Solvent effects on the n→π[sup ∗] electronic transition in formaldehyde: A combined coupled cluster/molecular dynamics study

Redfield Propagation of Photoinduced Electron Transfer Reactions in Vacuum and Solution

Dynamical simulations of ultrafast electron transfer reactions are of utmost interest. To allow for energy dissipation directly into an external surrounding environment, a solvent coupling model has been deduced, implemented, and utilized to describe the photoinduced electron transfer dynamics within a model triad system herein. The model is based on Redfield theory, and the environment is represented by harmonic oscillators filled with bosonic quanta. To imitate real solvents, the oscillators have been equipped with frequencies and polarization lifetimes characteristic of the corresponding solvent. The population was found to transfer through the energetically lowest electron transfer route regardless of the medium. The condensed population transfer dynamics were observed to be highly dependent on the solvent parameters. In particular, an increase in the solvent coupling entailed a detainment in the population transfer from the initially prepared diabatic state and a promotion in the population transfer through the other electron transfer route. Two explanations based on the diagonal and off-diagonal matrix elements of the Kohn-Sham Fock matrix, respectively, have been provided. The lifetime of the populated partially charge-separated state was prolonged with increasing solvent polarity, and it was explained in terms of attractive interactions between the solvent's dipole moments and the fragments' charges. The high-frequency vibrational fine-structure in the correlation function was demonstrated to be important for the transfer dynamics, and the importance of dephasing effects in polar solvents was verified and precised to concern the optical polarization of the solvents.

Investigation of the Structural and Thermochemical Properties of [2.2.2]-Bicyclooctadiene Photoswitches

Molecular photoswitches can under certain conditions be used to store solar energy in the so-called molecular solar thermal storage systems, which is an interesting technology for renewable energy solutions. The current investigations focus on the performance of seven different density functional theory (DFT) methods (B3LYP, CAM-B3LYP, PBE0, M06-2X, ωB97X-D, B2PLYP, and PBE0DH) when predicting geometries and thermochemical properties of the [2.2.2]-bicyclooctadiene (BOD) photoswitch. We find that all of the investigated DFT methods provide geometries that are in good agreement with those obtained using coupled cluster singles and doubles (CCSD) calculations. The dependence on the employed basis set is not large when predicting geometries. With respect to the thermochemical properties, we find that the M06-2X, CAM-B3LYP, PBE0, and ωB97X-D functionals all predict thermochemical properties that are in good agreement with the results of the CCSD, the CCSD including perturbative triples (CCSD(T)), and the explicitly correlated CCSD-F12 and CCSD(T)-F12 models. Lastly, for energy calculations, we tested the newly developed fourth-order cluster perturbation theory singles and doubles CPS(D-4) model, which in this study provides energy differences that are of CCSD and sometimes also CCSD(T) quality at a relatively low cost. We find that the CPS(D-4) model is an excellent choice for further investigation of BOD derivatives because accurate energies can be obtained routinely using this methodology. From the results, we also note that the predicted storage energies and storage energy densities for the BOD photoswitch are very large compared to other molecular solar thermal storage systems and that these systems could be candidates for such applications.

Synthesis and photophysical properties of deuteration of pirfenidone

In order to improve the metabolism of pirfenidone (5-methyl-1-phenylpyridin-2-one, PFD), the methyl-deuterated version of pirfenidone via the substitution of hydrogen (H) at C-5 by its isotope deuterium (D, 5D-PFD) was synthesized and its photophysical properties were investigated. The negative solvatochrom was observed in absorption and fluorescence spectra with increasing solvent polarity, which implied that intermolecular charge transfer (ICT) involved n → π* transition for both of PFD and 5D-PFD. The ground state and excited state dipole moment was calculated as 5.30 D and 3.30 D for PFD, and 3.70 D and 2.18 D for 5D-PFD, respectively, which suggested the more polar nature of PFD in the ground state than that of excited state compared with 5D-PFD. Density functional theory (DFT) results demonstrated a significant propensity of ICT from the electron-donor, methyl and carbonyl group to the amine group as an electron donor. The binding of metal ions with PFD or 5D-PFD induced a red-shift of π → π* transition and blue-shift of n → π* transition, respectively, indicating that the pyridone ring showed more stability upon binding of unoccupied orbital of metal ions with lone-pair electron of oxygen atom and thus prompted the electronic distribution on phenyl unit. Upon addition of metal ions, the aromatic region presented the characteristic upfield shifts, and the resonance contributed by 3-H showed a significant downfield chemical shift/deshielding effect, indicating the deduced resonance of 3-H and the improved electron distribution of phenyl unit. The binding and docking of human serum albumin showed that the affinity of 5D-PFD with HSA was lower than that of PFD, and also 5D-PFD might prefer to present free forms in the blood with better efficacy comparing with PFD. The pharmacokinetic of half-time (T_1/2) for oral and i.v. administration of 5D-PFD was found around 19 and 30 min, higher than that of i.v. administration of PFD, 8.6 min, reported by Giri et al. The results of this work suggest that the deuteration enhances the metabolism of PFD significantly with little change of physical-chemical property.

Synthesis of (d)-erythrose from glycolaldehyde aqueous solutions under electric field

A Miller-like numerical experiment demonstrates that ubiquitarious molecules such as water and glycolaldehyde can synthesize (d)-erythrose, one of the direct precursors of ribose.

Mechanistic insights into photoinduced damage of DNA and RNA nucleobases in the gas phase and in bulk solution

The mechanistic details of well-known photohydrate lesions are explored using state-of-the-art computational methods.

Predicting transport regime and local electrostatic environment from Coulomb blockade diamond sizes

Electron transport through a molecule is often described in one of the two regimes: the coherent tunnelling regime or the Coulomb blockade regime. The twilight zone of the two regimes still possesses many unsolved questions. A theoretical analysis of the oligophenylenevinylene OPV3 experiments by Bjørnholm and co-workers is performed. The experiments showed how two OPV3 derivatives performed very differently despite the strong similarity of the molecular structure, hence the experimental data showed two different transport mechanisms. The different transport mechanisms of the two OPV3 derivatives are explained from quantum mechanical calculations of the molecular redox energies and from the experimentally accessible window size.

Efficient determination of accurate atomic polarizabilities for polarizeable embedding calculations

We evaluate embedding potentials, obtained via various methods, used for polarizable embedding computations of excitation energies of para-nitroaniline in water and organic solvents as well as of the green fluorescent protein. We found that isotropic polarizabilities derived from DFTD3 dispersion coefficients correlate well with those obtained via the LoProp method. We show that these polarizabilities in conjunction with appropriately derived point charges are in good agreement with calculations employing static multipole moments up to quadrupoles and anisotropic polarizabilities for both computed systems. The (partial) use of these easily-accessible parameters drastically reduces the computational effort to obtain accurate embedding potentials especially for proteins. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

QM/MM-MD simulations of conjugated polyelectrolytes: a study of luminescent conjugated oligothiophenes for use as biophysical probes

A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state as well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (iii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.

Excited state properties of liquid water

In this paper, we give an overview of the state of the art in calculations of the electronic band structure and absorption spectra of water. After an introduction to the main theoretical and computational schemes used, we present results for the electronic and optical excitations of water. We focus mainly on liquid water, but spectroscopic properties of ice and vapor phase are also described. The applicability and the accuracy of first-principles methods are discussed, and results are critically presented.

Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins

The explicit treatment of polarization as a many-body interaction in condensed-phase systems represents a current problem in empirical force-field development. Although a variety of efficient models for molecular polarization have been suggested, polarizable force fields are still far from common use nowadays. In this work, we consider interactive polarization models employing Thole's short-range damping scheme and assess them for application on polypeptides. Despite the simplicity of the model, we find mean polarizabilities and anisotropies of amino acid side chains in excellent agreement with MP2/cc-pVQZ benchmark calculations. Combined with restrained electrostatic potential (RESP) derived atomic charges, the models are applied in a quantum-mechanical/molecular-mechanical (QM/MM) approach. An iterative scheme is used to establish a self-consistent mutual polarization between the QM and MM moieties. This ansatz is employed to study the influence of the protein polarizability on calculated optical properties of the protonated Schiff base of retinal in rhodopsin (Rh), bacterio-rhodopsin (bR), and pharaonis sensory rhodopsin II (psRII). The shifts of the excitation energy due to the instantaneous polarization response of the protein to the charge transfer on the retinal chromophore are quantified using the high level ab initio multireference spectroscopy-oriented configuration interaction (SORCI) method. The results are compared with those of previously published QM1/QM2/MM models for bR and psRII.

Structure of Low-Lying Excited States of Guanine in DNA and Solution: Combined Molecular Mechanics and High-Level Coupled Cluster Studies

High-level ab-initio equation-of-motion coupled-cluster methods with singles, doubles, and noniterative triples are used, in conjunction with the combined quantum mechanical molecular mechanics approach, to investigate the structure of low-lying excited states of the guanine base in DNA and solvated environments. Our results indicate that while the excitation energy of the first excited state is barely changed compared to its gas-phase counterpart, the excitation energy of the second excited state is blue-shifted by 0.24 eV.

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) method for a large number of configurations generated from MD simulations. The method includes electron correlation effects at the coupled cluster singles and doubles level and the use of a large correlation consistent basis set. A polarizable force field has been used for the molecular dynamics part in both the CC/MM method and in the MD simulation. We describe how the methodology can be optimized with respect to computational costs while maintaining the quality of the results. Using the optimized method we study the energetic properties including the heat of vaporization and electronic excitation energies as well as electric dipole and quadrupole moments, the frequency dependent electric (dipole) polarizability, and electric-field-induced second harmonic generation first and second hyperpolarizabilities. Comparisons with experiments are performed where reliable data are available. Furthermore, we discuss the important issue on how to compare the calculated microscopic nonlocal properties to the experimental macroscopic measurements.

Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde

A combined quantum mechanics/molecular mechanics (QM/MM) method is described, where the polarization between the solvent and solute is accounted for using a self-consistent scheme linear in the solvent polarization. The QM/MM method is implemented for calculation of energies and molecular response properties including the calculation of linear and quadratic response functions using the density-functional theory (DFT) and the Hartree-Fock (HF) theory. Sample calculations presented for ground-state energies, first-order ground-state properties, excitation energies, first-order excited state properties, polarizabilities, first-hyperpolarizabilities, and two-photon absorptions strengths of formaldehyde suggests that DFT may in some cases be a sufficiently reliable alternative to high-level theory, such as coupled-cluster (CC) theory, in modeling solvent shifts, whereas results obtained with the HF wave function deviate significantly from the CC results. Calculations carried out on water gives results that also are comparable with CC calculations in accuracy for ground-state and first-order properties. However, to obtain such accuracy an exchange-correlation functional capable of describing the diffuse Rydberg states must be chosen.

Coupled cluster calculation of the n --> pi* electronic transition of acetone in aqueous solution

The combined linear response coupled cluster/molecular mechanics (CC/MM) scheme including mutual polarization effects in the coupling Hamiltonian is applied together with supermolecular CC methods to the study of the gas-to-aqueous solution blue shift of the n --> pi* excitation energy in acetone. The aug-cc-pVDZ basis set is found to be adequate for the calculation of this excitation energy. In the condensed phase, the shift in the excitation energy is obtained by statistical averaging over 800 solute-solvent configurations extracted from a molecular dynamics simulation. We find the shift to be around 1100-1200 cm(-1) depending on the specific model used to describe solvent polarization. The importance of including explicit polarization in both the molecular dynamics simulation as well as the CC/MM calculations is emphasized. Furthermore, the significant dependence of the excitation energy on the CO bond length of acetone is discussed.

Calculations of Molecular Properties in Hybrid Coupled-Cluster and Molecular Mechanics Approach

We report benchmark calculations obtained with our new coupled-cluster singles and doubles (CCSD) code for calculating the first- and second-order molecular properties. This code can be easily incorporated into combined [Valiev, M.; Kowalski, K. J. Chem. Phys. 2006, 125, 211101] classical molecular mechanics (MM) and ab initio coupled-cluster (CC) calculations using NWChem, enabling us to study molecular properties in a realistic environment. To test this methodology, we discuss the results of calculations of dipole moments and static polarizabilities for the Cl2O system in the CCl4 solution using the CCSD (CC with singles and doubles) linear response approach. We also discuss the application of the asymptotic extrapolation scheme (AES) [Kowalski, K.; Valiev, M. J. Phys. Chem. A 2006, 110, 13106] in reducing the numerical cost of CCSD calculations.

Solvent Effects on NMR Isotropic Shielding Constants. A Comparison between Explicit Polarizable Discrete and Continuum Approaches

The gas-to-aqueous solution shifts of the 17O and 13C NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.