F. Bickelhaupt

Chemistry with ADF

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.

The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance

The view that the hydrogen bonds in Watson - Crick adenine - thy- mine (AT) and guanine - cytosine (GC) base pairs are in essence electrostatic interactions with substantial resonance assistance from the p electrons is ques- tioned. Our investigation is based on a state-of-the-art density functional theo- retical (DFT) approach (BP86/TZ2P) that has been shown to properly repro- duce experimental data. Through a quantitative decomposition of the hy- drogen bond energy into its various physical terms, we demonstrate that, contrary to the widespread belief, do- nor - acceptor orbital interactions (i.e., charge transfer) in s symmetry between N or O lone pairs on one base and NH s*-acceptor orbitals on the other base do provide a substantial bonding contri- bution which is, in fact, of the same order of magnitude as the electrostatic interaction term. The overall orbital interactions are reinforced by a small p component which stems from polariza- tion in the p-electron system of the individual bases. This p component is, however, one order of magnitude small- er than the s term. Furthermore, we have investigated the synergism in a base pair between charge transfer from one base to the other through one hydrogen bond and in the opposite direction through another hydrogen bond, as well as the cooperative effect between the donor - acceptor interac- tions in the s- and polarization in the p- electron system. The possibility of CH ··· O hydrogen bonding in AT is also examined. In the course of these analyses, we introduce an extension of the Voronoi deformation density (VDD) method which monitors the redistribution of the s- and p-electron densities individually out of (DQ> 0) or into (DQ< 0) the Voronoi cell of an atom upon formation of the base pair from the separate bases.

2,4,6-Tri-tert-butylphenylphosphene-dimesitylsilene; the first phosphasilaalkene

Abstract The title compound (1) was prepared from chlorodimesitylsilyl-2,4,6-tri- tert -butyl-phenylphosphine (4) with n -butyllithium and characterized by its spectral data and by its chemical conversion with methanol to the adduct 6.

Organomagnesium chemistry: Nearly hundred years but still fascinating

Abstract Victor Grignard discovered his famous reaction, the synthesis of organomagnesium halides or Grignard reagents from organic halides and magnesium, in 1900. Up to now, this reaction has proved tremendously useful in organic and organometallic synthesis, and many of the secrets of its formation, structure, and reactivity have been unravelled. Nevertheless, organomagnesium chemistry is still vital and full of surprises. This will be illustrated with a selection of recent developments, admittedly with a strong bias for results from the authors laboratory. The topics presented concern the intermediacy of carbanions during the conversion of organic halides to Grignard reagents, the induction of high coordination numbers of magnesium by (intramolecular) coordination of crown and polyethers which leads to special structures such as organometallic rotaxanes and catenanes as well as to increased reactivity, and finally small α,ω-di-Grignard reagents with one, two or three carbon atoms between the two magnesiums, which are of interest both for their unique structures and for their application in the synthesis of metallacycles and metal-carbene complexes.

E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.

We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.

Synthesis and structure of pentacarbonyl(mesityldiphenylmethylenephosphine)-chromium(0)

Abstract Mesityldiphenylmethylenephosphine (I), a stable all-carbon substituted phosphaalkene, reacts with Cr(CO)5 · THF to furnish the title compound II, a relatively air-stable complex. Spectral data suggest a close structural similarity between the free and the complexed ligand and indicate I to be a ligand of moderate basicity towards chromium. X-ray crystal and molecular structure determination showed the phosphaalkene moiety to be nearly planar with a typically short PC bond length of 1.679(4) » and a CPC bond angle of 109.8(2)°. From a discussion of the bond lengths, it is tentatively concluded that in II, I is a π-acceptor of intermediate strength.

X-ray structural analyses of organomagnesium compounds

Publisher Summary This chapter discusses the X–ray structural analyses of organomagnesium compounds. Organomagnesium compounds are well-established tools in organic chemistry. Compared to the long history of the synthetic applications of organomagnesium compounds, the investigation of their structure and bonding covers a much shorter period. By the use of gas-phase electron diffraction (GED), it is possible to determine the structure of molecules in the gas phase. A major drawback of GED is that only small molecules can be resolved completely; for larger molecules, the degrees of freedom must be limited during the calculations by assuming and optimizing values for many of the structural parameters. In almost all structure determinations of simple Grignard or diorganylmagnesium compounds, the magnesium atoms are surrounded by four ligands. In the absence of coordinating solvents such as ethers, most organomagnesium compounds tend to form polymeric structures. Solid and volatile organomagnesium compounds can be slowly sublimed in a static high vacuum. On the symmetrization of di-Grignard reagents to the analogous halogen-free compounds, both polymeric and cyclic species may be expected. Although the tetrahedral coordination geometry is preferred by organomagnesium compounds, many examples have been structurally characterized, which show deviating coordination numbers. Increased coordination numbers for magnesium are also found for an ethylmagnesium-chloride/magnesium-chloride adduct. Fascinating structures can be obtained on the complexation of organomagnesium compounds with polyether ligands.

Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes

Strain-promoted azide-alkyne cycloaddition (SPAAC) as a conjugation tool has found broad application in material sciences, chemical biology and even in vivo use. However, despite tremendous effort, SPAAC remains fairly slow (0.2-0.5 M(-1) s(-1)) and efforts to increase reaction rates by tailoring of cyclooctyne structure have suffered from a poor trade-off between cyclooctyne reactivity and stability. We here wish to report tremendous acceleration of strain-promoted cycloaddition of an aliphatic cyclooctyne (bicyclo[6.1.0]non-4-yne, BCN) with electron-deficient aryl azides, with reaction rate constants reaching 2.0-2.9 M(-1) s(-1). A remarkable difference in rate constants of aliphatic cyclooctynes versus benzoannulated cyclooctynes is noted, enabling a next level of orthogonality by a judicious choice of azide-cyclooctyne combinations, which is inter alia applied in one-pot three-component protein labelling. The pivotal role of azide electronegativity is explained by density-functional theory calculations and electronic-structure analyses, which indicates an inverse electron-demand mechanism is operative with an aliphatic cyclooctyne.

The formation of Grignard compounds—II

Detailed investigations of CIDNP phenomena during Grignard formation reactions are reported. CIDNP was found in the main product RMgX, as well as in the byproducts R(H) and R(-H) and in one case in the starting halide, i-C3H7I. The radical pairR Ris shown to be involved in the formation of the polarized products. Furthermore it is proposed that the first step in the reaction sequence is a one electron transfer from magnesium to the organic halide to form the radical anion R-X which dissociates rapidly to furnish radical R.

Matrix-isolation infrared investigation of the flash vacuum thermolysis of norbornadienone azine

Abstract The flash vacuum thermolysis of norbornadienone azine over the temperature range 300 to 800°C was investigated by matrixisolation IR methods. The following thermolysis products could be identified: isocyanogen, cyanogen, benzene, benzonitrile and hydrogen cyanide. A tentative assignment of the infrared-active ν 2 stretching vibration of diisocyanogen, CNNC, in an argon matrix is made. The peak positions of four fundamentals (ν 1 to ν 4 ) of isocyanogen, CNCN, and of two stretching fundamentals (ν 1 and ν 2 ) of 13 CNCN, CN 13 CN, C 15 NCN and CNC 15 N in an argon matrix were measured. Combination bands yielded a value for ν 5 of CNCN. A molecular force field for CNCN was determined.