Efficient and accurate approximations to the molecular spin-orbit coupling operator and their use in molecular g-tensor calculations

Approximations to the Breit-Pauli form of the spin-orbit coupling (SOC) operator are examined. The focus is on approximations that lead to an effective quasi-one-electron operator which leads to efficient property evaluations. In particular, the accurate spin-orbit mean-field (SOMF) method developed by Hess, Marian, Wahlgren, and Gropen is examined in detail. It is compared in detail with the "effective potential" spin-orbit operator commonly used in density functional theory (DFT) and which has been criticized for not including the spin-other orbit (SOO) contribution. Both operators contain identical one-electron and Coulomb terms since the SOO contribution to the Coulomb term vanishes exactly in the SOMF treatment. Since the DFT correlation functional only contributes negligibly to the SOC the only difference between the two operators is in the exchange part. In the SOMF approximation, the SOO part is equal to two times the spin-same orbit contribution. The DFT exchange contribution is of the wrong sign and numerically shown to be in error by a factor of 2-2.5 in magnitude. The simplest possible improvement in the DFT-SOC treatment [Veff(-2X)-SOC] is to multiply the exchange contribution to the Veff operator by -2. This is verified numerically in calculations of molecular g-tensors and one-electron SOC constants of atoms and ions. Four different ways of handling the computationally critical Coulomb part of the SOMF and Veff operators are discussed and implemented. The resolution of the identity approximation is virtually exact for the SOC with standard auxiliary basis sets which need to be slightly augmented by steep s functions for heavier elements. An almost as efficient seminumerical approximation is equally accurate. The effective nuclear charge model gives results within approximately 10% (on average) of the SOMF treatment. The one-center approximation to the Coulomb and one-electron SOC terms leads to errors on the order of approximately 5%. Small absolute errors are obtained for the one-center approximation to the exchange term which is consequently the method of choice [SOMF(1X)] for large molecules.     

Absolute Asymmetric Synthesis: The Origin, Control, and Amplification of Chirality

Biomolecular homochirality, the origin of which is still a puzzle, has challenged scientists to design chemical systems that provide chiral molecules through absolute asymmetric synthesis and to amplify a small stereochemical bias in such systems. The photoresolution of the enantiomers of helical-shaped, sterically overcrowded alkene 1 with circularly polarized light and the transduction of the stereochemical information by triggering the helical arrangement of a large collection of achiral molecules in a twisted nematic liquid crystalline phase (2) are examples of control and amplification of chirality.     

Standardization for oxygen isotope ratio measurement - still an unsolved problem

Numerous organic and inorganic laboratory standards were gathered from nine European and North American laboratories and were analyzed for their delta(18)O values with a new on-line high temperature pyrolysis system that was calibrated using Vienna standard mean ocean water (VSMOW) and standard light Antartic precipitation (SLAP) internationally distributed reference water samples. Especially for organic materials, discrepancies between reported and measured values were high, ranging up to 2 per thousand. The reasons for these discrepancies are discussed and the need for an exact and reliable calibration of existing reference materials, as well as for the establishment of additional organic and inorganic reference materials is stressed. Copyright 1999 John Wiley & Sons, Ltd.     

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.     

Experimental and computational investigation of thiolate alkylation in Ni(II) and Zn(II) complexes: role of the metal on the sulfur nucleophilicity

The biologically relevant S-alkylation reactions of thiolate ligands bound to a transition metal ion were investigated with particular attention paid to the role of the metal identity: Zn(II) versus Ni(II). The reactivity of two mononuclear diamine dithiolate Zn and Ni complexes with CH(3)I was studied. With the [ZnL] complex (1) (LH(2) = 2,2'-(2,2'-bipyridine-6,6'-diyl)bis(1,1-diphenylethanethiolate)), a double S-methylation occurs leading to [ZnL(Me2)I(2)] (1(Me2)), while with [NiL] (2), only the mono-S-methylated product [NiL(Me)]I (2(Me)) is formed. Complexes 1 and 1(Me2) have been characterized by X-ray crystallography, while the structures of 2 and 2(Me) have been previously described. The kinetics of the first S-methylation reaction, investigated by (1)H NMR, is found to follow a second-order rate law, and the activation parameters, ΔH(?) and ΔS(?), are similar for both 1 and 2. S K-edge X-ray absorption spectroscopy measurements have been carried out on 1, 2, and 2(Me), and a TD-DFT approach was employed to interpret the data. The electronic structures of 1 and 2 calculated by DFT reveal that the thiolate-metal bond is predominantly ionic in 1 and covalent in 2. However, evaluation of the molecular electrostatic potential minima around the lone pairs of the thiolate sulfur atoms gives similar values for 1 and 2, suggesting a comparable nucleophilicity. The DFT-optimized structures of the mono-S-methylation products have been calculated for the Zn and Ni complexes. Molecular electrostatic potential analysis of these products shows that (i) the nucleophilicity of the remaining thiolate sulfur atom is partly quenched for the Ni complex while it is conserved in the Zn complex and, more importantly, (ii) that the accessibility for the methyl transfer agent to the remaining thiolate is favored for the mono-S-methylated Zn complex compared to the Ni one. This explains the absence of a double S-methylation process in the case of the Ni complex at room temperature.     

Ab initio calculations of the photoionization of diatomic molecules

A review is presented of the calculation of photoionization spectra, particularly in the spectral range where electron autoionization of diatomic molecules takes place. In addition to some interesting results obtained over years that compare favourably with experiment, the emphasis here is put on the relation between the methods developed for the calculation of observables associated with the continuum energy spectrum of the electrons and the Alchemy system of programs. This system of programs serves as a basis for initial and intermediate calculations. The examples presented show that diatomic molecules not only in gas phase but also oriented in space or physisorbed at surfaces may be studied readily.     

Interaction between explosive and analyte layers in explosive matrix-assisted plasma desorption mass spectrometry

An HMX/insulin two-layer system was chosen as a model for further investigation of the matrix properties of explosive materials for protein analytes in plasma desorption mass spectrometry. The dependencies of the molecular ion yield and average charge state as a function of the analyte thickness were studied. An increase in the charge state of multiply protonated molecular species was confirmed as the major matrix effect, with the average charge state z at the smallest thickness studied being higher than in matrix-assisted laser desorption/ionization and closer to the value obtained in electrospray ionization under standard acidic conditions. Observed charge state distributions are significantly narrower than the corresponding Poisson distributions, which suggests that the protonation of insulin is limited in plasma desorption by the number of basic sites in the molecule, similar to electrospray ionization. Both the curve displaying total molecular ion yield and the one showing the total charge (proton) yield as a function of the insulin thickness have maxima at a thickness different from an insulin monolayer. These observations diminish the significance of a matrix/analyte interface mechanism for the explosive matrix assistance. Instead, a mechanism related to the chemical energy release during conversion of the explosive after the ion impact is proposed. As additional mechanisms, enhanced protonation of the analyte through collisions with products of the explosive decay is considered, as well as electron scavenging by other products, which leads to a higher survival probability of positively charged protein molecular ions. Copyright 1999 John Wiley & Sons, Ltd.