Jaap G. Snijders

Implementation of time-dependent density functional response equations

Time-dependent density functional theory provides a first principles method for the calculation of frequency-dependent polarizabilities, hyperpolarizabilities, excitation energies and many related response properties. In recent years, the molecular results obtained by several groups have shown that this approach is in general more accurate than the time-dependent Hartree-Fock approach, and is often competitive in accuracy with computationally more demanding conventional ab initio approaches. In this paper, our implementation of the relevant equations in the Amsterdam Density Functional program is described. We will focus on certain aspects of the implementation which are necessary for an efficient evaluation of the desired properties, enabling the treatment of large molecules. Such an efficient implementation is obtained by: using the full symmetry of the molecule, using a set of auxiliary functions for fitting the (zeroth- and first-order) electron density, using a highly vectorized and parallelized code, using linear scaling techniques, and, most importantly, by solving the response equations iteratively.

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.

Steric asymmetry in state-resolved NO-ar collisions

New experimental results are reported on state-dependent steric effects in NO-Ar inelastic scattering. The NO molecules are selected in the J = 1/2(-) l-doublet state of the electronic ground state and oriented relative to the incident Ar atoms. The steric asymmetry, S = (sigma(NO) - sigma(ON))/(sigma(NO) + sigma(ON)), has been measured as a function of the final rotational state J. In a previous study, quantum-mechanical scattering calculations were found to predict strong oscillations in S, but experimental evidence for this behavior was not conclusive. The results of experiments presented here provide clear evidence of the qualitative correctness of the theoretical calculations.

Calculation of the redox potential of the protein azurin and some mutants

Azurin from Pseudomonas aeruginosa is a small 128‐residue, copper‐containing protein. Its redox potential can be modified by mutating the protein. Free‐energy calculations based on classical molecular‐dynamics simulations of the protein and from mutants in aqueous solution at different pH values were used to compute relative redox potentials. The precision of the free‐energy calculations with the λ coupling‐parameter approach is evaluated as function of the number and sequence of λ values, the sampling time and initial conditions. It is found that the precision is critically dependent on the relaxation of hydrogen‐bonding networks when changing the atomic‐charge distribution due to a change of redox state or pH value. The errors in the free energies range from 1 to 10 kBT, depending on the type of process. Only qualitative estimates of the change in redox potential by protein mutation can be obtained.

On the nature of the first excited states of the uranyl ion

Abstract Results of calculations on the uranylion using the LCAO MO Hartree—Fock—Slater method including relativistic effects are reported. The highest occupied molecular orbital is calculated to be σ u , consisting predominantly of U 5f character. The σ u orbital is the HOMO partly because of “pushing-from-below” by the U 6p orbital, but also as a result of the change in potential of the U 5f electrons with the uranium core elections brought about by relativistic contraction of the core electrons. This effect also determines the character of the first virtual levels (δ u and Φ u , respectively) in equatorial ligand fields.

Time-dependent density functional study of the static second hyperpolarizability of BB-, NN- and BN-substituted C60

In this work we have investigated the effects of substituting carbon atoms with B and N on the second hyperpolarizability of C60 using time-dependent density functional theory. We have calculated the second hyperpolarizability of the double substitute-doped fullerenes C58NN, C58BB and C58BN. For C60 only small changes in the second hyperpolarizability were found when doping with either 2B or 2N. However, by doping C60 with both B and N, creating an donor-acceptor system, an increase in the second hyperpolarizability with about 50% was found.

Mean polarizabilities of organic molecules. A comparison of restricted Hartree Fock, density functional theory and direct reaction field results

Abstract The polarizabilities of 15 organic molecules are calculated using the Restricted Hartree Fock (RHF) method, the Time Dependent Density Functional Theory (TD-DFT) and the Direct Reaction Field (DRF) approach. The RHF method gives rather poor results, while the other two give average deviations comparable to the experimental uncertainty. The DRF approach is very fast (

On the Evaluation of Spin)Orbit Coupling Matrix Elements in a Spin-Adapted Basis

In the present article, we outline a simple scheme for generating configuration interaction matrix elements for spin)orbit interactions in molecules. The procedure leads to a close parallelism with spin-free permutation-group approaches. Unitary shift operators were successfully used on the orbital space to generate the matching permutations necessary to evaluate the required matrix elements. The procedure is adequately illustrated using examples. Q 1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 23)27, 1999