scholarly journals Erratum: “Density functional solvation model based on CM2 atomic charges” [J. Chem. Phys. 109, 9117 (1998)]

1999 ◽  
Vol 111 (12) ◽  
pp. 5624-5624 ◽  
Author(s):  
Tianhai Zhu ◽  
Jiabo Li ◽  
Gregory D. Hawkins ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Density Functional ◽  
Chem Phys ◽  
Atomic Charges ◽  
Solvation Model ◽  
Model Based

Erratum: “Density functional solvation model based on CM2 atomic charges” [J. Chem. Phys. 109, 9117 (1998); 111, 5624 (E) (1999)]

2000 ◽  
Vol 113 (9) ◽  
pp. 3930-3930
Author(s):  
Tianhai Zhu ◽  
Jiabo Li ◽  
Gregory D. Hawkins ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Density Functional ◽  
Chem Phys ◽  
Atomic Charges ◽  
Solvation Model ◽  
Model Based

Density functional solvation model based on CM2 atomic charges

1998 ◽  
Vol 109 (20) ◽  
pp. 9117-9133 ◽  
Author(s):  
Tianhai Zhu ◽  
Jiabo Li ◽  
Gregory D. Hawkins ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Density Functional ◽  
Atomic Charges ◽  
Solvation Model ◽  
Model Based

Analytical energy gradients of a self-consistent reaction-field solvation model based on CM2 atomic charges

1999 ◽  
Vol 110 (12) ◽  
pp. 5503-5513 ◽  
Author(s):  
Tianhai Zhu ◽  
Jiabo Li ◽  
Daniel A. Liotard ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Atomic Charges ◽  
Solvation Model ◽  
Reaction Field ◽  
Model Based ◽  
Self Consistent

Computational Investigation of the Asymmetry in Photosynthetic Reaction Center Models from First Principles

2020 ◽  
Author(s):  
Denis Artiukhin ◽  
Patrick Eschenbach ◽  
Johannes Neugebauer
Keyword(s):  
Spin Density ◽  
Reaction Center ◽  
Density Functional ◽  
Photosynthetic Reaction Center ◽  
Chem Phys ◽  
Molecular Structures ◽  
Error Characteristic ◽  
Molecular Systems ◽  
Density Distributions ◽  
The Asymmetry

We present a computational analysis of the asymmetry in reaction center models of photosystem I, photosystem II, and bacteria from <i>Synechococcus elongatus</i>, <i>Thermococcus vulcanus</i>, and <i>Rhodobacter sphaeroides</i>, respectively. The recently developed FDE-diab methodology [J. Chem. Phys., 148 (2018), 214104] allowed us to effectively avoid the spin-density overdelocalization error characteristic for standard Kohn–Sham Density Functional Theory and to reliably calculate spin-density distributions and electronic couplings for a number of molecular systems ranging from dimeric models in vacuum to large protein including up to about 2000 atoms. The calculated spin densities showed a good agreement with available experimental results and were used to validate reaction center models reported in the literature. We demonstrated that the applied theoretical approach is very sensitive to changes in molecular structures and relative orientation of molecules. This makes FDE-diab a valuable tool for electronic structure calculations of large photosynthetic models effectively complementing the existing experimental techniques.

`Diet GMKTN55' Offers Accelerated Benchmarking Through a Representative Subset Approach

2018 ◽  
Author(s):  
Tim Gould
Keyword(s):  
Density Functional ◽  
Chem Phys ◽  
Comprehensive Analysis ◽  
Genetic Approach ◽  
Representative Subset ◽  
Phys Chem Chem Phys

The GMTKN55 benchmarking protocol introduced by [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184] allows comprehensive analysis and ranking of density functional approximations with diverse chemical behaviours. But this comprehensiveness comes at a cost: GMTKN55's 1500 benchmarking values require energies for around 2500 systems to be calculated, making it a costly exercise. This manuscript introduces three subsets of GMTKN55, consisting of 30, 100 and 150 systems, as `diet' substitutes for the full database. The subsets are chosen via a stochastic genetic approach, and consequently can reproduce key results of the full GMTKN55 database, including ranking of approximations.

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

scholarly journals Octupole correlations in light actinides from the interacting boson model based on the Gogny energy density functional

2020 ◽  
Vol 102 (6) ◽  
Author(s):  
K. Nomura ◽  
R. Rodríguez-Guzmán ◽  
Y. M. Humadi ◽  
L. M. Robledo ◽  
J. E. García-Ramos
Keyword(s):  
Energy Density ◽  
Density Functional ◽  
Interacting Boson Model ◽  
Energy Density Functional ◽  
Model Based ◽  
Boson Model

scholarly journals Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy

2021 ◽  
Author(s):  
Maximilian Theiß ◽  
Merten Grupe ◽  
Tilman Lamparter ◽  
Maria Andrea Mroginski ◽  
Rolf Diller
Keyword(s):  
Density Functional ◽  
Transient Absorption ◽  
Vibrational Analysis ◽  
Density Functional Theory Calculations ◽  
Chem Phys ◽  
Molecular Structures ◽  
Ir Absorption ◽  
Time Resolved ◽  
Time Constants ◽  
Vis Spectroscopy

AbstractDeactivation processes of photoexcited (λex = 580 nm) phycocyanobilin (PCB) in methanol were investigated by means of UV/Vis and mid-IR femtosecond (fs) transient absorption (TA) as well as static fluorescence spectroscopy, supported by density-functional-theory calculations of three relevant ground state conformers, PCBA, PCBB and PCBC, their relative electronic state energies and normal mode vibrational analysis. UV/Vis fs-TA reveals time constants of 2.0, 18 and 67 ps, describing decay of PCBB*, of PCBA* and thermal re-equilibration of PCBA, PCBB and PCBC, respectively, in line with the model by Dietzek et al. (Chem Phys Lett 515:163, 2011) and predecessors. Significant substantiation and extension of this model is achieved first via mid-IR fs-TA, i.e. identification of molecular structures and their dynamics, with time constants of 2.6, 21 and 40 ps, respectively. Second, transient IR continuum absorption (CA) is observed in the region above 1755 cm−1 (CA1) and between 1550 and 1450 cm−1 (CA2), indicative for the IR absorption of highly polarizable protons in hydrogen bonding networks (X–H…Y). This allows to characterize chromophore protonation/deprotonation processes, associated with the electronic and structural dynamics, on a molecular level. The PCB photocycle is suggested to be closed via a long living (> 1 ns), PCBC-like (i.e. deprotonated), fluorescent species.

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