C. Fonseca Guerra

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.

Isohexide Derivatives from Renewable Resources as Chiral Building Blocks

The combination of rapidly depleting fossil resources and growing concerns about greenhouse gas emissions and global warming have stimulated extensive research on the use of biomass for energy, fuels, and chemicals.[1] Although biobased chemicals have the potential to reduce the amount of fossil feedstock consumed in the chemical industry today, the most abundant type of biobased feedstock, that is, carbohydrates, is often unsuitable for current high-temperature industrial chemical processes. Compared to hydrophobic aliphatic or aromatic feedstocks with a low degree of functionalization, carbohydrates such as polysaccharides are complex, overfunctionalized hydrophilic materials. One approach to overcome these drawbacks is to reduce the number of functional groups, resulting in more stable, industrially applicable bifunctional biobased building blocks,[2] such as furan-2,5-dicarboxylic acid,[3] levulinic acid,[4] and isosorbide.[5] Isosorbide (1,4:3,6-dianhydrosorbitol) is a rigid bicyclic diol that is derived from sorbitol and can ultimately be obtained from glucose-based polysaccharides such as starch and cellulose.[6] Apart from isosorbide, in which the hydroxyl groups on C2 and C5 are in the exo and endo positions, respectively, two other isohexides are known (Figure 1): the symmetrical endo-endo isomer isomannide (1,4:3,6-dianhydromannitol) and the exo-exo isomer isoidide (1,4:3,6-dianhydroiditol), derived from d-mannitol and l-iditol, respectively.

Towards excitation energies and (hyper)polarizability calculations of large molecules. Application of parallelization and linear scaling techniques to time-dependent density functional response theory

We document recent improvements in the efficiency of our implementation in the Amsterdam Density Functional program (ADF) of the response equations in time‐dependent density functional theory (TDDFT). Applications to quasi one‐dimensional polyene chains and to three‐dimensional water clusters show that, using our all‐electron atomic orbital (AO)‐based implementation, calculations of excitation energies and (hyper)polarizabilities on molecules with several hundred atoms and several thousand basis functions are now feasible, even on (a small cluster of) personal computers. The matrix elements, which are required in TDDFT, are calculated on an AO basis and the same linear scaling techniques as used in ADF for the iterative solution of the Kohn–Sham (KS) equations are applied to the determination of these matrix elements. Near linear scaling is demonstrated for this part of the calculation, which used to be the time‐determining step. Transformations from the AO basis to the KS orbital basis and back exhibit N3 scaling, but due to a very small prefactor this N3 scaling is still of little importance for currently accessible system sizes. The main CPU bottleneck in our current implementation is the multipolar part of the Coulomb potential, scaling quadratically with the system size. It is shown that the parallelization of our code leads to further significant reductions in execution times, with a measured speed‐up of 70 on 90 processors for both the SCF and the TDDFT parts of the code. This brings high‐level calculations on excitation energies and dynamic (hyper)polarizabilities of large molecules within reach.

Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug.

Abstract We have computationally studied the intercalation of the antitumor drug daunomycin into six stacks of Watson-Crick DNA base pairs i.e., AT-AT, AT-TA, GC-AT, CG-TA, GC-GC, GC-CG) using density functional theory (DFT). The proton affinity of the DNA intercalater daunomycin in water was computed to be 159.2 kcal/mol at BP86/TZ2P, which is in line with the experimental observation that daunomycin is protonated under physiological conditions. The intercalation interaction of protonated daunomycin with two stacked DNA base pairs was studied through a hybrid approach in which intercalation is treated at LDA/TZP while the molecular structure of daunomycin and hydrogen-bonded Watson-Crick pairs is computed at BP86/TZ2P We find that the affinity of the drug for the six considered base pair dimers decreases in the order AT-AT > AT-TA > GC-AT > GC-TA > GC-CG > GC-GC, in excellent agreement with experimental data on the thermodynamics of the interaction between daunomycin and synthetic polynucleotides in aqueous solution. Our analyses show that the overall stability of the intercalation complexes comes mainly from π-π stacking but an important contribution to the computed and experimentally observed sequence specificity comes from hydrogen bonding between daunomycin and hetero atoms in the minor groove of AT base pairs.

Covalency in Highly Polar Bonds. Structure and Bonding of Methylalkalimetal Oligomers (CH3M)n (M = Li−Rb; n = 1, 4)

We have carried out a theoretical investigation of the methylalkalimetal monomers CH3M and tetramers (CH3M)4 with M = Li, Na, K, and Rb and, for comparison, the methyl halides CH3X with X = F, Cl, Br, and I, using density functional theory (DFT) at BP86/TZ2P. Our purpose is to determine how the structure and thermochemistry (e.g., C-M bond lengths and strengths, oligomerization energies) of organoalkalimetal compounds depend on the metal atom and to understand the emerging trends in terms of quantitative Kohn-Sham molecular orbital (KS-MO) theory. The C-M bond becomes longer and weaker, both in the monomers and tetramers, if one descends the periodic table from Li to Rb. Quantitative bonding analysis shows that this trend is not only determined by decreasing electrostatic attraction but also, even to a larger extent, by the weakening in orbital interactions. The latter become less stabilizing along Li-Rb because the bond overlap between the singly occupied molecular orbitals (SOMOs) of CH3(•) and M(•) radicals decreases as the metal ns atomic orbital (AO) becomes larger and more diffuse. Thus, the C-M bond behaves as a typical electron-pair bond between the methyl radical and alkalimetal atom, and, in that respect, it is covalent. It is also shown that such an electron-pair bond can still be highly polar, in agreement with the large dipole moment. Interestingly, the C-M bond becomes less polar in the methylalkalimetal tetramers because metal-metal interactions stabilize the alkalimetal orbitals and, in that way, make the alkalimetal effectively less electropositive.

Neutral Six-Coordinate and Cationic Five-Coordinate Silicon(IV) Complexes with Two Bidentate Monoanionic N,S-Pyridine-2-thiolato(−) Ligands

A series of neutral six-coordinate silicon(IV) complexes (4-11) with two bidentate monoanionic N,S-pyridine-2-thiolato ligands and two monodentate ligands R(1) and R(2) was synthesized (4, R(1) = R(2) = Cl; 5, R(1) = Ph, R(2) = Cl; 6, R(1) = Ph, R(2) = F; 7, R(1) = Ph, R(2) = Br; 8, R(1) = Ph, R(2) = N3; 9, R(1) = Ph, R(2) = NCO; 10, R(1) = Ph, R(2) = NCS; 11, R(1) = Me, R(2) = Cl). In addition, the related ionic compound 12 was synthesized, which contains a cationic five-coordinate silicon(IV) complex with two bidentate monoanionic N,S-pyridine-2-thiolato ligands and one phenyl group (counterion: I(-)). Compounds 4-12 were characterized by elemental analyses, NMR spectroscopic studies in the solid state and in solution, and crystal structure analyses (except 7). These structural investigations were performed with a special emphasis on the sophisticated stereochemistry of these compounds. These experimental investigations were complemented by computational studies, including bonding analyses based on relativistic density functional theory.

The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics.

Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine–thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson–Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp2 to sp3, does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn–Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor–acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands

We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)2 <d(CpA)2 <d(ApT)2 <d(ApA)2 <d(GpT)2 <d(GpA)2 <d(ApG)2 <d(CpG)2 <d(GpG)2 <d(GpC)2, where the energy differences between the last four dimers, d(ApG)2, d(CpG)2, d(GpG)2 and d(GpC)2, is within 4.0 kcal mol−1, and the energy between the most and the least stable isomers is 13.4 kcal mol−1. This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5’- to the 3’-end.

Extension of a predictive substrate model for human cytochrome P4502D6

1. Metoprolol, indoramine, codeine, tamoxifen and prodipine, compounds which are clinically used, and MDMA (ecstasy) were fitted in a small molecule model for substrates of human cytochrome P4502D6. 2. For both the R- and S-enantiomer of metoprolol, the R- and S-enantiomer of MDMA, and for indoramine and codeine (all proven substrates of cytochrome P4502D6) an acceptable fit in the substrate model was obtained. 3. For tamoxifen, for which the involvement of cytochrome P4502D6 in the 4-hydroxylation is uncertain, no acceptable fit could be obtained in the substrate model. 4. For prodipine, a competitive inhibitor of P4502D6, for which the involvement of P4502D6 in the metabolism is uncertain, no acceptable fit in the substrate model could be obtained. 5. The substrate model was extended in a direction in which two large known substrates extend from the original substrate model. This extension did not change the flat hydrophobic region of the original substrate model.

How amino and nitro substituents direct electrophilic aromatic substitution in benzene: an explanation with Kohn–Sham molecular orbital theory and Voronoi deformation density analysis

The substituent effect of the amino and nitro groups on the electronic system of benzene has been investigated quantum chemically using quantitative Kohn-Sham molecular orbital theory and a corresponding energy decomposition analysis (EDA). The directionality of electrophilic substitution in aniline can accurately be explained with the amount of contribution of the 2pz orbitals on the unsubstituted carbon atoms to the highest occupied π orbital. For nitrobenzene, the molecular π orbitals cannot explain the regioselectivity of electrophilic substitution as there are two almost degenerate π orbitals with nearly the same 2pz contributions on the unsubstituted carbon atoms. The Voronoi deformation density analysis has been applied to aniline and nitrobenzene to obtain an insight into the charge rearrangements due to the substituent. This analysis method identified the orbitals involved in the C-N bond formation of the π system as the cause for the π charge accumulation at the ortho and para positions in the case of the NH2 group and the largest charge depletion at these same positions for the NO2 substituent. Furthermore, we showed that it is the repulsive interaction between the πHOMO of the phenyl radical and the πHOMO of the NH2 radical that is responsible for pushing up the πHOMO of aniline and therefore activating this π orbital of the phenyl ring towards electrophilic substitution.