Unraveling substituent effects on frontier orbitals of conjugated molecules using an absolutely localized molecular orbital based analysis

A B3LYP-D3 computational study of electronic, structural and torsional dynamic properties of mono-substituted naphthalenes: the effect of the nature and position of substituent

CONTEXT

The effects of selected substituent groups (-CH3, -Br, -CO2CH3, -COOH, and -NH2) and their relative positions on the electronic and structural properties of mono-substituted naphthalenes were investigated theoretically. In order to elucidate the suitability of the studied substituents in different fields including chemistry, spectroscopy, and materials sciences, accurate DFT calculations were performed at the dispersion-corrected B3LYP level of theory (B3LYP-D3/6-311 +  + G(d,p)), and the obtained results were then validated by extensive comparisons with available experimental data. Among the studied substituents, the -NH2 group causes the maximum reduction of the HOMO-LUMO energy gap. This result revealed clearly the suitability of the -NH2 group, compared to other studied substituents, in the chemical synthesis of future organic-semiconductors having small energy gaps. In addition, the level of theory adopted in this study allowed the fine discrimination between the chemical reactivity parameters of the studied congeners, which is very difficult to perform experimentally. On the other hand, the rotational barriers of the studied non-halogen substituent groups were predicted. The greater sensitivity of the rotational barrier heights to the local environments, arising from intra-molecular interactions, was attributed to the -CH3 group. The torsional frequencies, calculated within the harmonic approximation, were also employed to relatively explore the differences between the environments of the same substituent at two different positions. The usefulness of these results can be manifested in the vibrational spectroscopy field, especially, for the IR/ Raman spectral analysis of polycyclic-aromatic congeners.

METHOD

All calculations were conducted within the Density functional theory (DFT) using the so-called dispersion-corrected B3LYP functional (B3LYP-D3) with the carefully selected 6-311 +  + G(d,p) basis set. The B3LYP-D3/6-311 +  + G(d,p) calculations were performed using the Gaussian 09 program, and the obtained results were visualized by employing the GaussView 6.0.16 program.

Effect of regio-specific arylamine substitution on novel π-extended zinc salophen complexes: density functional and time-dependent density functional study on DSSC applications

A series of π-extended salophen-type Schiff-base zinc(ii) complexes, e.g., zinc-salophen complexes (ZSC), were investigated toward potential applications for dye-sensitized solar cells. The ZSC dyes adopt linear-, X-, or π-shaped geometries either with the functionalization of 1 donor/1 acceptor or 2 donors/2 acceptors to achieve a push-pull type molecular structure. The frontier molecular orbitals, light-harvesting properties as well as charge transfer characters against regio-specific substitution of donor/acceptor groups were studied by using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The results reveal that all ZSC dyes of D-ZnS-π-A geometry (where D, S, and A denote to donor, salophen ligand, and acceptor, respectively) exhibit relatively lower HOMO energy compared to the structurally resembled porphyrin dye YD2-o-C8. Natural transition orbital (NTO) and electron-hole separation (EHS) approaches clearly differentiate the linear type YD-series dyes from CL-, AJ1-, and AJ2-series dyes because of poor charge transfer (CT) properties. In contrast, the π-shaped AJ2-series and X-shaped AJ1-series dyes outperform the others in a manner of stronger CT characteristics, broadened UV-vis absorption as well as tunable bandgap simply via substitution of p-ethynylbenzoic acids (EBAs) and arylamine donors at salophen 7,8- and 2,3,12,13-positions, respectively. Both EHS and calculated exciton binding energies suggest the strength of CT character for ZSC dyes with an amino donor in the trend TPA > AN > DPA. This work has provided clear illustration toward molecular design of efficient dyes featuring a zinc-salophen backbone.

Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs

Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.

Functionalizing aromatic compounds with optical cycling centres

Molecular design principles provide guidelines for augmenting a molecule with a smaller group of atoms to realize a desired property or function. We demonstrate that these concepts can be used to create an optical cycling centre, the Ca(I)-O unit, that can be attached to a number of aromatic ligands, enabling the scattering of many photons from the resulting molecules without changing the molecular vibrational state. Such capability plays a central role in quantum state preparation and measurement, as well as laser cooling and trapping, and is therefore a prerequisite for many quantum science and technology applications. We provide further molecular design principles that indicate the ability to optimize and expand this work to an even broader class of molecules. This represents a great step towards a quantum functional group, which may serve as a generic qubit moiety that can be attached to a wide range of molecular structures and surfaces.

Evaluation of molecular photophysical and photochemical properties using linear response time-dependent density functional theory with classical embedding: Successes and challenges

Time-dependent density functional theory (TDDFT) based approaches have been developed in recent years to model the excited-state properties and transition processes of the molecules in the gas-phase and in a condensed medium, such as in a solution and protein microenvironment or near semiconductor and metal surfaces. In the latter case, usually, classical embedding models have been adopted to account for the molecular environmental effects, leading to the multi-scale approaches of TDDFT/polarizable continuum model (PCM) and TDDFT/molecular mechanics (MM), where a molecular system of interest is designated as the quantum mechanical region and treated with TDDFT, while the environment is usually described using either a PCM or (non-polarizable or polarizable) MM force fields. In this Perspective, we briefly review these TDDFT-related multi-scale models with a specific emphasis on the implementation of analytical energy derivatives, such as the energy gradient and Hessian, the nonadiabatic coupling, the spin–orbit coupling, and the transition dipole moment as well as their nuclear derivatives for various radiative and radiativeless transition processes among electronic states. Three variations of the TDDFT method, the Tamm–Dancoff approximation to TDDFT, spin–flip DFT, and spin-adiabatic TDDFT, are discussed. Moreover, using a model system (pyridine–Ag20 complex), we emphasize that caution is needed to properly account for system–environment interactions within the TDDFT/MM models. Specifically, one should appropriately damp the electrostatic embedding potential from MM atoms and carefully tune the van der Waals interaction potential between the system and the environment. We also highlight the lack of proper treatment of charge transfer between the quantum mechanics and MM regions as well as the need for accelerated TDDFT modelings and interpretability, which calls for new method developments.

Effect of the iodine atom position on the phosphorescence of BODIPY derivatives: a combined computational and experimental study

A new BODIPY derivative (o-I-BDP) containing an iodine atom in the ortho position of the meso-linked phenyl group was prepared. Photophysical and electrochemical properties of the molecule were compared to previously reported iodo BODIPY derivatives, as well as to the non-iodinated analog. While in the case of derivatives featuring iodine substituents in the BODIPY core, efficient population of the triplet state is accompanied by a substantial positive shift of the reduction potential compared to pristine BODIPY, o-I-BDP displays phosphorescence and simultaneously maintains the electrochemical properties of unsubstituted BODIPYs. A theoretical investigation was settled to analyze results and rationalize the influence of iodine position on electronic and photophysical properties, with the purpose of preparing a fully organic phosphorescent BODIPY derivative. TD-DFT and spin-orbit coupling calculations shed light on the subtle effects played by the introduction of iodine atom in different positions of BODIPY.

Unusual fluorescence behaviour of a heteroleptic Cu(i) complex featuring strong electron donating groups on a diimine ligand

Synthesis of a novel bulky diimine ligand and its corresponding heteroleptic Cu(i). Unusual fluorescence behavior of a novel Cu(i) complex due to a strong electron-donor diimine ligand.

Photoredox Chemistry with Organic Catalysts: Role of Computational Methods

Organic catalysts have the potential to carry out a wide range of otherwise thermally inaccessible reactions via photoredox routes. Early demonstrated successes of organic photoredox catalysts include one-electron CO₂ reduction and H₂ generation via water splitting. Photoredox systems are challenging to study and design owing to the sheer number and diversity of phenomena involved, including light absorption, emission, intersystem crossing, partial or complete charge transfer, and bond breaking or formation. Designing a viable photoredox route therefore requires consideration of a host of factors such as absorption wavelength, solvent, choice of electron donor or acceptor, and so on. Quantum chemistry methods can play a critical role in demystifying photoredox phenomena. Using one-electron CO₂ reduction with phenylene-based chromophores as an illustrative example, this perspective highlights recent developments in quantum chemistry that can advance our understanding of photoredox processes and proposes a way forward for driving the design and discovery of organic catalysts.

Substituent effects in aqueous solutions of carboxylate salts studied by x-ray absorption spectroscopy at the oxygen K-edge

The present study aims at probing the influence of different substituents of sodium carboxylate salts R-COO^-:Na⁺ in aqueous solutions, with R = H, CH₃, C₂H₅, CH₂Cl, CF₃, and C₆H₅. X-ray absorption spectroscopy was used in the oxygen K-edge region to highlight the effect of R on the energy position of the O1s-to-π_COO* resonance of the carboxylate ion. Ab initio static exchange and ΔSCF calculations are performed and confirm the experimental observations. We qualitatively discuss the results on the basis of the polar properties of these groups as well as on the basis of the π_COO* orbital energy in the ground states, the oxygen 1s orbital ionization energy, and the O1s-to-π_COO* resonance energy.

First-principles studies of substituent effects on squaraine dyes

Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used ab initio theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored via conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications.

Squaraine dyes are candidates for DNA-templated excitonic interactions. This work presents substituent effects on the electronic and photophysicalproperties of squaraine dyes and a correlation between empirical Hammettconstant and those properties.

Natural Blues: Structure Meets Function in Anthocyanins

Choices of blue food colourants are extremely limited, with only two options in the USA, synthetic blue no. 1 and no. 2, and a third available in Europe, patent blue V. The food industry is investing heavily in finding naturally derived replacements, with limited success to date. Here, we review the complex and multifold mechanisms whereby blue pigmentation by anthocyanins is achieved in nature. Our aim is to explain how structure determines the functionality of anthocyanin pigments, particularly their colour and their stability. Where possible, we describe the impact of progressive decorations on colour and stability, drawn from extensive but diverse physico-chemical studies. We also consider briefly how this understanding could be harnessed to develop blue food colourants on the basis of the understanding of how anthocyanins create blues in nature.

Elucidating the Electronic Structure of a Delayed Fluorescence Emitter via Orbital Interactions, Excitation Energy Components, Charge-Transfer Numbers, and Vibrational Reorganization Energies

Recently, Wang and co-workers carried out frontier molecule orbital engineering in the design of m-Cz-BNCz, a thermally activated delayed fluorescence (TADF) molecule that emits pure green light at an external quantum efficiency of 27%. To further understand the underlying molecular design principles, we employed four advanced electronic structure analysis tools. First, an absolutely localized molecular orbitals (ALMO-) based analysis indicates an antibonding combination between the highest occupied molecular orbitals (HOMOs) of the donor 3,6-di-tert-butylcarbazole fragment and the acceptor BNCz fragment, which raises the HOMO energy and red-shifts the fluorescence emission wavelength. Second, excitation energy component analysis reveals that the S₁-T₁ gap is dominated by two-electron components of the excitation energies. Third, charge transfer number analysis, which is extended to use fragment-based Hirshfeld weights, indicates that the S₁ and T₁ excited states of m-Cz-BNCz (within time-dependent density functional theory) have notable charge transfer characters (27% for S₁ and 12% for T₁). This provides a balance between a small single-triplet gap and a substantial fluorescence intensity. Last, a vibrational reorganization energy analysis pinpoints the torsional motion between the BNCz and Cz moieties of m-Cz-BNCz as the source for its wider emission peak than that of p-Cz-BNCz. These four types of analyses are expected to be very valuable in the study and design of other TADF and functional dye molecules.

Hypoxia-activated probe for NIR fluorescence and photoacoustic dual-mode tumor imaging

Construction of tumor microenvironment responsive probe with more than one imaging modality, in particular toward hypoxia of solid tumors, is an appealing yet significantly challenging task. In this work, we designed a hypoxia-activated probe TBTO (Triphenylamine-Benzothiadiazole-Triphenylamine derivative featuring four diethylamino N-Oxide groups) for in vivo imaging. TBTO could undergo bioreduction in a hypoxic microenvironment to yield compound TBT sharing both near-infrared (NIR) aggregation-induced emission and strong twisted intramolecular charge transfer features, which endows the probe with excellent performance in NIR fluorescence and photoacoustic dual-mode tumor imaging. This study offers useful insights into designing a new generation agent for clinical cancer diagnosis.

Doubly N-confused phlorin and phlorinone analogue

A doubly N-confused phlorin and phlorinone analogue were synthesized from a β,β'-linked dipyrromethane precursor and characterized by means of NMR and UV-Vis spectroscopies, X-ray crystallography, and electrochemistry. Solvents have a considerable impact on the optical absorption of the doubly N-confused phlorin so that it can differentiate simple alcohols such as methanol and ethanol.

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.

Hammett Relationship in Oxidase-Mimicking Metal-Organic Frameworks Revealed through a Protein-Engineering-Inspired Strategy

While the unique physicochemical properties of nanomaterials that enable regulation of nanozyme activities are demonstrated in many systems, quantitative relationships between the nanomaterials structure and their enzymatic activities remain poorly understood, due to the heterogeneity of compositions and active sites in these nanomaterials. Here, inspired by metalloenzymes with well-defined metal-ligand coordination, a set of substituted metal-organic frameworks (MOFs) with similar coordination is employed to investigate the relationship between structure and oxidase-mimicking activity. Both experimental results and density functional theory calculations reveal a Hammett-type structure-activity linear free energy relationship (H-SALR) of MIL-53(Fe) (MIL = Materials of Institute Lavoisier) nanozymes, in which increasing the Hammett σ_m value with electron-withdrawing ligands increases the oxidase-mimicking activity. As a result, MIL-53(Fe) NO₂ with the strongest electron-withdrawing NO₂ substituent shows a tenfold higher activity than the unsubstituted MIL-53(Fe). Furthermore, the generality of H-SALR is demonstrated for a range of substrates, one other metal (Cr), and even one other MOF type (MIL-101). Such biologically inspired quantitative studies demonstrate that it is possible to identify quantitative structure-activity relationships of nanozymes, and to provide detailed insight into the catalytic mechanisms as those in native enzymes, making it possible to use these relationships to develop high-performance nanomaterials.

Analysis and visualization of energy densities. II. Insights from linear-response time-dependent density functional theory calculations

Inspired by the analysis of Kohn-Sham energy densities by Nakai and coworkers, we extended the energy density analysis to linear-response time-dependent density functional theory (LR-TDDFT) calculations. Using ethylene-tetrafluoroethylene and oxyluciferin-water complexes as examples, distinctive distribution patterns were demonstrated for the excitation energy densities of local excitations (within a molecular fragment) and charge-transfer excitations (between molecular fragments). It also provided a simple way to compute the effective energy of both hot carriers (particle and hole) from charge-transfer excitations via an integration of the excitation energy density over the donor and acceptor grid points.

Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding

Hybrid quantum mechanical and molecular mechanical (QM/MM) approaches facilitate computational modeling of large biological and materials systems. Typically, in QM/MM, a small region of the system is modeled with an accurate quantum mechanical method and its surroundings with a more efficient alternative, such as a classical force field or the effective fragment potential (EFP). The reliability of QM/MM calculations depends largely on the treatment of interactions between the two subregions, also known as embedding. The polarizable embedding, which allows mutual polarization between solvent and solute, is considered to be essential for describing electronic excitations in polar solvents. In this work, we employ the QM/EFP model and extend the polarizable embedding by incorporating two short-range terms-a charge penetration correction to the electrostatic term and the exchange-repulsion term-both of which are modeled with one-electron contributions to the quantum Hamiltonian. We evaluate the accuracy of these terms by computing excitation energies across 37 molecular clusters consisting of biologically relevant chromophores surrounded by polar solvent molecules. QM/EFP excitation energies are compared to the fully quantum mechanical calculations with the configuration interaction singles (CIS) method. We find that the charge penetration correction diminishes the accuracy of the QM/EFP calculations. On the other hand, while the effect of exchange-repulsion is negligible for most ππ* transitions, the exchange-repulsion significantly improves description of nπ* transitions with blue solvatochromic shifts. As a result, addition of the exchange-repulsion term improves the overall accuracy of QM/EFP. Performances of QM/EFP models remain similar when excitation energies are modeled with cc-pVDZ and aug-cc-pVDZ basis sets.

Computational Analysis of Electron Transfer Kinetics for CO2 Reduction with Organic Photoredox Catalysts

We present a fundamental description of the electron transfer (ET) step from substituted oligo(p-phenylene) (OPP) radical anions to CO₂, with the larger goal of assessing the viability of underexplored, organic photoredox routes for utilization of anthropogenic CO₂. This work varies the electrophilicity of para-substituents to OPP and probes the dependence of rate coefficients and interfragment interactions on the substituent Hammett parameter, σ_p, using constrained density functional theory (CDFT) and energy decomposition analysis (EDA). Large electronic couplings across substituents indicates an adiabatic electron transfer process for reactants at contact. As one might intuitively expect, free energy changes dominate trends in ET rate coefficients in most cases, and rates increase with substituent electron-donating ability. However, we observe an unexpected dip in rate coefficients for the most electron-donating groups, due to the combined impact of flattening free energies and a steep increase in reorganization energies. Our analysis shows that, with decreasing σ_p, flattening OPP LUMO levels lower the marginal increase in free energy. EDA reveals trends in electrostatics and charge transfer interactions between the catalyst and substrate fragments that influence free energy changes across substituents. Reorganization energies do not exhibit a direct dependence on σ_p and are largely similar across systems, with the exception of substituents containing lone pairs of electrons that exhibit significant deformation upon electron transfer. Our study therefore suggests that while a wide range of ET rates are observed, there is an upper limit to rate enhancements achievable by only tuning the substituent electrophilicity.

Regulating the Structures of Self-Assembled Mechanically Interlocked Moleculecular Constructs via Dianion Precursor Substituent Effects

Substituent effects play critical roles in both modulating reaction chemistry and supramolecular self-assembly processes. Using substituted terephthalate dianions (p-phthalic acid dianions; PTADAs), the effect of varying the type, number, and position of the substituents was explored in terms of their ability to regulate the inherent anion complexation features of a tetracationic macrocycle, cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene) (referred to as the Texas-sized molecular box; 1⁴⁺), in the form of its tetrakis-PF₆^- salt in DMSO. Several of the tested substituents, including 2-OH, 2,5-di(OH), 2,5-di(NH₂), 2,5-di(Me), 2,5-di(Cl), 2,5-di(Br), and 2,5-di(I), were found to promote pseudorotaxane formation in contrast to what was seen for the parent PTADA system. Other derivatives of PTADA, including those with 2,3-di(OH), 2,6-di(OH), 2,5-di(OMe), 2,3,5,6-tetra(Cl), and 2,3,5,6-tetra(F) substituents, led only to so-called outside binding, where the anion interacts with 1⁴⁺ on the outside of the macrocyclic cavity. The differing binding modes produced by the choice of PTADA derivative were found to regulate further supramolecular self-assembly when the reaction components included additional metal cations (M). Depending on the specific choice of PTADA derivatives and metal cations (M = Co²⁺, Ni²⁺, Zn²⁺, Cd²⁺, Gd³⁺, Nd³⁺, Eu³⁺, Sm³⁺, Tb³⁺), constructs involving one-dimensional polyrotaxanes, outside-type rotaxanated supramolecular organic frameworks (RSOFs), or two-dimensional metal-organic rotaxane frameworks (MORFs) could be stabilized. The presence and nature of the substituent were found to dictate which specific higher order self-assembled structure was obtained using a given cation. In the specific case of the 2,5-di(OH), 2,5-di(Cl), and 2,5-di(Br) PTADA derivatives and Eu³⁺, so-called MORFs with distinct fluorescence emission properties could be produced. The present work serves to illustrate how small changes in guest substitution patterns may be used to control structure well beyond the first interaction sphere.

Controlling the Cleavage of Carbon-Carbon Bonds To Generate α,α-Difluorobenzyl Carbanions for the Construction of Difluoromethylbenzenes

Controlling the cleavage of carbon-carbon bonds during a chemical reaction is a substantial challenge; however, synthetic methods that accomplish this objective produce valuable and often unexplored reactivity. We have designed a mild process to generate α,α-difluorobenzyl carbanions in the presence of potassium carbonate by exploiting the cleavage of C-C bonds during the release of trifluoroacetate. The initiating reagent is potassium carbonate, which represents an improvement over existing protocols that require a strong base. Fragmentation studies across substituted arenes and heteroarenes were conducted along with computational analyses to elucidate reactivity trends. Furthermore, the mildly generated α,α-difluorobenzyl carbanions from electron-deficient aromatics and heteroaromatic rings can react with aldehydes to create derivatives of difluoromethylbenzenes, which are valuable synthetic targets.

Sulfur-substituted perylene diimides: efficient tuning of LUMO levels and visible-light absorptionviasulfur redox

A series of sulfide and sulfone substituted perylene diimides (PDIs) with different LUMO levels covering a range of 0.72 eV were synthesized through simple sulfur redox chemistry.