Biomedical subjects

Christel M Marian

Publications and source records attributed to Christel M Marian.

9 recordsLinked to original sources

PubMed2006

Electronically excited states of tryptamine and its microhydrated complex.

The lowest electronically excited singlet states of tryptamine and the tryptamine (H2O)1 cluster have been studied, using time dependent density functional theory for determination of the geometries and multireference configuration interaction for the vertical and adiabatic excitation energies, the permanent dipole moments, and the transition dipole moment orientations. All molecular properties of the seven experimentally observed conformers of tryptamine could be reproduced with high accuracy. A strong solvent reorientation has been found upon electronic excitation of the 1:1 water cluster of tryptamine to the L(a) and L(b) states. The adiabatically lowest excited singlet state in case of the tryptamine monomer is the L(b) state, while for the 1:1 water complex, the L(a) is calculated below the L(b) state.

Computer Simulation↗

PubMed2006

SPOCK.CI: a multireference spin-orbit configuration interaction method for large molecules.

We present SPOCK.CI, a selecting direct multireference spin-orbit configuration interaction (MRSOCI) program based on configuration state functions. It constitutes an extension of the spin-free density functional theory/multireference configuration interaction (DFT/MRCI) code by Grimme and Waletzke [J. Chem. Phys. 111, 5645 (1999)] and includes spin-orbit interaction on the same footing with electron correlation. Key features of SPOCK.CI are a fast determination of coupling coefficients between configuration state functions, the use of a nonempirical effective one-electron spin-orbit atomic mean-field Hamiltonian, the application of a resolution-of-the-identity approximation to computationally expensive spin-free four-index integrals, and the use of an efficient multiroot Davidson diagonalization scheme for the complex Hamiltonian matrix. SPOCK.CI can be run either in ab initio mode or as semiempirical procedure combined with density functional theory (DFT/MRSOCI). The application of these techniques and approximations makes it possible to compute spin-dependent properties of large molecules in ground and electronically excited states efficiently and with high confidence. Second-order properties such as phosphorescence rates are known to converge very slowly when evaluated perturbationally by sum-over-state approaches. We have investigated the performance of SPOCK.CI on these properties in three case studies on 4H-pyran-4-thione, dithiosuccinimide, and free-base porphin. In particular, we have studied the dependence of the computed phosphorescence lifetimes on various technical parameters of the MRSOCI wave function such as the size of the configuration space, selection of single excitations, diagonalization thresholds, etc. The results are compared to the outcome of extensive quasidegenerate perturbation theory (QDPT) calculations as well as experiment. In all three cases, the MRSOCI approach is found to be superior to the QDPT expansion and yields results in very good agreement with experimental findings. For molecules up to the size of free-base porphin, MRSOCI calculations can easily be run on a single-processor personal computer. Total CPU times for the evaluation of the electronic excitation spectrum and the phosphorescence lifetime of this molecule are below 40 h.

Journal Article↗

PubMed2006

Vibronic absorption, fluorescence, and phosphorescence spectra of psoralen: a quantum chemical investigation.

Excited state potential energy hypersurfaces of 7H-furo[3,2-g][1]benzopyran-7-one (psoralen) have been explored employing (time-dependent) Kohn-Sham density functional theory. At selected points, we have determined electronic excitation energies and electric dipole (transition) moments utilizing a combined density functional/multireference configuration interaction method. Spin-orbit coupling has been taken into account employing an efficient, non-empirical spin-orbit mean-field Hamiltonian. Franck-Condon factors have been computed for vibrational modes with large displacements in the respective Dushinsky transformations. The simulated band spectra closely resemble experimental band shapes and thus validate the theoretically determined nuclear structures at the S(0), S(1), and T(1) minima. In the S(1) (pi(HOMO)-->pi*(LUMO)) state, the lactone bond of the pyrone ring is significantly elongated. From excited vibrational levels of the S(1) state a conical intersection between a (pi-->sigma*) excited state and the electronic ground state may be energetically accessible. Fast non-radiative decay via this relaxation pathway could explain the low fluorescence quantum yield of psoralen. The T(1) (pi(HOMO-1)-->pi*(LUMO)) exhibits a diradicaloid electronic structure with a broken C(5)-C(6) double bond in the pyrone ring. A variational multireference spin-orbit configuration interaction procedure yields a phosphorescence lifetime of 3 s, in excellent agreement with experimental estimates.

Absorption↗

PubMed2006

The 15N chemical shifts in mixed NB2Si and NBSi2 environments of Si3B3N7--a theoretical investigation.

Nuclear magnetic resonance (NMR) chemical shifts in solids may be calculated by ab initio methods approximating the solid state by molecular clusters. We employed this technique to obtain estimates of (15)N chemical shifts in NB(2)Si and NBSi(2) environments in the solid state. Such nitrogen environments are found in amorphous (Si/B/N-)ceramics which exhibit very interesting features such as high thermal and mechanical stability. We based our calculations on cutouts of hypothetical Si(3)B(3)N(7) crystals suggested by Kroll and Hoffmann [Silicon boron nitrides: hypothetical polymorphs of Si(3)B(3)N(7), Angew. Chem. Int. Ed. 37 (1998) 2527]. Taking the systematic errors of our calculations into account we expect the chemical shifts in NBSi(2) environments around -293+/-5ppm. Chemical shifts in NB(2)Si environments are expected at -272+/-6ppm. The range of the calculated chemical shifts in NBSi(2) environments coincides with experimental chemical shifts in molecular compounds. Experimental chemical shifts of NB(2)Si nitrogen in molecules appear at lower field than our calculated chemical shifts in the solid state.

Journal Article↗

PubMed2005

Quantum chemical investigation of the electronic spectra of the keto, enol, and keto-imine tautomers of cytosine.

The low-lying excited singlet states of the keto, enol, and keto-imine tautomers of cytosine have been investigated employing a combined density functional/multireference configuration interaction (DFT/MRCI) method. Unconstrained geometry optimizations have yielded out-of-plain distorted structures of the pi --> pi and n --> pi excited states of all cytosine forms. For the keto tautomer, the DFT/MRCI adiabatic excitation energy of the pi --> pi state (4.06 eV including zero-point vibrational energy corrections) supports the resonant two-photon ionization (R2PI) spectrum (Nir et al. Phys. Chem. Chem. Phys. 2002, 5, 4780). On its S1 potential energy surface, a conical intersection between the 1pipi state and the electronic ground state has been identified. The barrier height of the reaction along a constrained minimum energy path amounts to merely 0.2 eV above the origin and explains the break-off of the R2PI spectrum. The 1pipi minimum of the enol tautomer is found at considerably higher excitation energies (4.50 eV). Because of significant geometry shifts with respect to the ground state, long vibrational progressions are expected, in accord with experimental observations. For the keto-imine tautomer, a crossing of the 1pipi potential energy surface with the ground-state surface has been found, too. Its n --> pi minimum (3.27 eV) is located well below the conical intersection between the pi --> pi and S0 states, but it will be difficult to observe because of its small transition moment. The identified conical intersections of the pi --> pi excited states of the keto cytosine tautomers are made responsible for the ultrafast decay to the electronic ground states and thus may explain their subpicoseconds lifetimes.

Cytosine↗

PubMed2005

Tautomers and electronic states of jet-cooled 2-aminopurine investigated by double resonance spectroscopy and theory.

We present resonant two-photon ionization (R2PI), IR-UV, and UV-UV double resonance spectra of jet-cooled 2-aminopurine (2AP) as well as Fourier transform infrared (FTIR) gas phase spectra. 2AP is a fluorescing isomer of the nucleobase adenine. The results show that there is only one tautomer of 2AP which absorbs in the wavelength range 32,300-34,500 cm(-1). The comparison with the calculated IR spectra of 9H- and 7H-2AP points to 9H-2AP as the dominating tautomer in the gas phase but the spectra are too similar to allow an unambiguous assignment to the respective tautomer. Hence, we determined vertical and adiabatic excitation energies of both tautomers employing combined density functional theory and multi-reference configuration interaction techniques. For the 0-0 band of the first 1pipi* transition of 9H-2AP we obtain a theoretical value of 32,328 cm(-1), in excellent agreement with the band origin of our R2PI spectrum at 32,371 cm(-1). The first singlet pipi* transition of the less stable 7H-2AP tautomer is predicted to be red-shifted by about 1700 cm(-1) with respect to the corresponding transition in 9H-2AP. From the absence of experimental bands in the energy region between 30,300 and 32,350 cm(-1) we conclude that 7H-2AP is not present to an appreciable extent in the molecular beam. Our calculations yield nearly equal energies for the 1npi* and 1pipi* minima of isolated 2AP, similar to the situation in adenine. The hitherto existing argument that the energetic order of states is responsible for the different spectroscopic properties of these isomers therefore does not hold. Rather, vibronic levels close to the origin of the 1pipi* transition cannot access the conical intersection between the 1pipi* and S(0) states along a puckering coordinate of the six-membered ring, in contrast to the situation in electronically excited 9H-adenine. As a consequence, a rich vibrational structure can be observed in the R2PI spectrum of 2AP whereas the spectrum of 9H-adenine breaks off at low energies.

2-Aminopurine↗

PubMed2005

A new pathway for the rapid decay of electronically excited adenine.

Combined density functional and multireference configuration interaction methods have been used to calculate the electronic spectrum of 9H-adenine, the most stable tautomer of 6-aminopurine. In addition, constrained minimum energy paths on excited potential energy hypersurfaces have been determined along several relaxation coordinates. The minimum of the first (1)[n-->pi*] state has been located at an energy of 4.54 eV for a nuclear arrangement in which the amino group is pyramidal whereas the ring system remains planar. Close by, another minimum on the S(1) potential energy hypersurface has been detected in which the C(2) center is deflected out of the molecular plane and the electronic character of S(1) corresponds to a nearly equal mixture of (1)[pi-->pi*] and (1)[n-->pi*] configurations. The adiabatic excitation energy of this minimum amounts to 4.47 eV. Vertical and adiabatic excitation energies of the lowest n-->pi* and pi-->pi* transitions as well as transition moments and their directions are in very good agreement with experimental data and lend confidence to the present quantum chemical treatment. On the S(1) potential energy hypersurface, an energetically favorable path from the singlet n-->pi* minimum toward a conical intersection with the electronic ground state has been identified. Close to the conical intersection, the six-membered ring of adenine is strongly puckered and the electronic structure of the S(1) state corresponds to a pi-->pi* excitation. The energetic accessibility of this relaxation path at about 0.1 eV above the singlet n-->pi* minimum is presumably responsible for the ultrafast decay of 9H-adenine after photoexcitation and explains why sharp vibronic peaks can only be observed in a rather narrow wavelength range above the origin. The detected mechanism should be equally applicable to adenosine and 9-methyladenine because it involves primarily geometry changes in the six-membered ring whereas the nuclear arrangement of the five-membered ring (including the N(9) center) is largely preserved.

Journal Article↗

PubMed2002

Spin-orbit coupling of DFT/MRCI wavefunctions: method, test calculations, and application to thiophene.

During the past decade the one-center mean-field approximation has proven to be a very appropriate framework for the accurate description of spin-orbit effects at the correlated all-electron level. Here, a new efficient code, SPOCK, is introduced that calculates spin-orbit matrix elements in the one-center mean-field approximation for multireference CI wave functions. For the first time, the computation of spin-dependent interactions within a Kohn-Sham orbital based CI (DFT/MRCI) scheme1 is made possible. The latter approach is suitable for large scale systems with up to 100-200 valence electrons. Test calculations are performed on well-known diatomic molecules and the thiocarbonyl pyranthione. Spin-orbit matrix elements show good agreement with their Hartree-Fock orbital based counterparts but are obtained at considerably lower expense, thus demonstrating the power of the method. As an application singlet-triplet couplings in thiophene are investigated that are important for the photophysics and photochemistry. Spin-orbit matrix elements between all pi --> pi* excited states are found to be small. Considerably larger spin-orbit matrix elements are observed only for cases in which pi --> sigma* excited configurations are involved.

Journal Article↗

PubMedDate not supplied

Fully automated flexible docking of ligands into flexible synthetic receptors using forward and inverse docking strategies.

The prediction of the structure of host-guest complexes is one of the most challenging problems in supramolecular chemistry. Usual procedures for docking of ligands into receptors do not take full conformational freedom of the host molecule into account. We describe and apply a new docking approach which performs a conformational sampling of the host and then sequentially docks the ligand into all receptor conformers using the incremental construction technique of the FlexX software platform. The applicability of this approach is validated on a set of host-guest complexes with known crystal structure. Moreover, we demonstrate that due to the interchangeability of the roles of host and guest, the docking process can be inverted. In this inverse docking mode, the receptor molecule is docked around its ligand. For all investigated test cases, the predicted structures are in good agreement with the experiment for both normal (forward) and inverse docking. Since the ligand is often smaller than the receptor and, thus, its conformational space is more restricted, the inverse docking approach leads in most cases to considerable speed-up. By having the choice between two alternative docking directions, the application range of the method is significantly extended. Finally, an important result of this study is the suitability of the simple energy function used here for structure prediction of complexes in organic media.

Algorithms↗