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Chemistry with ADF

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TLDR
The “Activation‐strain TS interaction” (ATS) model of chemical reactivity is reviewed as a conceptual framework for understanding how activation barriers of various types of reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis.
Abstract
We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001

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Citations
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Mapping the sites for selective oxidation of guanines in DNA.

TL;DR: The calculated distributions of a positive charge in sequences of two or three adjacent guanines, flanked by other nucleobases, provide an explanation for experimental literature data on the site-selective oxidation of DNA.
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Amide linkage isomerism as an activity switch for organometallic osmium and ruthenium anticancer complexes.

TL;DR: It is shown that the binding mode adopted by picolinamide derivatives in organometallic Os (II) and Ru(II) half-sandwich complexes can lead to contrasting cancer cell cytotoxicity and dynamic interconversion between N,O and N,N configurations can occur in solution and is time- and temperature- as well as pH-dependent.
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Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies.

TL;DR: Methods that can be applied for theoretical analyses of environmental effects are reviewed, ranging from continuum and point-charge models to explicit quantum chemical subsystem methods for environmental effects, and connections to physical model theories are outlined.
Journal ArticleDOI

Comparison of frozen-density embedding and discrete reaction field solvent models for molecular properties.

TL;DR: This work investigates the performance of two discrete solvent models in connection with density functional theory (DFT) for the calculation of molecular properties and finds that both solvent models agree for ground state properties, while there are significant differences in the description of response properties.
Journal ArticleDOI

Li+ Solvation in Pure, Binary, and Ternary Mixtures of Organic Carbonate Electrolytes

TL;DR: In this paper, classical molecular dynamics simulations and quantum chemical density functional theory (DFT) calculations have been employed in the present study to investigate the solvation of lithium cations in pure organic carbonate solvents.
References
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Journal ArticleDOI

Density‐functional thermochemistry. III. The role of exact exchange

TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
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Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

TL;DR: Numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, show that density-functional formulas for the correlation energy and correlation potential give correlation energies within a few percent.
Journal ArticleDOI

Self-Consistent Equations Including Exchange and Correlation Effects

TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
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Density-functional exchange-energy approximation with correct asymptotic behavior.

TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
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Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation.

TL;DR: A way is found to visualize and understand the nonlocality of exchange and correlation, its origins, and its physical effects as well as significant interconfigurational and interterm errors remain.
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