Chirality Sensing of Cryptochiral Guests with Prism[n]arenes

Optical chirality sensing has gained significant attention in recent years. Within this field, the quest for stereodynamic chiroptical probes capable of detecting cryptochiral guests presents a formidable challenge. Macrocycles exhibiting planar chirality have emerged as promising candidates for amplifying the chirality of cryptochiral guests. In this study, we demonstrate that the formation of host-guest complexes between cryptochiral molecules and planar chiral prismarenes triggers electronic circular dichroism (ECD) signals via host-guest complexation-induced chirality amplification. The absolute configuration of the most stable chiral macrocyclic host-guest complex has been established by resorting to both exciton model and DFT computations. Furthermore, we demonstrated that this supramolecular chirality sensing system can be employed to determine the enantiomeric composition of scalemic mixtures by measuring the ECD bands intensity. The information described here opens the way for the use of prismarenes as stereodynamic probes for sensing of cryptochiral guests.

De novo design of proteins housing excitonically coupled chlorophyll special pairs

Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.

A Perspective on the Simulation of Electronic Circular Dichroism and Circularly Polarized Luminescence Spectra in Chiral Solid Materials

Chiral materials have shown tremendous potential for many technological applications, such as optoelectronics, sensing, magnetism, information technology, and imaging. Characterization of these materials is mostly based on chiroptical spectroscopies, such as electronic circular dichroism (ECD) and circularly polarized luminescence (CPL). These experimental measurements would greatly benefit from theoretical simulations for interpretation of the spectra as well as predictions on new materials. While ECD and CPL simulations are well established for molecular systems, they are not for materials. In this Perspective, we describe the theoretical quantities necessary to simulate ECD and CPL spectra in oriented systems. Then, we discuss the approximate strategies currently used to perform these calculations, what computational machinery is already available to develop more general approaches, and some of the open challenges for the simulation of ECD and CPL spectra in solid materials. When methods that are as reliable and computationally efficient as those for molecules are developed, these simulations will provide invaluable insight and guidance for the rational design of optically active materials.

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints

The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.

Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization

In this study, we exploit a recently developed fragment diabatization-based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine-rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c-Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time-dependent density functional theory (TD-DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD-DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD-DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K + $$ {}^{+} $$ cation in the calculation.

Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity

OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.

Role of Dielectric Screening in Calculating Excited States of Solvated Azobenzene: A Benchmark Study Comparing Quantum Embedding and Polarizable Continuum Model for Representing the Solvent

The low energy excited states of the conformational isomers of solvated azobenzene are calculated with several DFT methods accounting for the solute-solvent interaction implicitly with the polarizable continuum model or explicitly with subsystem DFT. For the latter, embedding potentials are calculated for 21 sampled snapshots of the solvent molecules. First, we find that accounting for the solvent implicitly or explicitly has little effect on the predicted cis-trans S₁ excitation energy gap. Second, we find that azobenzene's S₁ cis and trans energies are accurate as long as a screened range-separated hybrid exchange-correlation functional is employed. Finally, we also tested a simplified workflow whereby a single, averaged, embedding potential is used. Unfortunately, we find larger deviations against the experiment for the simplified workflow. This highlights a basic flaw in the approach, where the time scale of solvent averaging is much longer than that of the solute's electronic polarization.

Near-infrared circular dichroism of the ytterbium DOTMA complex: an ab initio investigation

The electronic structure and circular dichroism spectra of the ytterbium(III) complex [Yb(DOTMA)]^- are calculated using complete and restricted active space self-consistent field wavefunction methods with the spin-orbit coupling treated by the state interaction approach. The influence of the dynamical correlation effect is then included via the 2nd order perturbation method. The experimental circular dichroism spectrum is well reproduced by calculations, both in terms of relative energy excitations and in terms of rotatory strength intensities. The results allow highlighting the mechanism that drives the chiroptical properties in Yb(III) complexes and reveal the importance of taking into account the 4f¹²5d¹ electronic configurations in the calculated wavefunctions to properly describe the chiroptical properties of the 4f-4f transitions.

Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5′TGGGTGGGTGGGTGGG3′), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.

Excitonic Model for Strongly Coupled Multichromophoric Systems: The Electronic Circular Dichroism Spectra of Guanine Quadruplexes as Test Cases

We here propose a general and flexible approach, based on fragment diabatization, which incorporates charge transfer states and significantly increases the reliability of excitonic Hamiltonians for systems where the chromophores are very close. This model (FrDEx) is used to compute the electronic circular dichroism and absorption spectra of two prototype guanine-rich DNA sequences folded in quadruple helices (GQs), i.e., a fragment of the human telomeric sequence (Tel21, antiparallel), and (TGGGGT)₄ (TG4T, parallel). Calculations on different subsets of Tel21 and TG4T, from dimers to tetramers, show that FrDEx provides spectra close to the reference full quantum mechanical (QM) ones (obtained with time-dependent density functional theory), with significant improvements with respect to "standard" excitonic Hamiltonians. Furthermore, these tests enable the most cost-effective procedure for the whole GQ to be determined. FrDEx spectra of Tel21 and TG4T are also in good agreement with the QM and experimental ones and give access to interesting insights into the chemical-physical effects modulating the spectral signals. FrDEx could be profitably used to investigate many other biological and nanotechnological materials, from DNA to (opto)electronic polymers.

Chiroptical Symmetry Analysis of Trianglimines: A Case Study

It is well established that chiroptical responses, based on the unique reaction to circularly polarized light by chiral non-racemic systems, are sensitive to the stereochemistry of the featuring systems. This behavior has promoted the use of chiroptical spectroscopies as a mandatory tool in the structure determination of molecules for decades. Recently, the higher sensitivity of chiroptical techniques compared to the conventional UV/Vis absorption and fluorescence spectroscopies or electrochemistry has awakened much interest in the development of chiroptical everyday applications. While chiroptical responses could be predicted by ab initio calculations, large systems calculated at a high level of theory may have an important computational cost; therefore, more intuitive methods are desired to design systems with tailored chiroptical responses. In this regard, the exciton chirality method has been often used in conformationally stable systems incorporating at least two independent chromophores. Taking this method into consideration, in our previous work, we described the chiroptical symmetry analysis (CSA) based on symmetry selection rules. To explore the scope of the CSA, herein we perform the chiroptical symmetry analysis of diverse trianglimines and draw general conclusions to assist on the design of chiroptical systems with high symmetry.

Ab Initio Study of Circular Dichroism and Circularly Polarized Luminescence of Spin-Allowed and Spin-Forbidden Transitions: From Organic Ketones to Lanthanide Complexes

Complete and restricted active space self-consistent field (CAS-/RAS-SCF) wave function methods are applied for the calculation of circular dichroism (CD) and circularly polarized luminescence (CPL) of a series of molecules comprising four organic ketones, the chiral cobalt(III) complex [Co(en)₃]³⁺, and the europium(III) complex [Eu(DPA)₃]^3-. The ab initio results are in good agreement with the experimental data and previous results obtained with Kohn-Sham density functional theory in the case of the spin-allowed transitions. CD and CPL properties are calculated ab initio for the spin-forbidden transitions of both a transition metal and a lanthanide complex.

Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules

Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.

Effective computational route towards vibrational optical activity spectra of chiral molecules in aqueous solution

A polarizable QM/MM approach to accurately compute the Vibrational Optical Activity (VOA) spectra of chiral systems is proposed and applied to aqueous solutions of (l)-methyl lactate and (S)-glycidol.

EXAT: EXcitonic analysis tool

We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G-quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/. © 2017 Wiley Periodicals, Inc.

Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum

We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.

A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved?

We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.

Assembly and Folding of Twisted Baskets in Organic Solvents

A synthetic method for obtaining enantiopure and twisted baskets of type (P)-3 is described. These chiral cavitands were found to fold quinoline gates, at the rim of their twisted platform, in acetonitrile and give molecular capsules that assemble into large unilamellar vesicles. In a less polar dichloromethane, however, cup-shaped (P)-3 packed into vesicles but with the quinoline gates in an unfolded orientation. The ability of twisted baskets to form functional nanostructured materials could be of interest for building stereoselective sensors and catalysts.

Synthesis of enantiomerically pure helicene-like mono 1,3-oxazines from 1,1′-binaphthyl-2,2′,7-triol and study of their chiroptical properties

Several helicene-like molecules have been synthesized and characterized. The effect of helicene-like structural arrangement was more prominent in the chiroptical properties as compared to the stereogenic center of the diastereomeric compounds.

Bicamphor: a prototypic molecular system to investigate vibrational excitons

Vibrational circular dichroism (VCD) and IR spectra have been recorded in the fingerprint and carbonyl stretching regions for endo,endo-bicamphor (1), exo,exo-bicamphor (2), endo,exo-bicamphor (3), 3,3'-bicamphorylidene (4), and exo,exo-bis-thiocamphor (5). The C2 symmetry possessed by these molecular systems (except in one case), as well as their limited conformational mobility associated with well-defined degrees of freedom, allow for optimal test of the vibrational circular dichroism exciton chirality (VCDEC) rule introduced by Taniguchi and Monde. Density functional theory calculations are employed not only to predict the entire aspect of the VCD and IR spectra but also to study how the VCDEC rule may be impacted by the coupling between C═O stretchings and from C═O stretchings with other vibrational modes and by the rotation about the C-C bond connecting the two camphors. Comments are provided about the limitations and potentialities of the VCDEC method and about the manifestation of different vibrational excitons in other regions of the VCD spectra, either in the mid-IR or in the CH-stretching regions.

DNA Electronic Circular Dichroism on the Inter-Base Pair Scale: An Experimental-Theoretical Case Study of the AT Homo-Oligonucleotide

A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment.

The electronic circular dichroism of nicotine in aqueous solution: a test case for continuum and mixed explicit-continuum solvation approaches

In this paper, we extend an integrated QM/MM/polarizable continuum model (PCM) method, which combines a fluctuating charge (FQ) approach to the MM polarization with the PCM, to describe electronic circular dichroism (ECD) spectra of systems in aqueous solution. The main features of the approach are presented, and then applications to the UV and ECD spectra of neutral (S)-nicotine in aqueous solution are reported. The performance of the QM/FQ/PCM is compared with that of the PCM against newly measured UV ECD spectra, which are in agreement with previous findings. The inclusion of specific solvation effects via the QM/FQ/PCM method leads to an improvement in the calculated spectra compared to the experimental findings, though the pure PCM results are still qualitatively correct and are a useful tool for the characterization of the states.

Twisted baskets

A preparative procedure for obtaining a pair of twisted molecular baskets, each comprising a chiral framework with either right ((P)-1syn) or left ((M)-1syn) sense of twist and six ester groups at the rim has been developed and optimized. The racemic (P/M)-1syn can be obtained in three synthetic steps from accessible starting materials. The resolution of (P/M)-1syn is accomplished by its transesterification with (1R,2S,5R)-(-)-menthol in the presence of a Ti(IV) catalyst to give diastereomeric 8(P) and 8(M). It was found that dendritic-like cavitands 8(P) and 8(M), in CD2Cl2, undergo self-inclusion ((1)H NMR spectroscopy) with a menthol moiety occupying the cavity of each host. Importantly, the degree of inclusion of the menthol group was ((1)H NMR spectroscopy) found to be greater in the case of 8(P) than 8(M). Accordingly, it is suggested that different folding characteristic of 8(P) and 8(M) ought to affect the physicochemical characteristics of the hosts to permit their effective separation by column chromatography. The absolute configuration of 8(P)/8(M), encompassing right- and left-handed "cups", was determined with the exciton chirality method and also verified in silico (DFT: B3LYP/TZVP). Finally, the twisted baskets are strongly fluorescent due to three naphthalene chromophores, having a high fluorescence quantum yield within the rigid framework of 8(P)/8(M).

The role of magnetic–electric coupling in exciton-coupled ECD spectra: the case of bis-phenanthrenes

The intrinsic magnetic moment of phenanthrene¹B_btransition has a strong impact on exciton-coupled CD spectra of some bis(phenanthrenes).

The Fenna-Matthews-Olson protein revisited: a fully polarizable (TD)DFT/MM description

We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen-bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short-range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex.