A TDDFT Study of the Optical Response of DNA Bases, Base Pairs, and Their Tautomers in the Gas Phase

DNA sequencing by Förster resonant energy transfer

We propose a new DNA sequencing concept based on nonradiative Förster resonant energy transfer (FRET) from a donor quantum dot (QD) to an acceptor molecule. The FRET mechanism combined with the nanopore-based DNA translocation is suggested as a novel concept for sequencing DNA molecules. A recently-developed hybrid quantum/classical method is employed, which uses time-dependent density functional theory and quasistatic finite difference time domain calculations. Due to the significant absorbance of DNA bases for photon energies higher than 4 eV, biocompatibility, and stability, we use Zinc-Oxide (ZnO) QD as a donor in the FRET mechanism. The most sensitivity for the proposed method to DNA is achieved for the Hoechst fluorescent-dye acceptor and 1 nm ZnO-QD. Results show that the insertion of each type of DNA nucleobases between the donor and acceptor changes the frequency of the emitted light from the acceptor molecule between 0.25 to 1.6 eV. The noise analysis shows that the method can determine any unknown DNA nucleobases if the signal-to-noise ratio is larger than 5 dB. The proposed concept and excellent results shed light on a new promising class of DNA sequencers.

Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.

First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases

TD-DFT characterization of the high-energy singlet excited state manifold of the canonical DNA/RNA nucleobasesin vacuumis assessed against RASPT2 reference computations for reliable simulations of linear and non-linear electronic spectra.

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.

A potential sensing mechanism for DNA nucleobases by optical properties of GO and MoS2 Nanopores

We propose a new DNA sensing mechanism based on optical properties of graphene oxide (GO) and molybdenum disulphide (MoS2) nanopores. In this method, GO and MoS2 is utilized as quantum dot (QD) nanopore and DNA molecule translocate through the nanopore. A recently-developed hybrid quantum/classical method (HQCM) is employed which uses time-dependent density functional theory and quasi-static finite difference time domain approach. Due to good biocompatibility, stability and excitation wavelength dependent emission behavior of GO and MoS2 we use them as nanopore materials. The absorption and emission peaks wavelengths of GO and MoS2 nanopores are investigated in the presence of DNA nucleobases. The maximum sensitivity of the proposed method to DNA is achieved for the 2-nm GO nanopore. Results show that insertion of DNA nucleobases in the nanopore shifts the wavelength of the emitted light from GO or MoS2 nanopore up to 130 nm. The maximum value of the relative shift between two different nucleobases is achieved by the shift between cytosine (C) and thymine (T) nucleobases, ~111 nm for 2-nm GO nanopore. Results show that the proposed mechanism has a superior capability to be used in future DNA sequencers.

New Properties of a Bioinspired Pyridine Benzimidazole Compound as a Novel Differential Staining Agent for Endoplasmic Reticulum and Golgi Apparatus in Fluorescence Live Cell Imaging

In this study, we explored new properties of the bioinspired pyridine benzimidazole compound B2 (2,4-di-tert-butyl-6-(3H-imidazo[4,5-c]pyridine-2-yl)phenol) regarding its potential use as a differential biomarker. For that, we performed 1D ¹HNMR (TOCSY), UV-Vis absorption spectra in different organic solvents, voltammetry profile (including a scan-rate study), and TD-DFT calculations that including NBO analyses, to provide valuable information about B2 structure and luminescence. In our study, we found that the B2 structure is highly stable, where the presence of an intramolecular hydrogen bond (IHB) seems to have a crucial role in the stability of luminescence, and its emission can be assigned as fluorescence. In fact, we found that the relatively large Stokes Shift observed for B2 (around 175 nm) may be attributed to the stability of the B2 geometry and the strength of its IHB. On the other hand, we determined that B2 is biocompatible by cytotoxicity experiments in HeLa cells, an epithelial cell line. Furthermore, in cellular assays we found that B2 could be internalized by passive diffusion in absence of artificial permeabilization at short incubation times (15 min to 30 min). Fluorescence microscopy studies confirmed that B2 accumulates in the endoplasmic reticulum (ER) and Golgi apparatus, two organelles involved in the secretory pathway. Finally, we determined that B2 exhibited no noticeable blinking or bleaching after 1 h of continuous exposure. Thus, B2 provides a biocompatible, rapid, simple, and efficient way to fluorescently label particular organelles, producing similar results to that obtained with other well-established but more complex methods.

Exponential integrators in time-dependent density-functional calculations

The integrating factor and exponential time differencing methods are implemented and tested for solving the time-dependent Kohn-Sham equations. Popular time propagation methods used in physics, as well as other robust numerical approaches, are compared to these exponential integrator methods in order to judge the relative merit of the computational schemes. We determine an improvement in accuracy of multiple orders of magnitude when describing dynamics driven primarily by a nonlinear potential. For cases of dynamics driven by a time-dependent external potential, the accuracy of the exponential integrator methods are less enhanced but still match or outperform the best of the conventional methods tested.

TDDFT Study of the Optical Excitation of Nucleic Acid Bases-C60 Complexes

The potential of C₆₀ as a nucleic acid base (NAB) optical sensor is theoretically explored. We investigate the adsorption of four NABs, namely, adenine, cytosine, guanine, and thymine, on C₆₀ in the gas phase. For the optimal NAB@C₆₀ adsorption configurations, obtained using a dispersion-corrected density functional, we calculate the vis-near-ultraviolet optical response using time-dependent density functional theory. While the isolated C₆₀ and NAB molecules do not exhibit visible optical excitation, we find that C₆₀/NAB conjugation gives rise to distinct spectral features in the visible range. These results suggest that C₆₀ conjugation can be applied for photodetection of individual NABs.

Investigating the features in differential absorbance spectra of NOM associated with metal ion binding: A comparison of experimental data and TD-DFT calculations for model compounds

In this study, seven model compounds containing typical functional groups (phenolic and carboxylic groups) present in nature organic matter (NOM) were used to ascertain the nature of the characteristic bands in differential absorbance spectra (DAS) of NOM that are induced by metal ion binding. Some similarities were found between the DAS of the examined model compounds, caffeic acid, ferulic acid, sinapic acid, terephthalic acid, isophthalic acid, esculetin and myricetin and those of NOM. The binding of Cu(II) with carboxylic group might produce two peaks, A1 and A2, while the binding of Cu(II) with phenolic group might produce all four Gaussian peaks, from A1 to A4 displayed in the DAS of NOM. The UV-visible spectra predicted using time-dependent density functional theory (TD-DFT)-based methods met well with the experimental DAS of model compounds at different stages of Cu(II) binding. It demonstrates that the features in absorbance spectra are chiefly caused by HOMO (Highest Occupied Molecular Orbital) - LUMO (Lowest Unoccupied Molecular Orbital) transitions in the molecule and that the appearance of peaks in DAS reflects the changes of the molecular orbitals around reactive functional groups in a molecule before and after metal ion binding. The basis of the DAS features of NOM that are induced by metal ion binding could be identified primarily by the frontier molecular orbital theory.

Ultrafast Nuclear Dynamics of Photoexcited Guanosine-5'-Monophosphate in Three Singlet States

We report measurement of resonance Raman (RR) spectra of guanosine-5'-monophosphate (GMP), a DNA nucleotide at excitation wavelengths throughout its ππ* absorption band (B_b) in the 210-230 nm range. From these data, we constructed wavelength-dependent Raman intensity excitation profiles (REPs) for all observed modes. These profiles and the absorption spectrum were then modeled using self-consistent simulations based on the time-dependent wave packet propagation formalism. We inferred the initial structural dynamics of GMP immediately after photoexcitation in terms of dimensionless displacements. The simulations also provide linewidth-broadening parameters that in turn report on the time scale of dynamics. We compared deduced structural changes in the purine ring upon photoabsorption into the B_b state with those deduced for the two lowest lying ππ* (L_a and L_b at 280 and 248 nm, respectively) excited states of GMP. We find that excitation to the L_b state lengthens C₆-N₁ and C₂═N₃ bonds, which lie along the formation coordinate of various oxidative adducts but B_b excitation does not. We also find that photoabsorption by the B_b state weakens the C₈-N₉ bond and thus might assist imidazole ring opening via cleavage of the same bond. Electronic excitation to different ππ* states of the guanine chromophore results in contrasting structural changes; although absorption by the L_a and L_b states induces expansion of pyrimidine and contraction of imidazole rings, excitation results in overall shrinkage of both the rings. Computed absolute changes in internal coordinates imply that photoexcitation to any of the three singlet states of GMP does not lead directly to the formation of a cation radical of guanine.

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.

Ultrafast charge-transfer in organic photovoltaic interfaces: geometrical and functionalization effects

Understanding the microscopic mechanisms of electronic excitation in organic photovoltaic cells is a challenging problem in the design of efficient devices capable of performing sunlight harvesting. Here we develop and apply an ab initio approach based on time-dependent density functional theory and Ehrenfest dynamics to investigate photoinduced charge transfer in small organic molecules. Our calculations include mixed quantum-classical dynamics with ions moving classically and electrons quantum mechanically, where no experimental external parameter other than the material geometry is required. We show that the behavior of photocarriers in zinc phthalocyanine (ZnPc) and C60 systems, an effective prototype system for organic solar cells, is sensitive to the atomic orientation of the donor and the acceptor units as well as the functionalization of covalent molecules at the interface. In particular, configurations with the ZnPc molecules facing on C60 facilitate charge transfer between substrate and molecules that occurs within 200 fs. In contrast, configurations where ZnPc is tilted above C60 present extremely low carrier injection efficiency even at longer times as an effect of the larger interfacial potential level offset and higher energetic barrier between the donor and acceptor molecules. An enhancement of charge injection into C60 at shorter times is observed as binding groups connect ZnPc and C60 in a dyad system. Our results demonstrate a promising way of designing and controlling photoinduced charge transfer on the atomic level in organic devices that would lead to efficient carrier separation and maximize device performance.

The Importance of Short- and Long-Range Exchange on Various Excited State Properties of DNA Monomers, Stacked Complexes, and Watson-Crick Pairs

We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.

Charge-transfer optical absorption mechanism of DNA:Ag-nanocluster complexes

Optical properties of DNA:Ag-nanoclusters complexes have been successfully applied experimentally in Chemistry, Physics, and Biology. Nevertheless, the mechanisms behind their optical activity remain unresolved. In this work, we present a time-dependent density functional study of optical absorption in DNA:Ag_{4}. In all 23 different complexes investigated, we obtain new absorption peaks in the visible region that are not found in either the isolated Ag_{4} or isolated DNA base pairs. Absorption from red to green are predominantly of charge-transfer character, from the Ag_{4} to the DNA fragment, while absorption in the blue-violet range are mostly associated to electronic transitions of a mixed character, involving either DNA-Ag_{4} hybrid orbitals or intracluster orbitals. We also investigate the role of exchange-correlation functionals in the calculated optical spectra. Significant differences are observed between the calculations using the PBE functional (without exact exchange) and the CAM-B3LYP functional (which partly includes exact exchange). Specifically, we observe a tendency of charge-transfer excitations to involve purines bases, and the PBE spectra error is more pronounced in the complexes where the Ag cluster is bound to the purines. Finally, our results also highlight the importance of adding both the complementary base pair and the sugar-phosphate backbone in order to properly characterize the absorption spectrum of DNA:Ag complexes.

Coupled-cluster and density functional theory studies of the electronic 0–0 transitions of the DNA bases

The 0–0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations.

ABSORPTION SPECTRA OF NUCLEIC ACID BASES IN WATER ENVIRONMENT: INSIGHTS INTO FROM COMBINED QM/MM AND CLUSTER-CONTINUUM MODEL CALCULATIONS

Electronic spectra of uracil, thymine, adenine, guanine, and cytosine in the gas phase and aqueous solution have been studied by extensive time-dependent density functional calculations. Calculations show that the Quantum mechanics/molecular mechanics (QM/MM) geometry optimization based on the molecular dynamics (MD) equilibrated configuration can locate an optimal solvated cluster for the base solvation, and the combined QM/MM and cluster-continuum computational protocol is capable of handling the solvent effect on the excited states of nucleic acid bases and providing realistic absorption spectra in water environment with relatively low computational costs. Generally, the vertical excitation energies in aqueous solution by PCM/TD-X3LYP calculations show excellent agreement with the experimental observations and the maximum deviation is less than 0.2 eV. The present results reveal that the hydrogen bond network around the excited-state base and its dipole moment change may remarkably modify the absorption spectra of nucleic acid bases in aqueous solution.

Ab initio determination of coarse-grained interactions in double-stranded DNA

We derive the coarse-grained interactions between DNA nucleotides from ab initio total-energy calculations based on density functional theory (DFT). The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-base interactions. The interaction energies of each contribution are calculated from DFT for a wide range of configurations and are fitted by simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This model is not derived from experimental data, yet it successfully reproduces the stable B-DNA structure and gives good predictions for the persistence length. It may be used to realistically probe dynamics of DNA strands in various environments at the μs time scale and the μm length scale.

Theoretical studies on molecular and structures of mono- and binuclear chromium carbazole derivatives for optoelectronics

Studies on the molecular geometries, electronic properties and second-order nonlinearities of a series of mono- and binuclear chromium carbazole complexes: (N-vinylcarbazole)Cr(CO)(3) (M1), (N-vinylcarbazole)Cr(CO)(2)PPh(3) (M2), (CO)(3)Cr(N-vinylcarbazole)Cr(CO)(3) (B1), and (CO)(3)Cr(N-vinylcarbazole)Cr(CO)(2)PPh(3) (B2) were carried out, using the density functional theory (DFT) at the B3LYP//LanL2DZ/6-31G(d) level. The experimental singlet metal-to-ligand charge transfer ((1)MLCT) spectra of these complexes can also be well simulated and discussed by the time-dependent DFT (TDDFT) at the B3LYP//LanL2DZ/6-311+G(d) level associated with the polarizable continuum model (PCM). The computational results show that an unusual characteristic of chromium carbazole structures is explained in terms of interaction between frontier molecular orbitals of the metal and its ligands. The highest occupied molecular orbitals (HOMOs) of these complexes are composed of a set of distorted degenerated Cr 3d orbitals, whereas the lowest unoccupied molecular orbitals (LUMOs) are predominantly the N-vinylcarbazole ligand π* orbitals. The HOMO-LUMO energy gaps decrease in the order NVC > M1 > B1 > M2 > B2. The considerable coupling between the carbazole and (CO)(3) in M1 creates an asymmetric environment about the chromium atom, leading to modest second-order responses. The PPh(3) ligand is acting as a donor which increases the donating strength of the d(π) orbitals in chromium carbazole species, resulting in the large electronic asymmetry in M2. As for the binuclear chromium carbazole chromophores, a wide-range (1)MLCT band and large oscillator strength are found, allowing for the electronic interactions between two metal centers which can be modified by altering the ligand bound to the metals to induce peculiar asymmetry. Essentially, Cr(CO)(3) acceptor and Cr(CO)(2)PPh(3) donor units in B2 make significant contribution to the charge-transfer process or NLO responses via conventional push-pull chromophoric architecture.

TDDFT STUDY OF NUCLEOBASE THIOANALOGUES AND OXO-DERIVATIVES EXCITED STATES

Thioanalogues of nucleic-acid bases have been shown to be the place of preferential charge or energy localization when incorporated in the system of respective regular bases. Most evidence of such behavior is based on experiments using γ-ray or other ionizing radiation. Here time dependent density functional theory (TDDFT) has been applied to investigate singlet and triplet excited state spectra of thioanalogues and some oxo-derivatives of nucleic-acid bases and compare the spectra to the calculated spectra of the regular bases as well as to the existing experimental data. It has been shown that thioanalogues have lower excitation singlet and triplet energies than are the respective energies in the regular bases. Energy localization on thioanalogues and their spectroscopic properties are related to the effect of sulfur substitution in such systems.

Electron and hole dynamics in dye-sensitized solar cells: influencing factors and systematic trends

We investigate electron and hole dynamics upon photon excitation in dye-sensitized solar cells, using a recently developed method based on real-time evolution of electronic states through time-dependent density functional theory. The systems we considered consist of organic sensitizers and nanocrystalline TiO(2) semiconductors. We examine the influence of various factors on the dynamics of electrons and holes, including point defects (vacancies) on the TiO(2) surface, variations in the dye molecular size and binding geometry, and thermal fluctuations which result in different alignments of the electronic energy levels. Two clear trends emerge: (a) dissociated adsorption of the dye molecules leads to faster electron injection dynamics by reducing interfacial dipole moments; (b) oxygen vacancy defects stabilize dye adsorption and facilitate charge injection, at the cost of lower open circuit voltage and higher electron-hole recombination rate. Understanding of these effects at the atomic level suggests tunable parameters through which the electronic characteristics of dye-sensitized solar cell devices can be improved and their efficiency can be maximized.