Alexander A. Granovsky

Gas Phase Absorption Studies of Photoactive Yellow Protein Chromophore Derivatives

Photoabsorption spectra of deprotonated trans p-coumaric acid and two of its methyl substituted derivatives have been studied in gas phase both experimentally and theoretically. We have focused on the spectroscopic effect of the location of the two possible deprotonation sites on the trans p-coumaric acid which originate to either a phenoxide or a carboxylate. Surprisingly, the three chromophores were found to have the same absorption maximum at 430 nm, in spite of having different deprotonation positions. However, the absorption of the chromophore in polar solution is substantially different for the distinct deprotonation locations. We also report on the time scales and pathways of relaxation after photoexcitation for the three photoactive yellow protein chromophore derivatives. As a result of these experiments, we could detect the phenoxide isomer within the deprotonated trans p-coumaric acid in gas phase; however, the occurrence of the carboxylate is uncertain. Several computational methods were used simultaneously to provide insights and assistance in the interpretation of our experimental results. The calculated excitation energies S(0)-S(1) are in good agreement with experiment for those systems having a negative charge on a phenoxide moiety. Although our augmented multiconfigurational quasidegenerate perturbation theory calculations agree with experiment in the description of the absorption spectrum of anions with a carboxylate functional group, there are some puzzling disagreements between experiment and some calculational methods in the description of these systems.

C20H4(C4F8)3: A Fluorine-Containing Annulated Corannulene that Is a Better Electron Acceptor Than C60†

At sixes and sevens: The reaction of corannulene with 35 equivalents of 1,4-C4F8I2 is an efficient and a relatively selective process that yields two main products in which six H atoms are substituted with three C4F8 moieties that form six- and seven-membered rings. Low-temperature photoelectron spectroscopy showed the electron affinity of the major isomer (shown) exceeds that of C60 (2.74±0.02 and 2.689±0.008 eV, respectively).

Hybrid diatomics-in-molecules-based quantum mechanical/molecular mechanical approach applied to the modeling of structures and spectra of mixed molecular clusters Arn(HCl)m and Arn(HF)m

A new hybrid QM/DIM approach aimed at describing equilibrium structures and spectroscopic properties of medium size mixed molecular clusters is developed. This methodology is applied to vibrational spectra of hydrogen chloride and hydrogen fluoride clusters with up to four monomer molecules embedded in argon shells Arn(H(Cl/F))m (n = 1-62, m = 1-4). The hydrogen halide complexes (QM part) are treated at the MP2/aug-cc-pVTZ level, while the interaction between HX molecules and Ar atoms (MM part) is described in terms of the semiempirical DIM methodology, based on the proper mixing between neutral and ionic states of the system [Grigorenko et al., J. Chem. Phys. 104, 5510 (1996)]. A detailed analysis of the resulting topology of the QM/DIM potential energy (hyper-)surface in the triatomic subsystem Ar-HX reveals more pronounced nonadditive atomic induction and dispersion contributions to the total interaction energy in the case of the Ar-HCl system. An extension of the original analytical DIM-based potential in the frame of the present model as well as the current limitations of the method are discussed. A modified algorithm for the gradient geometry optimization, along with partly analytical force constant matrix evaluation, is developed to treat large cages of argon atoms around molecular clusters. Calculated frequency redshifts of HX stretching vibrations in the mixed clusters relative to the isolated hydrogen-bonded complexes are in good agreement with experimental findings.

Modeling photoabsorption of the asFP595 chromophore.

The fluorescent protein asFP595 is a promising photoswitchable biomarker for studying processes in living cells. We present the results of a high level theoretical study of photoabsorption properties of the model asFP595 chromophore molecule in biologically relevant protonation states: anionic, zwitterionic, and neutral. Ground state equilibrium geometry parameters are optimized in the PBE0/(aug)-cc-pVDZ density functional theory approximation. An augmented version of multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) following the state-averaged CASSCF/(aug)-cc-pVDZ calculations is used to estimate the vertical S0-S1 excitation energies for all chromophore species. An accuracy of this approach is validated by comparing the computed estimates of the S0-S1 absorption maximum of the closely related chromophore from the DsRed protein to the known experimental value in the gas phase. An influence of the CASSCF active space on the aug-MCQDPT2 excitation energies is analyzed. The zwitterionic form of the asFP595 chromophore is found to be the most sensitive to a particular choice and amount of active orbitals. This observation is explained by the charge-transfer type of the S0-S1 transition involving the entire conjugated pi-electron system for the zwitterionic protonation state. According to the calculation results, the anionic form in the trans conformation is found to possess the most red-shifted absorption band with the maximum located at 543 nm. The bands of the zwitterionic and neutral forms are considerably blue-shifted compared to those of the anionic form. These conclusions are at variance with the results obtained in the TDDFT approximation for the asFP595 chromophore. The absorption wavelengths computed in the aug-MCQDPT2/CASSCF theory are as follows: 543 (535), 470 (476), and 415 (417) nm for the anionic, zwitterionic, and neutral forms of the trans and cis (in parentheses) isomers of the asFP595 chromophore. These data can be used as a reference for further theoretical studies of the asFP595 chromophore in different media and for modeling photoabsorption properties of the asFP595 fluorescent protein.

Classical vibrational predissociation dynamics: The effects of phase-space bifurcations

Extensive classical investigation of the vibrational predissociation dynamics of the model He⋯Br2 and Rg⋯I2 (Rg=He, Ne, and Ar) van der Waals complexes is performed. Classical trajectory calculations of the fragmentation rates are accomplished with the numerical analysis of the phase-space structure within the two-dimensional T-shaped model. Various bifurcations of the phase portrait with increasing excitation energy are found to produce a remarkable effect on the fragmentation dynamics causing irregular variations of the decay rate. This effect is proven to be quite persistent and pertinent to the more realistic three-dimensional dynamics as well. The implications of the results for studying quantum-classical correspondence for metastable states are indicated.

Communication: An efficient approach to compute state-specific nuclear gradients for a generic state-averaged multi-configuration self consistent field wavefunction

We present a new, very efficient semi-numerical approach for the computation of state-specific nuclear gradients of a generic state-averaged multi-configuration self consistent field wavefunction. Our approach eliminates the costly coupled-perturbed multi-configuration Hartree-Fock step as well as the associated integral transformation stage. The details of the implementation within the Firefly quantum chemistry package are discussed and several sample applications are given. The new approach is routinely applicable to geometry optimization of molecular systems with 1000+ basis functions using a standalone multi-core workstation.

Accurate modeling of the S0-S1 photo-absorption in biological chromophores

We address the problem of quantitative evaluation of the absorption S0-S1 peaks &lgr; max of biological chromophores in vacuo by using the state-of-art computational methods of quantum theory. In particularly, we rely on the second order multiconfigurational quasidegenerate perturbation theory (MCQDPT2) following the complete active space selfconsistent field (CASSCF) calculations. The use of augmented effective Hamiltonian operators in the MCQDPT2 framework allows us to correct deficiencies of the standard multistate approaches and to obtain stable saturated solutions for the target low-lying excited states. A high accuracy of the proposed methodology is illustrated for several photoactive protein chromophores in the gas phase including all-trans retinal, green fluorescent protein type chromophores and photoactive yellow protein chromophores. It is shown that our approach provides correct ordering of states and predicts maxima of absorption bands for the S0-S1 transitions within only a few nanometers from experimental data.

Application of the vibrational self-consistent field and correlation techniques to the SH/D(Ã)⋯Rg (Rg=Ar, Kr) van der Waals complexes

Abstract The vibrational energy levels for the SH/D(A)⋯Ar/Kr complexes are computed with the vibrational self-consistent field (VSCF), configuration interaction (CI-VSCF) and direct variational approaches and the results are compared to the previously reported discrete variable representation (DVR) data. The same empirical potential energy surfaces as for the DVR treatment are used. It is concluded that the deviations of the lowest VSCF excitation energies from the reference values do not exceed 2.5%, and the correlation-corrected approach CI-VSCF permits to reduce the errors at least twice at low expenses.

Vibrational spectra of C 60 polymers: experiment and first-principle assignment

The infrared and Raman spectra of orthorhombic and tetragonal polymers of C60 are thoroughly studied and interpreted on the base of DFT vibrational calculations of their finite fragments. Complete assignment of the spectra serves to establish the genetic relationships of the polymer vibrations to the parent fullerene modes and to follow the vibrations associated with some particular intramolecular motions.

CAP-XMCQDPT2 method for molecular electronic resonances

Metastable electronic states decaying via autoionization or autodetachment are common gateway states for chemical processes initiated by electron-molecule interactions or photo-excitation and are ubiquitous in highly energetic environments. We present a robust theoretical approach for calculating positions and widths of electronic resonances. The method is based on the extended multiconfigurational quasidegenerate perturbation theory combined with complex absorbing potential technique (CAP-XMCQDPT2). The theory is capable of describing the resonance position and width for shape and Feshbach resonances with high accuracy and low computational cost. Importantly, the resonance parameters are extracted at a cost of a single electronic structure calculation. Resonances positions and widths computed for shape and Feshbach molecular resonances are in a good agreement with the experimental data and with the previous theoretical estimates.