Systems ◽  
The Impact

Vibrational spectroscopy represents an active frontier for the identification and characterization of molecular species in the context of astrochemistry and astrobiology. As new missions will provide more data over broader ranges and at higher resolution, especially in the infrared region, which could be complemented with new spectrometers in the future, support from laboratory experiments and theory is crucial. In particular, computational spectroscopy is playing an increasing role in deepening our understanding of the origin and nature of the observed bands in extreme conditions characterizing the interstellar medium or some planetary atmospheres, not easily reproducible on Earth. In this connection, the best compromise between reliability, feasibility and ease of interpretation is still a matter of concern due to the interplay of several factors in determining the final spectral outcome, with larger molecular systems and non-covalent complexes further exacerbating the dichotomy between accuracy and computational cost. In this context, second-order vibrational perturbation theory (VPT2) together with density functional theory (DFT) has become particularly appealing. The well-known problem of the reliability of exchange-correlation functionals, coupled with the treatment of resonances in VPT2, represents a challenge for the determination of standardized or “black-box” protocols, despite successful examples in the literature. With the aim of getting a clear picture of the achievable accuracy and reliability of DFT-based VPT2 calculations, a multi-step study will be carried out here. Beyond the definition of the functional, the impact of the basis set and the influence of the resonance treatment in VPT2 will be analyzed. For a better understanding of the computational aspects and the results, a short summary of vibrational perturbation theory and the overall treatment of resonances for both energies and intensities will be given. The first part of the benchmark will focus on small molecules, for which very accurate experimental and theoretical data are available, to investigate electronic structure calculation methods. Beyond the reliability of energies, widely used for such systems, the issue of intensities will also be investigated in detail. The best performing electronic structure methods will then be used to treat larger molecular systems, with more complex topologies and resonance patterns.

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