Magdalena Pecul

The Ab Initio Calculation of Optical Rotation and Electronic Circular Dichroism

Abstract We review the theory of the lowest-order manifestations of natural optical activity: optical rotation (OR) and electronic circular dichroism (ECD), and discuss the applications of modern ab initio methods to the calculation of these properties, with particular emphasis put on the challenges facing such calculations, including the gauge origin problem. We review the recent applications of ab initio methods to calculations of OR and ECD, giving examples of the kind of molecules and questions that can now be addressed using ab initio methodology.

Chiral bias of amyloid fibrils revealed by the twisted conformation of Thioflavin T: An induced circular dichroism/DFT study

Since it was implicated in a number of neurodegenerative conditions, such as Alzheimer disease, formation of β‐sheet‐rich protein fibrils (amyloids) has been drawing a lot of attention. One of elusive aspects of amyloidogenesis concerns the mechanisms of specific binding of molecules such as Congo red, or Thioflavin T by amyloid fibrils. A comprehensive understanding of these docking interactions is needed, however, for the sake of furthering biochemical studies and developing molecular, pharmacological strategies preventing proliferation of amyloids in vivo. Through the application of circular dichroism, here we show that upon binding to insulin fibrils, a twisted conformation is enforced in molecules of Thioflavin T, manifested in a strong negative Cotton effect around 450 nm, which is supported by density functional theory–based calculations. This finding may lead to circular dichroism of Thioflavin T becoming a new diagnostic technique for protein fibrils, complementary to fluorescence spectroscopy.

Explicit versus implicit solvent modeling of Raman optical activity spectra.

Raman and Raman optical activity (ROA) spectra of molecules reflect not only molecular structure and conformation but also the dynamics and interactions with the solvent. For polar, biologically relevant molecules in aqueous environment, this often complicates the band assignment and interpretation of the spectra. In the present study, implicit dielectric and explicit solvent models are compared with respect to the influence of the choice of solvent model on the spectral shape. Lactamide and 2-aminopropanol were selected as model compounds, and the Raman and ROA spectra were measured for both enantiomers. Geometries of explicitly solvated clusters were derived from quantum-mechanical calculations, classical (MD), and Car-Parrinello (CPMD) molecular dynamics. The results indicate that although the dielectric model reasonably well reproduces the main spectral features, more faithful intensity profiles, including the inhomogeneous band broadening, are obtained from the explicit MD and CPMD clusters. Additionally, the CPMD clusters are capable of reproducing most spectral features better than the classical dynamics, provided the simulation time is long enough to allow for a complete sampling of the conformational space. The hydrogen-bonded water molecules of the first hydration shell significantly influence the spectral intensities, whereas the effect of loosely attached or distant solvent molecules is minor. In order to average the signal, however, a relatively large number of MD geometries need to be considered, as was also exemplified by simulations of the ROA spectrum of the achiral molecule glycine. An explicit solvent modeling of sizable systems thus requires extensive computations, which became possible only recently due to the development of efficient analytical computational techniques.

A simple scheme for magnetic balance in four-component relativistic Kohn–Sham calculations of nuclear magnetic resonance shielding constants in a Gaussian basis

We report the implementation of nuclear magnetic resonance (NMR) shielding tensors within the four-component relativistic Kohn-Sham density functional theory including non-collinear spin magnetization and employing London atomic orbitals to ensure gauge origin independent results, together with a new and efficient scheme for assuring correct balance between the large and small components of a molecular four-component spinor in the presence of an external magnetic field (simple magnetic balance). To test our formalism we have carried out calculations of NMR shielding tensors for the HX series (X = F, Cl, Br, I, At), the Xe atom, and the Xe dimer. The advantage of simple magnetic balance scheme combined with the use of London atomic orbitals is the fast convergence of results (when compared with restricted kinetic balance) and elimination of linear dependencies in the basis set (when compared to unrestricted kinetic balance). The effect of including spin magnetization in the description of NMR shielding tensor has been found important for hydrogen atoms in heavy HX molecules, causing an increase of isotropic values of 10%, but negligible for heavy atoms.

Characterization of dihydrogen-bonded D-H...H-A complexes on the basis of infrared and magnetic resonance spectroscopic parameters

The structural, energetic, and spectroscopic properties of the dihydrogen-bonded complexes LiH⋯H2, LiH⋯CH4, LiH⋯C2H6, and LiH⋯C2H2 are investigated. In particular, the interaction energy is decomposed into physically meaningful contributions, and the calculated vibrational frequencies, the magnetic resonance shielding constants, and inter- and intramolecular spin–spin coupling constants are analyzed in terms of their correlation with the interaction energy. Unlike the other three complexes, which can be classified as weak van der Waals complexes, the LiH⋯C2H2 complex resembles a conventional hydrogen-bonded system. The complexation-induced changes in the vibrational frequencies and in the magnetic resonance shielding constants correlate with the interaction energy, as does the reduced coupling 2hJHX between the proton of LiH and hydrogen or carbon nucleus of the proton donor, while 1hJHH do not correlate with the interaction energy. The calculations have been carried out using Moller–Plesset perturbation ...

High-order correlation effects on dynamic hyperpolarizabilities and their geometric derivatives: A comparison with density functional results

Second harmonic generation hyperpolarizabilities and their geometric derivatives have been calculated for HF, HCl, CO, and LiF, using the coupled cluster hierarchies, CCS, CC2, CCSD, CC3, and large correlation-consistent basis sets. The full configuration interaction results have been used to test the accuracy of the coupled cluster results. The CCS and CC2 methods do not improve on the Hartree-Fock results while CCSD is robust and gives significant improvements compared to CCS and CC2. The effects of triples in CC3 are in some cases substantial. Higher order correlation effects are significant for LiF. Including core-valence correlation effects is required only if high accuracy is desired. The coupled cluster results have been used as benchmarks for the results obtained by means of density functional theory using various exchange-correlation functionals. For the hyperpolarizability B3LYP was found to perform best, i.e., to give the results closest to the CC3 ones, while for the geometric derivatives none of the considered functionals was able to give a consistent description for all the considered molecules.

Polarizable continuum model study of solvent effects on electronic circular dichroism parameters

We present an implementation of the polarizable continuum model for the calculation of solvent effects on electronic circular dichroism spectra. The computational model used is density functional theory in the length-gauge formulation, and gauge-origin independence is ensured through the use of London atomic orbitals. Results of calculations carried out for methyloxirane and bicyclic ketones, camphor, norcamphor, norbornenone, and fenchone are presented, and the theoretically obtained solvent effects are compared with experimental observations.

Electric field effects on the shielding constants of noble gases: A four-component relativistic Hartree-Fock study

Second derivatives of nuclear shielding constants with respect to an electric field, i.e., shielding polarizabilities, have been calculated for the noble gas atoms from helium to xenon. The calculations have been carried out using the four-component relativistic Hartree-Fock method. In order to assess the importance of the individual relativistic corrections, the shielding polarizabilities have also been calculated at the nonrelativistic Hartree-Fock level, with spin-orbit and scalar (Darwin and mass-velocity) effects having been established by perturbative methods. Electron correlation effects have been estimated using the second-order polarization propagator approach. The relativistic effects on the tensor components of the shielding polarizabilities are found to be larger and changing less regularly with the atomic number than for the shielding constant itself. However, there is a partial cancellation of the contributions to the parallel and perpendicular components of the shielding polarizability and as a consequence the mean shielding polarizability is far less affected than the individual components.

Comprehensive ab initio studies of nuclear magnetic resonance shielding and coupling constants in XH⋯O hydrogen-bonded complexes of simple organic molecules

The influence of hydrogen-bond formation on the scalar spin–spin coupling constants and NMR shielding constants in CH2O–H2O, C2H2–H2O, CH3OH–H2O, and (HCOOH)2 complexes has been calculated using correlated MO (MCSCF and MP2) methods. The hydrogen-bond transmitted spin–spin coupling constants are also reported. The iso- and anisotropic 1H shielding constants are found to be the most general parameters of the hydrogen bond. The changes in 1J(XH) coupling in the proton donor also correlate with the XH⋯Y hydrogen bond strength. A similar correlation is found in the intermolecular 1hJ(HY) and 2hJ(XY) couplings. These couplings are substantial and dominated by the Fermi-contact term in contrast to the longer-range hydrogen-bond transmitted couplings where the noncontact terms prevail.

Solvent effects on NMR spectrum of acetylene calculated by ab initio methods

Abstract The NMR spectrum of acetylene in the gas phase and in the solution was calculated on the SCF and CASSCF level. The calculated NMR parameters were studied in relation to the active space dimension and the basis set. Solvent-induced changes of acetylene coupling constants were calculated by the reaction field method; for shielding constants the supermolecular method was also used. The shielding and coupling constants calculated for the isolated molecule showed a strong electron correlation dependence as contrasted with the changes caused by the presence of a dielectric medium. Comparison with the experimental values confirmed an exceptional magnitude of the 1 J CC solvent-induced changes in acetylene. The coupling constants changes calculated by the reaction field method are consistent with the experimental values; the shielding constants changes revealed a large discrepancy. On this basis we conclude that the shielding constants in solution are affected mainly by the short-range specific interactions while for the coupling constants the long-range electrostatic interactions also contribute significantly.