Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. The relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein-Frenkel Hamiltonian model.

Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA

DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.

Molecular factors determining brightness in fluorescence-encoded infrared vibrational spectroscopy

Fluorescence-encoded infrared (FEIR) spectroscopy is a recently developed technique for solution-phase vibrational spectroscopy with detection sensitivity at the single-molecule level. While its spectroscopic information content and important criteria for its practical experimental optimization have been identified, a general understanding of the electronic and nuclear properties required for highly sensitive detection, i.e., what makes a molecule a "good FEIR chromophore," is lacking. This work explores the molecular factors that determine FEIR vibrational activity and assesses computational approaches for its prediction. We employ density functional theory (DFT) and its time-dependent version (TD-DFT) to compute vibrational and electronic transition dipole moments, their relative orientation, and the Franck-Condon factors involved in FEIR activity. We apply these methods to compute the FEIR activities of normal modes of chromophores from the coumarin family and compare these predictions with experimental FEIR cross sections. We discuss the extent to which we can use computational models to predict the FEIR activity of individual vibrations in a candidate molecule. The results discussed in this work provide the groundwork for computational strategies for choosing FEIR vibrational probes or informing the structure of designer chromophores for single-molecule spectroscopic applications.

Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites

Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of 'internally-labeled' (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions.

Studies of DNA breathing in exciton-coupled (iCy3)2 dimer-labeled DNA constructs by polarization-sweep single-molecule fluorescence (PS-SMF) microscopy

Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in the assembly of protein-DNA complexes. We present a single-molecule fluorescence method to sensitively measure the local conformational fluctuations of exciton-coupled cyanine [(iCy3)2] dimer-labeled DNA fork constructs in which the dimer probes are placed at varying positions relative to the DNA fork junction. These systems exhibit spectroscopic signals that are sensitive to the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probe label positions. The (iCy3)2 dimer has one symmetric (+) and one anti-symmetric (-) exciton with respective transition dipole moments oriented perpendicular to one another. We excite single molecule samples using a continuous-wave, linearly polarized laser with its polarization direction rotated at a frequency of 1 MHz. The ensuing fluorescence signal is modulated as the laser polarization alternately excites the symmetric and anti-symmetric excitons of the (iCy3)2 dimer probe. Phase-sensitive detection of the signal at the photon-counting level provides information about the distribution of local conformations and conformational dynamics. We analyze our data using a kinetic network model, which we use to parametrize the free energy surface of the system. In addition to observing DNA breathing at and near ss-dsDNA junctions, the approach can be used to study the effects of proteins that bind and function at these sites.

Prediction of fluorescence quantum yields using the extended thawed Gaussian approximation

Spontaneous emission and internal conversion rates are calculated within harmonic approximations and compared to the results obtained within the semi-classical extended thawed Gaussian approximation (ETGA). This is the first application of the ETGA in the calculation of internal conversion and emission rates for real molecular systems, namely, formaldehyde, fluorobenzene, azulene, and a dicyano-squaraine dye. The viability of the models as black-box tools for prediction of spontaneous emission and internal conversion rates is assessed. All calculations were done using a consistent protocol in order to investigate how different methods perform without previous experimental knowledge using density functional theory (DFT) and time-dependent DFT (TD-DFT) with B3LYP, PBE0, ωB97XD, and CAM-B3LYP functionals. Contrasting the results with experimental data shows that there are further improvements required before theoretical predictions of emission and internal conversion rates can be used as reliable indicators for the photo-luminescence properties of molecules. We find that the ETGA performs rather similar to the vertical harmonical model. Including anharmonicities in the calculation of internal conversion rates has a moderate effect on the quantitative results in the studied systems. The emission rates are fairly stable with respect to computational parameters, but the internal conversion rate reveals itself to be highly dependent on the choice of the spectral line shape function, particularly the width of the Lorentzian function, associated with homogeneous broadening.

Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer

The indocarbocyanine Cy3 dye is widely used to probe the dynamics of proteins and DNA. Excitonically coupled Cy3 dimers exhibit very unique spectral signatures that depend on the interchromophoric geometrical orientation induced by the environment, making them powerful tools to infer the dynamics of their surroundings. Understanding the origin of the dimeric spectral signatures is a necessity for an accurate interpretation of the experimental results. In this work, we simulate the vibronic spectrum of an experimentally well-studied Cy3 dimer, and we explain the origin of the experimental signatures present in its linear absorption spectrum. The Franck-Condon harmonic approximations, among other tests, are used to probe the factors contributing to the spectrum. It is found that the first peak in the absorption spectrum originates from the lower energy excitonic state, while the next two peaks are vibrational progressions of the higher energy excitonic state. The polar solvent plays a crucial role in the appearance of the spectrum, being responsible for the localized S1 minimum, which results in an increased intensity of the first peak.

Multiscale QM/MM modelling of catalytic systems with ChemShell

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

Studies of Local DNA Backbone Conformation and Conformational Disorder Using Site-Specific Exciton-Coupled Dimer Probe Spectroscopy

The processes of genome expression, regulation, and repair require direct interactions between proteins and DNA at specific sites located at and near single-stranded-double-stranded DNA (ssDNA-dsDNA) junctions. Here, we review the application of recently developed spectroscopic methods and analyses that combine linear absorbance and circular dichroism spectroscopy with nonlinear 2D fluorescence spectroscopy to study the local conformations and conformational disorder of the sugar-phosphate backbones of ssDNA-dsDNA fork constructs that have been internally labeled with exciton-coupled cyanine (iCy3)2 dimer probes. With the application of these methods, the (iCy3)2 dimer can serve as a reliable probe of the mean local conformations and conformational distributions of the sugar-phosphate backbones of dsDNA at various critical positions. The results of our studies suggest a possible structural framework for understanding the roles of DNA breathing in driving the processes of protein-DNA complex assembly and function.

Internal conversion rates from the extended thawed Gaussian approximation: Theory and validation

The theoretical prediction of the rates of nonradiative processes in molecules is fundamental in assessing their emissive properties. In this context, global harmonic models have been widely used to simulate vibronic spectra as well as internal conversion rates and to predict photoluminescence quantum yields. However, these simplified models suffer from the limitations that are inherent to the harmonic approximation and can have a severe effect on the calculated internal conversion rates. Therefore, the development of more accurate semiclassical methods is highly desirable. Here, we introduce a procedure for the calculation of nonradiative rates in the framework of the time-dependent semi-classical Extended Thawed Gaussian Approximation (ETGA). We systematically investigate the performance of the ETGA method by comparing it to the adiabatic and vertical harmonic methods, which belong to the class of widely used global harmonic models. Its performance is tested in potentials that cannot be treated adequately by global harmonic models, beginning with Morse potentials of varying anharmonicity followed by a double well potential. The calculated radiative and nonradiative internal conversion rates are compared to reference values based on exact quantum dynamics. We find that the ETGA has the capability to predict internal conversion rates in anharmonic systems with an appreciable energy gap, whereas the global harmonic models prove to be insufficient.