Biomedical subjects

Jochen Autschbach

Publications and source records attributed to Jochen Autschbach.

At least 19 recordsLinked to original sources

PubMed2007

Calculation of static and dynamic linear magnetic response in approximate time-dependent density functional theory.

We report implementations and results of time-dependent density functional calculations (i) of the frequency-dependent magnetic dipole-magnetic dipole polarizability, (ii) of the (observable) translationally invariant linear magnetic response, and (iii) of a linear intensity differential (LID) which includes the dynamic dipole magnetizability. The density functional calculations utilized density fitting. For achieving gauge-origin independence we have employed time-periodic magnetic-field-dependent basis functions as well as the dipole velocity gauge, and have included explicit density-fit related derivatives of the Coulomb potential. We present the results of calculations of static and dynamic magnetic dipole-magnetic dipole polarizabilities for a set of small molecules, the LID for the SF6 molecule, and dispersion curves for M-hexahelicene of the origin invariant linear magnetic response as well as of three dynamic polarizabilities: magnetic dipole-magnetic dipole, electric dipole-electric dipole, and electric dipole-magnetic dipole. We have also performed comparison of the linear magnetic response and magnetic dipole-magnetic dipole polarizability over a wide range of frequencies for H2O and SF6.

Journal Article↗

PubMed2006

Study of static and dynamic first hyperpolarizabilities using time-dependent density functional quadratic response theory with local contribution and natural bond orbital analysis.

We apply time-dependent density-functional quadratic response theory to investigate the static and dynamic second-order polarizabilities (first hyperpolarizability) beta. A new implementation using Slater-type basis functions, numerical integration, and density fitting techniques is reported. The second order coupled perturbed Kohn-Sham equations are solved and the second-order perturbed charge density is obtained. It is useful to highlight atomic and bond contributions to understand the relation between molecular structure and properties. Four moderately sized molecules (para-nitroaniline and derivatives thereof) are investigated to assess the accuracy of the time-dependent density-functional theory computations and to investigate the distribution of the second-order charge density as well as the "beta density." Our results highlight the contributions from atoms and bonds on different functional groups to the total value of beta with Mulliken-type and natural bond orbital (NBO) analyses, and demonstrate in some cases how contributions from a particular bond may be identified easily by visual inspection of the beta density. In addition, the position of side group substitution on carbon-carbon bonds significantly affects the hyperpolarizability. A contribution analysis as performed here might be helpful for the design of new materials with desired properties.

Journal Article↗

PubMed2006

Time dependent density functional theory modeling of specific rotation and optical rotatory dispersion of the aromatic amino acids in solution.

Time Dependent Density Functional Theory (TDDFT) along with the COnductor-like Screening MOdel (COSMO) has been applied to model the specific rotation at 589.3 nm and the optical rotatory dispersion (ORD) of the aromatic amino acids phenylalanine, tyrosine, histidine, and tryptophan. Solution structures at low, neutral, and high pH were determined. Both the anomalous dispersion absorbing (resonance) region and the lower energy (transparent) region of the ORD of the compounds were modeled. Linear response calculation of the specific rotation and ORD as well as Kramers-Kronig transformations of calculated circular dichroism spectra to model resonant ORD were compared with experimental data from the literature.

Amino Acids, Aromatic↗

PubMed2006

Calculation of circular dichroism spectra from optical rotatory dispersion, and vice versa, as complementary tools for theoretical studies of optical activity using time-dependent density functional theory.

A comparison of two theoretical methods based on time-dependent density functional theory for the calculation of the linear dispersive and absorptive properties of chiral molecules has been made. For this purpose, a recently proposed computational method for the calculation of circular dichroism (CD) spectra from the imaginary part of the optical rotation parameter has been applied to six rigid organic molecules. The results have been compared to the CD spectra obtained from the rotatory strengths and from the Kramers-Kronig transformation of optical rotatory dispersion (ORD) curves. We have also investigated a criterion based on the Kramers-Kronig integration formula to determine a number of excitations in truncated CD spectra which may yield a reasonable low frequency resonant ORD. It has been tested by calculating the ORD from the sum-over-states formula both in the nonresonant and resonant regions. Finally, we have applied these methods to model the resonant optical activity of proline at low pH.

Circular Dichroism↗

PubMed2006

Computational modeling of polyoxotungstates by relativistic DFT calculations of (183)W NMR chemical shifts.

The (183)W nuclear shielding in a variety of tungsten polyoxometalates (POM) (Lindqvist, Anderson, decatungstates, Keggin) of different shapes and charges has been modeled by DFT calculations that take into account relativistic effects, by means of the zero-order regular approximation (ZORA), and solvent effects, by the conductor-like screening model (COSMO) continuum method. The charge/surface area ratio (q/A) is proposed as an indicator of the charge density to which the solvation energies of all POMs are correlated in a satisfactory way. Among the various theoretical levels tested (ZORA scalar or spin-orbit, frozen-core or all-electron basis set, geometry optimization in the gas phase or in the continuum solvent, etc.), the best results are obtained when both geometry optimization in solvent and spin-orbit shielding are included (mean absolute error of delta=35 ppm). The quality of the computed chemical shifts depends systematically on the charge density as expressed by q/A; thus, POMs with low q/A ratios display the best agreement with experimental data. The performance of the method is such that computed values can aid the assignment of the (183)W NMR spectra of polyoxotungstates, as shown by the case of alpha-[PW(11)TiO(40)](5-), whose six signals are ranked computationally so as to almost reproduce the experimental ordering even though the signals are spaced by as little as 5 ppm.

Journal Article↗

PubMed2006

Density functional study of the 13C NMR chemical shifts in small-to-medium-diameter infinite single-walled carbon nanotubes.

NMR chemical shifts were calculated for semiconducting (n,0) single-walled carbon nanotubes (SWNTs) with n ranging from 7 to 17. Infinite isolated SWNTs were calculated using a gauge-including projector-augmented plane-wave (GIPAW) approach with periodic boundary conditions and density functional theory (DFT). In order to minimize intertube interactions in the GIPAW computations, an intertube distance of 8 A was chosen. For the infinite tubes, we found a chemical shift range of over 20 ppm for the systems considered here. The SWNT family with lambda = mod(n, 3) = 0 has much smaller chemical shifts compared to the other two families with lambda = 1 and lambda = 2. For all three families, the chemical shifts decrease roughly inversely proportional to the tube's diameter. The results were compared to calculations of finite capped SWNT fragments using a gauge-including atomic orbital (GIAO) basis. Direct comparison of the two types of calculations could be made if benzene was used as the internal (computational) reference. The NMR chemical shifts of finite SWNTs were found to converge very slowly, if at all, to the infinite limit, indicating that capping has a strong effect (at least for the (9,0) tubes) on the calculated properties. Our results suggest that (13)C NMR has the potential for becoming a useful tool in characterizing SWNT samples.

Carbon Isotopes↗

PubMed2006

Temperature dependence of the optical rotation of fenchone calculated by vibrational averaging.

On the basis of vibrational averaging, the temperature dependence of the optical rotation for fenchone has been calculated using TDDFT with the B3LYP hybrid functional at three wavelengths. The results show that very good agreement is obtained between theory and experiment. It is concluded that temperature-dependent vibrational effects are likely to account for much of the observed temperature dependence in optical rotation exhibited by rigid organic molecules in case there is only a weak temperature-dependent interaction with the solvent.

Journal Article↗

PubMed2006

Zero-point corrections and temperature dependence of HD spin-spin coupling constants of heavy metal hydride and dihydrogen complexes calculated by vibrational averaging.

Vibrational corrections (zero-point and temperature dependent) of the H-D spin-spin coupling constant J(HD) for six transition metal hydride and dihydrogen complexes have been computed from a vibrational average of J(HD) as a function of temperature. Effective (vibrationally averaged) H-D distances have also been determined. The very strong temperature dependence of J(HD) for one of the complexes, [Ir(dmpm)Cp*H2]2 + (dmpm = bis(dimethylphosphino)methane) can be modeled simply by the Boltzmann average of the zero-point vibrationally averaged JHD of two isomers. For this complex and four others, the vibrational corrections to JHD are shown to be highly significant and lead to improved agreement between theory and experiment in most cases. The zero-point vibrational correction is important for all complexes. Depending on the shape of the potential energy and J-coupling surfaces, for some of the complexes higher vibrationally excited states can also contribute to the vibrational corrections at temperatures above 0 K and lead to a temperature dependence. We identify different classes of complexes where a significant temperature dependence of J(HD) may or may not occur for different reasons. A method is outlined by which the temperature dependence of the HD spin-spin coupling constant can be determined with standard quantum chemistry software. Comparisons are made with experimental data and previously calculated values where applicable. We also discuss an example where a low-order expansion around the minimum of a complicated potential energy surface appears not to be sufficient for reproducing the experimentally observed temperature dependence.

Journal Article↗

PubMed2006

Calculation of origin-independent optical rotation tensor components in approximate time-dependent density functional theory.

We outline an implementation of the origin-independent optical rotation tensor, which includes electric dipole-magnetic dipole and electric dipole-electric quadrupole polarizability. The method is based on approximate time-dependent density functional theory. We utilize time-periodic magnetic-field-dependent basis functions as well as a modified velocity-gauge formulation of dynamic polarizability tensors in order to obtain a gauge-origin independence. To ensure gauge-origin independence of the results within a given numerical accuracy, density fit coefficient derivatives are employed. A damping constant has been introduced into the linear response equations to treat both resonance and nonresonance regions of optical activity. We present calculations for trans-2,3-dimethyloxirane and derivatives thereof as well as calculations for androst-4,17-dien-3-one. In the Appendix, we derive the equivalence between the common-gauge origin and gauge-including atomic orbitals formulations for the optical rotation tensor in time-dependent DFT.

Journal Article↗

PubMed2006

Spectral and structural characterization of amidate-bridged platinum-thallium complexes with strong metal-metal bonds.

The reactions of [Pt(NH3)2(NHCOtBu)2] and TlX3 (X = NO3-, Cl-, CF3CO2-) yielded dinuclear [{Pt(ONO2)(NH3)2(NHCOtBu)}Tl(ONO2)2(MeOH)] (2) and trinuclear complexes [{PtX(RNH2)2(NHCOtBu)2}2Tl]+ [X = NO3- (3), Cl- (5), CF3CO2- (6)], which were spectroscopically and structurally characterized. Strong Pt-Tl interaction in the complexes in solutions was indicated by both 195Pt and 205Tl NMR spectra, which exhibit very large one-bond spin-spin coupling constants between the heteronuclei (1J(PtTl)), 146.8 and 88.84 kHz for 2 and 3, respectively. Both the X-ray photoelectron spectra and the 195Pt chemical shifts reveal that the complexes have Pt centers whose oxidation states are close to that of Pt(III). Characterization of these complexes by X-ray diffraction analysis confirms that the Pt and Tl atoms are held together by very short Pt-Tl bonds and are supported by the bridging amidate ligands. The Pt-Tl bonds are shorter than 2.6 Angstrom, indicating a strong metal-metal attraction between these two metals. Compound 2 was found to activate the C-H bond of acetone to yield a platinum(IV) acetonate complex. This reactivity corresponds to the property of Pt(III) complexes. Density functional theory calculations were able to reproduce the large magnitude of the metal-metal spin-spin coupling constants. The couplings are sensitive to the computational model because of a delicate balance of metal 6s contributions in the frontier orbitals. The computational analysis reveals the role of the axial ligands in the magnitude of the coupling constants.

Journal Article↗

PubMed2006

Toward an accurate determination of 195Pt chemical shifts by density functional computations: the importance of unspecific solvent effects and the dependence of Pt magnetic shielding constants on structural parameters.

Density functional theory using the zero-order regular approximate two-component relativistic Hamiltonian has been applied to calculate the 195Pt chemical shifts for the complexes [PtCl6]2-, [PtCl4]2-, and [Pt2(NH3)2Cl2((CH3)3CCONH)2(CH2COCH3)]Cl. It is demonstrated that, in contrast to recent findings by other authors, platinum chemical shift calculations require not only a basis set beyond polarized triple-zeta quality for the metal atom but also, in principle, the consideration of explicit solvent molecules in addition to a continuum model for the first two complexes. We find that the inclusion of direct solvent-solute interactions at the quantum mechanical level is important for obtaining reasonable results despite that fact that these solvent effects are rather nonspecific. The importance of solvent effects has also implications on how experimental data should be interpreted. Further, in contrast to several previous studies of heavy-metal NMR parameters, functionals beyond the local density approximation were required both in the geometry optimization and the NMR calculations to obtain reasonable agreement between the computed and experimental NMR data. This comes with the disadvantage, however, of increased Pt-ligand bond distances leading to less good agreement with experiment for structural data. A detailed analysis of the results for the two chloroplatinate complexes is presented. The same computational procedure has then been applied to the dinuclear Pt(III) complex. Chemical shifts have been calculated with respect to both [PtCl6]2- and [PtCl4]2- chosen as the NMR reference, yielding good agreement with experiment. The determination of preferred solvent locations around the complexes studied turned out to be important for reproducing experimental data.

Journal Article↗

PubMed2006

Time dependent density functional theory modeling of chiroptical properties of small amino acids in solution.

Time dependent density functional theory (TDDFT) and the conductor-like screening model (COSMO) of solvation were used to model the specific rotation and optical rotatory dispersion (ORD) of alanine, proline and serine solutions. Zwitterionic, cationic and anionic forms of amino acids were investigated and the results compared with experimental literature data obtained in neutral, acidic and basic conditions, respectively. It was found that TDDFT consistently underestimated the electronic excitation energies of the molecules, leading to calculated optical rotations that are of the correct sign but somewhat larger in magnitude than those of experiment. An additional challenge was encountered in the modeling of serine, an amino acid with a strong tendency to form intramolecular hydrogen bonds. The model used overestimated the extent of such hydrogen bonding for the zwitterions while possibly underestimating such bonding for the cationic form. This effect on the calculated mole fractions of the different conformers had an impact on the specific rotation.

Alanine↗

PubMed2006

Time-dependent density functional calculations of optical rotatory dispersion including resonance wavelengths as a potentially useful tool for determining absolute configurations of chiral molecules.

The optical rotations for six organic molecules (verbenone, fenchone, camphor, nopinone, Tröger's base, dimethyl-cyclopropane) and the transition metal complex [Co(en)(3)](3+) were calculated as a function of wavelength using time-dependent density functional theory (TDDFT). In the calculations, a realistic behavior of the optical rotation in the vicinity of an electronic transition was obtained by using a phenomenological damping parameter of the order of 0.2 eV (0.007 au). In comparison with experiment, for the molecules studied here the sign and order of magnitude of the optical rotation as well as the excitation energies were reasonably well reproduced in most computations. These findings apply to the investigated wavelength ranges typically between about 200 and 650 nm even when using comparatively small basis sets. Such calculations might therefore routinely be applied to help assigning the absolute configurations of chiral molecules. Supplementary calculations of the circular dichroism (CD) and comparison with experimental CD were used for further assessment of the optical rotation calculations. In particular, a combined study of optical rotation and CD turned out to be useful in cases where the optical rotatory dispersion in a specific energy range exhibits a considerable blue or red shift or where it is difficult to reproduce because of an interplay of several competing Cotton effects. The influence of basis set, density functional, and the damping parameter was also investigated.

Journal Article↗

PubMed2006

Density functional computations of 99Ru chemical shifts: relativistic effects, influence of the density functional, and study of solvent effects on fac-[Ru(CO)3I3]-.

Solvent effects on the 99Ru NMR chemical shift of the complex fac-[Ru(CO)3I3]- are investigated computationally using density functional theory. Further, benchmark calculations of the 99Ru shift for a set of ten Ru complexes have been performed in order to calibrate the computational model and to determine the importance of relativistic effects on the 99Ru nuclear magnetic shielding and on the chemical shift. A computational model for fac-[Ru(CO)3I3]- that includes both explicit solvent molecules and a continuum model is shown to yield the best agreement with experiment. Relativistic corrections are shown to be of minor importance for determining 99Ru chemical shifts. On the other hand, the nature of the density functional is of importance. In agreement with literature data for ligand trends of 99Ru chemical shifts, the chemical shift range for different solvents is also best reproduced by a hybrid functional.

Journal Article↗

PubMed2005

Magnitude of zero-point vibrational corrections to optical rotation in rigid organic molecules: a time-dependent density functional study.

The zero-point vibrational corrections (ZPVCs) to the optical rotation of 22 rigid organic molecules have been calculated using time-dependent density functional theory with the B3LYP hybrid functional. We outline an implementation for calculating ZPVCs that can be applied with a variety of quantum chemistry programs and methods. It is shown that the ZPVCs to optical rotation have a wide range of values and can be quite significant depending on the molecule. On average, it has been determined that vibrational corrections can account for about 20% of the optical rotation for the equilibrium value. It is also concluded that vibrational effects alone cannot be the only factor in improving the calculated values of optical rotation with respect to experimental data measured in solution.

Journal Article↗

PubMed2005

Calculation of optical rotation with time-periodic magnetic-field-dependent basis functions in approximate time-dependent density-functional theory.

We report the implementation of a method for the calculation of optical rotation. This method is based on the time-dependent density-functional theory and utilizes time-periodic magnetic-field-dependent basis functions. The calculations are based on a density fit. It is demonstrated that additional terms in the analytical expression appearing from derivatives of the approximated Coulomb potential are necessary to provide the gauge-origin independence of the results within a given numerical accuracy. Contributions from these terms also restore the symmetry between the electric and magnetic perturbations in the optical rotation tensor.

Algorithms↗

PubMed2005

Importance of vibronic effects on the circular dichroism spectrum of dimethyloxirane.

We present a theoretical study on the vibrational structure of a circular dichroism (CD) spectrum using time-dependent density-functional theory in combination with a Franck-Condon-type approach. This method is applied to analyze the complex CD spectrum of dimethyloxirane, which involves delicate cancellations of positive and negative CD bands. Our approach reveals that these cancellations are strongly affected by the shapes of the CD bands, and that it is vital for an accurate simulation of the spectrum to take the different envelopes of these bands into account. One crucial point in some former theoretical studies on this compound, which were restricted to vertical excitations, was the appearance of a strong negative CD band in the energy range of 7.0-7.5 eV, which is not present in the experimental spectrum. We can explain the disappearance of this 2B band by a strong vibrational progression along normal modes with C-O stretching character, so that the band extends over an energy range of almost 1.1 eV. Thus, it overlaps with many other (mostly positive) CD bands, leading to a cancellation of its intensity. The dominant vibrational features in the experimental spectrum can be assigned to the 1B, 3B, and 5B bands, which show several clear vibrational peaks and a total bandwidth of only 0.3-0.5 eV. In order to obtain close agreement between the simulated and the experimental spectrum we have to apply small shifts to the vertical excitation energies that enter the calculation. These shifts account both for possible errors in the time-dependent density-functional theory calculations and for the neglect of differential zero-point energy between ground and excited states in our gradient-based vertical Franck-Condon approach.

Journal Article↗

PubMed2005

Density functional calculation of the electronic circular dichroism spectra of the transition metal complexes [M(phen)3]2+ (M = Fe, Ru, Os).

The circular dichroism spectra of the tris-bidentate metal complexes Lambda-[M(phen)3]2+, with M = Fe, Ru, Os and phen = 1,10-tris-phenanthroline, are investigated computationally, employing time-dependent density functional theory. Good agreement with experimental spectra is obtained for Ru and Os. The Lambda-[Os(phen)3]2+ spectrum is analyzed in detail. It is shown how relativistic effects red shift CD bands where the Os 5d-orbital participates to a large extent in the excitations. Further, the participation of the metal in the ligand pi --> pi exciton CD is determined to be of the order of 10%. Though solvent effects can have a noticeable effect on individual transitions and rotatory strengths, they are demonstrated to have only a very small overall effect on the resulting simulated CD spectra. For Lambda-[Fe(phen)3]2+, the results are shown to be rather sensitive to the choice of the applied hybrid and nonhybrid density functionals, and the optimized geometries based thereupon. In particular, the sign pattern of the lower-energy part (up to 33 x 10(3) cm(-1)) of the Lambda-[Fe(phen)3]2+ CD spectrum is difficult to reproduce. Some combinations of functionals and geometries yield good agreement with experiment, but no "best" approach can be devised based on the available results. Possible sources of errors in the spectrum of Lambda-[Fe(phen)3]2+ due to deficiencies in the functionals and the exchange-correlation kernels are investigated.

Circular Dichroism↗