Algebraic Diagrammatic Construction Schemes Employing the Intermediate State Formalism: Theory, Capabilities, and Interpretation

Algebraic diagrammatic construction (ADC) schemes represent a family of ab initio methods for the calculation of excited electronic states and electron-detached and -attached states. All ADC methods have been demonstrated to possess great potential for molecular applications, e.g., for the calculation of absorption or photoelectron spectra or electron attachment processes. ADC originates from Green's function or propagator theory; however, most recent ADC developments heavily rely on the intermediate state representation or effective Liouvillian formalisms, which comprise new ADC methods and computational schemes for high-order properties. The different approaches for the calculation of excitation energies, ionization potentials, and electron affinities are intimately related, and they provide a coherent description of these quantities at equivalent levels of theory and with comparable errors. Most quantum chemical program packages contain ADC methods; however, the most complete ADC suite of methods can be found in the recent release of Q-Chem.

Recent progress in atomistic modeling of light-harvesting complexes: a mini review

In this mini review, we focus on recent advances in the atomistic modeling of biological light-harvesting (LH) complexes. Because of their size and sophisticated electronic structures, multiscale methods are required to investigate the dynamical and spectroscopic properties of such complexes. The excitation energies, in this context also known as site energies, excitonic couplings, and spectral densities are key quantities which usually need to be extracted to be able to determine the exciton dynamics and spectroscopic properties. The recently developed multiscale approach based on the numerically efficient density functional tight-binding framework followed by excited state calculations has been shown to be superior to the scheme based on pure classical molecular dynamics simulations. The enhanced approach, which improves the description of the internal vibrational dynamics of the pigment molecules, yields spectral densities in good agreement with the experimental counterparts for various bacterial and plant LH systems. Here, we provide a brief overview of those results and described the theoretical foundation of the multiscale protocol.

On the origin of the inverted singlet-triplet gap of the 5th generation light-emitting molecules

Excitation energies of the lowest singlet and triplet state of molecules whose first excited singlet state lies energetically below the first triplet state have been studied computationally at (time-dependent) density functional theory, coupled-cluster, and second-order multiconfiguration perturbation theory levels. The calculations at the ab initio levels show that the singlet-triplet gap is inverted as compared to the one expected from Hund's rule, whereas all density functionals yield the triplet state as the lowest excited state. Double excitations responsible for the inverted singlet-triplet gap have been identified. Employing the spin-flip and ΔSCF methods, singlet-triplet inversion was obtained at the density functional theory level for some of the studied molecules.

Intramolecular axial α/β-coordination of the 132-terminal pyridyl group to the central zinc atom in chlorophyll-a derivatives

Chlorophyll(Chl)-a derivatives possessing a zinc center and a C13²-alkanoate residue with a terminal pyridyl group were synthesized. Their C13²-epimerically pure products were isolated by preparative reverse phase HPLC. The C13²-stereochemistry resulted in two directed terminal pyridinyl groups that coordinate with the central zinc atom in each stereoisomeric molecule: α/β-intramolecular axial coordination. The asymmetric axial coordinations mimic the immobilization manner of Chl-a in photosynthetically active proteins. The diastereomerically dependent conformers in solution were characterized by 1D/2D NMR, UV-visible absorption, and fluorescence emission as well as circular dichroism (CD) spectroscopy. The ¹H NMR and DOSY spectra revealed that the stereoselectively intramolecular coordination occurred in less coordinative deuterated chloroform, whereas a highly coordinative deuterated pyridine molecule replaced the terminal pyridine moiety as the axial ligand to form a mixture of α/β-coordinated species. Their optical spectra in pyridine were nearly independent of the C13²-stereochemistry and the linkers in the C13²-substituents. The CD bands of β-coordinated species in chloroform were more intense than those of the corresponding α-coordinated stereoisomers, indicating that the former had a larger distortion of the chlorin π-plane than the latter. Therefore, the α-coordinated Chl complex is more conformationally stable than the β-complex.

Exploration for the Optical Properties and Fluorescent Prediction of Nitrotriazole and Nitrofurazan: First-Principles and TD-DFT Calculations

High-energy materials containing azole and furazan have revealed numerous properties; however, the underlying optical properties need to be solved. Meanwhile, the uncertainty for the choice of fluorescent matrix materials and the flexible situational conditions prompted us to estimate the optical and fluorescent properties of 5,5'-dinitro-2H,2H'-3,3'-bi-1,2,4-triazole (DNBT), 4,4'-dinitroazolefurazan (DNAF), and 4,4'-dinitro-3,3'-4,3'-ter-1,2,5-oxadiazole (DNTO). The first-principles calculation with improved dispersion correction terms and time-dependent density functional theory were utilized to calculate the absorbance and excitation energy of DNBT, DNAF, and DNTO, as well as characterization for their crystal structure, electronic structure, molecular orbitals, and so forth, synchronously. In this work, the absorbance anisotropy of DNBT and DNTO is stronger than that of DNAF. The absorbance for each of the (0,0,1) crystal planes in the three compounds is greater than that of the other two crystal planes. Moreover, DNBT has the maximum absorbance on the (0,0,1) crystal plane. The N-N-H from DNBT and N-O-N from DNTO and DNAF are responsible for these results, while N=N in DNAF weakens the performance of N-O-N. UV-vis spectra show that the maximum absorption wavelengths λ_max for DNBT, DNAF, and DNTO are 225, 228, and 201 nm, respectively. The number of five-membered rings and the coplanarity of groups in the intermolecular non-conjugation interaction potentially improve this ability due to the results from the crystal diffraction analysis. In addition, the polarization rate DNBT > DNTO > DNAF based on the molecular orbital analysis and the electrostatic potential calculation implies that the excitation energy of DNBT is less than DNTO, and the excitation energy of DNTO is less than DNAF. This work is beneficial to the expansion of energetic materials into the optical field and the accelerated application process of the related industry.

The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol

The function of light-harvesting complexes is determined by a complex network of dynamic interactions among all the different components: the aggregate of pigments, the protein, and the surrounding environment. Complete and reliable predictions on these types of composite systems can be only achieved with an atomistic description. In the last few decades, there have been important advances in the atomistic modeling of light-harvesting complexes. These advances have involved both the completeness of the physical models and the accuracy and effectiveness of the computational protocols. In this Perspective, we present an overview of the main theoretical and computational breakthroughs attained so far in the field, with particular focus on the important role played by the protein and its dynamics. We then discuss the open problems in their accurate modeling that still need to be addressed. To illustrate an effective computational workflow for the modeling of light harvesting complexes, we take as an example the plant antenna complex CP29 and its H111N mutant.

Assessment of the Ab Initio Bethe-Salpeter Equation Approach for the Low-Lying Excitation Energies of Bacteriochlorophylls and Chlorophylls

Bacteriochlorophyll and chlorophyll molecules are crucial building blocks of the photosynthetic apparatus in bacteria, algae, and plants. Embedded in transmembrane protein complexes, they are responsible for the primary processes of photosynthesis: excitation energy and charge transfer. Here, we use ab initio many-body perturbation theory within the GW approximation and Bethe-Salpeter equation (BSE) approach to calculate the electronic structure and optical excitations of bacteriochlorophylls a, b, c, d, and e and chlorophylls a and b. We systematically study the effects of the structure, basis set size, partial self-consistency in GW, and the underlying exchange-correlation approximation and compare our calculations with results from time-dependent density functional theory, multireference RASPT2, and experimental literature results. We find that optical excitations calculated with GW+BSE are in excellent agreement with experimental data, with an average deviation of less than 100 meV for the first three bright excitations of the entire family of (bacterio)chlorophylls. Contrary to state-of-the-art time-dependent density functional theory (TDDFT) with an optimally tuned range-separated hybrid functional, this accuracy is achieved in a parameter-free approach. Moreover, GW+BSE predicts the energy differences between the low-energy excitations correctly and eliminates spurious charge transfer states that TDDFT with (semi)local approximations is known to produce. Our study provides accurate reference results and highlights the potential of the GW+BSE approach for the simulation of larger pigment complexes.

Divergent Carbocatalytic Routes in Oxidative Coupling of Benzofused Heteroaryl Dimers: A Mechanistic Update

Mildly thermal air or HNO3 oxidized activated carbons catalyse oxidative dehydrogenative couplings of benzo[b]fused heteroaryl 2,2'-dimers, e.g., 2-(benzofuran-2-yl)-1H-indole, to chiral 3,3'-coupled cyclooctatetraenes or carbazole-type migrative products under O2 atmosphere. DFT calculations show that the radical cation and the Scholl-type arenium cation mechanisms lead to different products with 2-(benzofuran-2-yl)-1H-indole, being in accord with experimental product distributions.

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.

Accurate Computation of the Absorption Spectrum of Chlorophyll a with Pair Natural Orbital Coupled Cluster Methods

The ability to accurately compute low-energy excited states of chlorophylls is critically important for understanding the vital roles they play in light harvesting, energy transfer, and photosynthetic charge separation. The challenge for quantum chemical methods arises both from the intrinsic complexity of the electronic structure problem and, in the case of biological models, from the need to account for protein–pigment interactions. In this work, we report electronic structure calculations of unprecedented accuracy for the low-energy excited states in the Q and B bands of chlorophyll a. This is achieved by using the newly developed domain-based local pair natural orbital (DLPNO) implementation of the similarity transformed equation of motion coupled cluster theory with single and double excitations (STEOM-CCSD) in combination with sufficiently large and flexible basis sets. The results of our DLPNO–STEOM-CCSD calculations are compared with more approximate approaches. The results demonstrate that, in contrast to time-dependent density functional theory, the DLPNO–STEOM-CCSD method provides a balanced performance for both absorption bands. In addition to vertical excitation energies, we have calculated the vibronic spectrum for the Q and B bands through a combination of DLPNO–STEOM-CCSD and ground-state density functional theory frequency calculations. These results serve as a basis for comparison with gas-phase experiments.

Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. Here we briefly outline the challenges associated with such computations and review the progress made in this field.

Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation

Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light-harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins.

Dimerization Behavior of Methyl Chlorophyllide a as the Model of Chlorophyll a in the Presence of Water Molecules-Theoretical Study

A dimerization of methyl chlorophyllide a molecules and a role of water in stabilization and properties of methyl chlorophyllide a dimers were studied by means of symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), density-functional theory (DFT), and time-dependent DFT approaches. The quantification of various types of interactions, such as π-π stacking, coordinative, and hydrogen bonding by applying the F-SAPT energy decomposition scheme shows the major role of the magnesium atom and the pheophytin macrocycle in the stability of the complex. The examination of interaction energy components with respect to a mutual orientation of monomers and in the presence or absence of water molecules reveals that the dispersion energy is the main binding factor of the interaction, while water molecules tend to weaken the attraction between methyl chlorophyllide a species. The dimerization can be seen in computed UV-vis spectra, and results in a doubling of the lowest peaks, as compared to the monomer spectrum, and in an intensity rise of the lowest 1.8 and 2.4 eV peaks at a cost of the 3.5 eV peaks for the majority of dimer configurations. The complexation of water has little effect on the peaks' position; however, it affects the overall shape of simulated spectra through changes in peak intensities, which is strongly dependent on the structure of the complex. The VCD spectra for the dimers show several characteristic features attributed to the interaction of substituting groups and/or water ligand attached to macrocycle groups belonging to different monomers. VCD is sensitive to the type of the formed dimer, but not to the number of water molecules it contains. This and several other features, as well as the differential UV-vis spectra, may serve as the indicator of the presence of a given dimer structure in the experiment.