TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids

The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute-Solvent Interactions and Non-Adiabatic Couplings

In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. Cytosine is interesting because it is characterized by several close-lying and coupled electronic states, challenging the approach commonly used to compute the vRR for systems where the excitation frequency is in quasi-resonance with a single state. We adopt two recently developed time-dependent approaches, based either on quantum dynamical numerical propagations of vibronic wavepackets on coupled PES or on analytical correlation functions for cases in which inter-state couplings were neglected. In this way, we compute the vRR spectra, considering the quasi-resonance with the eight lowest-energy excited states, disentangling the role of their inter-state couplings from the mere interference of their different contributions to the transition polarizability. We show that these effects are only moderate in the excitation energy range explored by experiments, where the spectral patterns can be rationalized from the simple analysis of displacements of the equilibrium positions along the different states. Conversely, at higher energies, interference and inter-state couplings play a major role, and the adoption of a fully non-adiabatic approach is strongly recommended. We also investigate the effect of specific solute-solvent interactions on the vRR spectra, by considering a cluster of cytosine, hydrogen-bonded by six water molecules, and embedded in a polarizable continuum. We show that their inclusion remarkably improves the agreement with the experiments, mainly altering the composition of the normal modes, in terms of internal valence coordinates. We also document cases, mostly for low-frequency modes, in which a cluster model is not sufficient, and more elaborate mixed quantum classical approaches, in explicit solvent models, need to be applied.

Damped (linear) response theory within the resolution-of-identity coupled cluster singles and approximate doubles (RI-CC2) method

An implementation of a complex solver for the solution of the linear equations required to compute the complex response functions of damped response theory is presented for the resolution-of-identity (RI) coupled cluster singles and approximate doubles (CC2) method. The implementation uses a partitioned formulation that avoids the storage of double excitation amplitudes to make it applicable to large molecules. The solver is the keystone element for the development of the damped coupled cluster response formalism for linear and nonlinear effects in resonant frequency regions at the RI-CC2 level of theory. Illustrative results are reported for the one-photon absorption cross section of C₆₀, the electronic circular dichroism of n-helicenes (n = 5, 6, 7), and the C₆ dispersion coefficients of a set of selected organic molecules and fullerenes.

Natural and magnetic circular dichroism spectra of nucleosides: effect of the dynamics and environment

Chiroptical spectroscopic methods are excellent tools to study structure and interactions of biomolecules. However, their sensitivity to different structural aspects varies. To understand the dependence of absorption, electronic and magnetic circular dichroism (ECD, MCD) intensities on the structure, dynamics and environment, we measured and simulated spectra of nucleosides and other nucleic acid model components. The conformation space was explored by molecular dynamics (MD), the electronic spectra were generated using time dependent density functional theory (TDDFT). The sum over state (SOS) method was employed for MCD. The results show that accounting for the dynamics is crucial for reproduction of the experiment. While unpolarized absorption spectroscopy is relatively indifferent, ECD reflects the conformation and geometry dispersion more. MCD spectra provide variable response dependent on the wavelength and structural change. In general, MCD samples the structure more locally than ECD. Simple computational tests suggest that the optical spectroscopies coupled with the computational tools provide useful information about nucleic acid components, including base pairing and stacking.

Magnetic Circular Dichroism of Naphthalene Derivatives: A Coupled Cluster Singles and Approximate Doubles and Time-Dependent Density Functional Theory Study

The UV-vis absorption and magnetic circular dichroism spectra of naphthalene and some of its derivatives have been simulated at the Coupled Cluster Singles and Approximate Doubles (CC2) level of theory, and at the Time-Dependent Density Functional Theory (TD-DFT) level using the B3LYP and CAM-B3LYP functionals. DFT and CC2 predict in general opposite energetic ordering of the L_b and L_a transitions (in gas phase), as previously observed in adenine. The CC2 simulations of UV and MCD spectra show the best agreement with the experimental data. Analysis of the Cartesian components of the electric dipole transition strengths and the magnetic dipole transition moment between the excited states have been considered in the interpretation of the electronic transitions and the Faraday B term inversion among the naphthalene derivatives.

Characterization of tetrakis(thiadiazole)porphyrazine metal complexes by magnetic circular dichroism and magnetic circularly polarized luminescence

The magnetic circular dichroism (MCD) spectra of metal complexes of tetrakis(thiadiazole)porphyrazines ([TTDPzM] with M = 2H^I , Zn^II , Mg^II (H₂ O), and Cd^II ) have been recorded in dimethyl formamide solution. Together with the UV-Vis spectra, the MCD spectra provide useful information about the structure and electronic properties of the complexes. The experimental UV-Vis and MCD spectra compare pretty well with DFT calculations of two sorts, based either on the sum-over-states (SOS) approach or on the complex polarization propagator approach. They further corroborate the findings and interpretation of MCD spectra of porphyrazines based on the model of Michl for peripheral molecular orbitals. Magnetic circularly polarized luminescence (MCPL) spectra, quite uncommon in the literature, have been recorded for [TTDPzM] (M = 2H^I , Zn^II , Mg^II (H₂ O)).

Core–valence-separated coupled-cluster-singles-and-doubles complex-polarization-propagator approach to X-ray spectroscopies

The iterative subspace algorithm to solve the CCSD complex linear response equations has been modified to include a core–valence separation projection step to overcome convergence problems. Illustrative results are reported for XAS, XCD, XES and RIXS.

Role of Explicit Solvation in the Simulation of Resonance Raman Spectra within Short-Time Dynamics Approximation

In short-time dynamics approximation, relative resonance Raman (RR) intensity of a vibrational mode primarily depends on the magnitude of square of the excited-state gradient along the corresponding normal coordinate, ground-state normal mode eigenvector, and harmonic vibrational wavenumbers. In this study, through simulation of RR spectra of guanosine-5'-monophosphate (GMP) in two ππ* singlet excited states, we analyze how the explicitly hydrogen-bonded local solvation structure of the chromophore dictates intensities of the RR active modes in an unprecedented manner. We show that the accuracy of the structural model of solvated chromophore plays a decisive role in determining an optimal theoretical method for prediction of the Franck-Condon region of the ππ* excited states. 9-Methylguanine (9-meG) in complex with six water molecules (9-meG·6H₂O) is found out to be the most accurate one for describing GMP in two different bright electronic states. We find that explicit hydrogen-bonded water molecules strongly influence computed RR intensities of GMP by modulating both the ground-state normal mode vectors and the excited-state energy gradients. We find that simultaneous inclusion of six explicit waters to describe the solute-solvent interaction near all hydration sites is essential for reliable prediction of the features of RR spectra in L_b and B_b electronic states of GMP.

Initial excited-state structural dynamics of 2′-deoxyadenosine

Purine nucleobases (adenosine and guanosine) are prone to spontaneous breaking of the nucleosidic bond to form abasic sites in both DNA and RNA. However, the purines also undergo photochemical reactions, including oxidation and cycloaddition, to form damage sites, albeit at lower photochemical quantum yields than the pyrimidines. In this study, we use ultraviolet resonance Raman spectroscopy to measure the initial excited-state structural dynamics in the nucleoside, 2′-deoxyadenosine. The resonance Raman-derived initial excited-state structural dynamics throughout the 260 nm La excited electronic state of adenine are found to be smaller in the nucleoside than in the previously reported 9-methyladenine nucleobase derivative, consistent with what is found for the pyrimidines thymine and uracil. Interestingly, resonance-enhanced vibrational modes in this electronic state also contain internal coordinates localized on the sugar, which may represent a different energy dissipation mechanism than in the pyrimidine nucleosides. The results will be discussed in terms of the initial excited-state photophysics and photochemistry of DNA and RNA.

Optical absorption and magnetic circular dichroism spectra of thiouracils: a quantum mechanical study in solution

The excited electronic states of thiouracils, the analogues of uracil where the carbonyl oxygens are substituted by sulphur atoms, have been investigated by computing the magnetic circular dichroism (MCD) and one-photon absorption (OPA) spectra at the TD-DFT level of theory.

Ultrafast structural dynamics of photoexcited adenine

Ultraviolet Resonance Raman (UVRR) spectroscopy derives distinct electronic properties of adenine in the L_a (260 nm) and B_b (210 nm) excited states.

Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism

The detailed electronic structures of fluorescent chromophores are important for their use in imaging of living cells. A series of green fluorescent protein chromophore derivatives is examined by magnetic circular dichroism (MCD) spectroscopy, which allows the resolution of more bands than plain absorption and fluorescence. Observed spectral patterns are rationalized with the aid of time-dependent density functional theory (TDDFT) computations and the sum-over-state (SOS) formalism, which also reveals a significant dependence of MCD intensities on chromophore conformation. The combination of organic and theoretical chemistry with spectroscopic techniques also appears useful in the rational design of fluorescence labels and understanding of the chromophore's properties. For example, the absorption threshold can be heavily affected by substitution on the phenyl ring but not much on the five-member ring, and methoxy groups can be used to further tune the electronic levels.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion

A schematic representation of magneto-chiral effects.