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

Chemistry with ADF

The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.

The hydrogen bond in the solid state.

The Gaussian‐2 theoretical procedure (G2 theory), based on a b i n i t i o molecular orbital theory, for calculation of molecular energies (atomization energies, ionization potentials,electron affinities, and proton affinities) of compounds containing first‐ (Li–F) and second‐row atoms (Na–Cl) is presented. This new theoretical procedure adds three features to G1 theory [J. Chem. Phys. 9 0, 5622 (1989)] including a correction for nonadditivity of diffuse‐s p and 2d f basis set extensions, a basis set extension containing a third d function on nonhydrogen and a second p function on hydrogen atoms, and a modification of the higher level correction. G2 theory is a significant improvement over G1 theory because it eliminates a number of deficiencies present in G1 theory. Of particular importance is the improvement in atomization energies of ionic molecules such as LiF and hydrides such as C2H6, NH3, N2H4, H2O2, and CH3SH. The average absolute deviation from experiment of atomization energies of 39 first‐row compounds is reduced from 1.42 to 0.92 kcal/mol. In addition, G2 theory gives improved performance for hypervalent species and electron affinities of second‐row species (the average deviation from experiment of electron affinities of second‐row species is reduced from 1.94 to 1.08 kcal/mol). Finally, G2 atomization energies for another 43 molecules, not previously studied with G1 theory, many of which have uncertain experimental data, are presented and differences with experiment are assessed.

Gaussian-2 theory for molecular energies of first- and second-row compounds

In this Account we have compiled a list of reliable bond energies that are based on a set of critically evaluated experiments. A brief description of the three most important experimental techniques for measuring bond energies is provided. We demonstrate how these experimental data can be applied to yield the heats of formation of organic radicals and the bond enthalpies of more than 100 representative organic molecules.

Bond Dissociation Energies of Organic Molecules

The first acidity scale to be established in a pure solvent other than water was the result of the pioneering work of Conant, Wheland, and McEwen in ether or ben~ene .~ During the past 20 years an ion-pair acidity scale covering an \"effective pKa rangefrom about 15 to 40 has been developed in cyclohexylamine (CHA),6 and similar studies in other low-dielectric-constant solvents including 1,2-dimethoxyethane (DME)7a and tetrahydrofuran (THF)7b*c have been carried out. A more limited ion-pair acidity scale has been developed in liquid NH,.7d Also, during this period, acidity scales have been established in the polar non-hydrogenbond-donor (NHBD) solvents dimethyl sulfoxide (Me$0)8 and N-methylpyrrolidin-2-one (NMP)? which have relatively high dielectric constants. The pK,'s measured in these solvents differ from ion-pair pK,'s in that they are absolute, in the sense that they are based on Me2S0 and NMP as the standard states, which allows direct comparisons to be made with H20 and gas-phase pK,'s. A truly absolute acidity scale has been established in the gas phase, which, for the first time, provides intrinsic measures of structural effects free of solvent effects.1° Our purpose in this Account is (a) to discuss briefly acidities in various solvent media, (b) to present a table of representative equilibrium acidity constants in M e 8 0 solution, and (c) to illustrate ways in which these pK, data can be used. In an accompanying Account we compare acidities in Me2S0 solution with intrinsic gas-phase acidities and discuss some of the insights into solvation effects provided thereby. Acidities in H 2 0 and Me2S0. It is important to recognize that pKa values are solvent dependent. The

/pdf/equilibrium-acidities-in-dimethyl-sulfoxide-solution-av3qyewuun.pdf

Equilibrium Acidities in Dimethyl Sulfoxide Solution

Estimation of effective ion temperatures in a quadrupole ion trap

Ab Initio Studies of Amino Acid Conformations. 1. The Conformers of Alanine, Serine, and Cysteine

Over the past several decades, quadrupole ion traps have become important instruments in the study of gas phase ion/molecule reactions. As a part of this work, they have been employed in a number of studies focused on fundamental organic reaction mechanisms. In this review, the general features and limitations of quadrupole ion traps are discussed followed by a description of representative ion trap studies of organic reaction mechanisms such as substitution, elimination, and acyl transfer reactions.

Quadrupole ion trap studies of fundamental organic reactions

Gas phase acidities of the α amino acids

High-level ab initio calculations are used to investigate the potential energy surfaces of the identity proton transfers between CH4, NH3, OH2, FH, SiH4, PH3, SH2, and ClH and their conjugate bases. Energies are reported at the MP4/6-311+G(d,p)//MP2/6-31+G(d,p) and G2+ levels. At the highest level, there is a good correlation between the calculated and experimental proton affinities of the conjugate bases (average error, ±0.5 kcal/mol). The proton-transfer potential energy surfaces vary from single wells with stable, symmetric intermediates (FH) to double wells with significant central barriers (CH 4 , NH 3 , SiH 4 , and PH 3 )

Theoretical studies of proton transfers. 1. The potential energy surfaces of the identity reactions of the first- and second-row non-metal hydrides with their conjugate bases

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