Small Polyenes Research Articles

Capturing the Elusive Curve-Crossing in Low-Lying States of Butadiene with Dressed TDDFT.

A striking example of the need to accurately capture states of double-excitation character in molecules is seen in predicting photoinduced dynamics in small polyenes. Due to the coupling of electronic and nuclear motions, the dark 21Ag state, known to have double-excitation character, can be reached after an initial photoexcitation to the bright 11Bu state via crossings of their potential energy surfaces. However, the shapes of the surfaces are so poorly captured by most electronic structure methods, that the crossing is missed or substantially mis-located. We demonstrate that the frequency-dependent kernel of dressed TDDFT beyond Tamm-Dancoff successfully captures the curve-crossing, providing an energy surface close to the highly accurate but more expensive δ-CR-EOMCC(2,3) benchmark reference. This, along with its accurate prediction of the excitation character of the state makes dressed TDDFT a practical and accurate route to electronic structure quantities needed in modeling ultrafast dynamics in molecules.

Geometric Isomerisation of Bifunctional Vinyl Fluoride Linchpins: Stereodivergence in Amide and Polyene Bioisostere Synthesis.

Amide groups are pervasive across the chemical space continuum, where their structural and pharmacological importance, juxtaposed with the hydrolytic vulnerabilities, continues to fuel bioisostere development. Vinyl fluorides have a venerable history as effective mimics (Ψ[CF=CH]) owing to the planarity of the motif and intrinsic polarity of the C(sp2)-F bond. However, emulating the s-cis to the s-trans isomerisation of a peptide bond with fluoro-alkene surrogates remains challenging, and current synthetic solutions only enable access to a single configuration. Through the design of an ambiphilic linchpin based on a fluorinated β-borylacrylate, it has been possible to leverage energy transfer catalysis to affect this unprecedented isomerisation process: this provides geometrically-programmable building blocks that can be functionalized at either terminus. Irradiation at λmax = 402 nm with inexpensive thioxanthone as a photocatalyst enables rapid, effective isomerisation of tri- and tetra-substituted species (up to E/Z 98:2 in 1 h), providing a stereodivergent platform for small molecule amide and polyene isostere discovery. Application of the methodology in target synthesis and initial laser spectroscopic studies are disclosed together with crystallographic analyses of representative products.

Geometric Isomerisation of Bifunctional Alkenyl Fluoride Linchpins: Stereodivergence in Amide and Polyene Bioisostere Synthesis

AbstractAmide groups are pervasive across the chemical space continuum, where their structural and pharmacological importance, juxtaposed with the hydrolytic vulnerabilities, continues to fuel bioisostere development. Alkenyl fluorides have a venerable history as effective mimics (Ψ[CF=CH]) owing to the planarity of the motif and intrinsic polarity of the C(sp2)−F bond. However, emulating the s‐cis to the s‐trans isomerisation of a peptide bond with fluoro‐alkene surrogates remains challenging, and current synthetic solutions only enable access to a single configuration. Through the design of an ambiphilic linchpin based on a fluorinated β‐borylacrylate, it has been possible to leverage energy transfer catalysis to affect this unprecedented isomerisation process: this provides geometrically‐programmable building blocks that can be functionalised at either terminus. Irradiation at λmax=402 nm with inexpensive thioxanthone as a photocatalyst enables rapid, effective isomerisation of tri‐ and tetra‐substituted species (up to E/Z 98 : 2 in 1 h), providing a stereodivergent platform for small molecule amide and polyene isostere discovery. Application of the methodology in target synthesis and initial laser spectroscopic studies are disclosed together with crystallographic analyses of representative products.

Theoretical Studies of Mutual Effects between 6-m-r Hemiketalization and 26-m-r Lactonization in Pimaricin Thioesterase.

Pimaricin is a small polyene macrolide antibiotic and has been broadly used as an antimycotic and antiprotozoal agent in both humans and foods. As a thioesterase in type-I polyketide synthase, pimTE controls the 26-m-r macrolide main chain release in pimaricin biosynthesis. In this work, we sought to determine whether the 6-m-r hemiketal formation was linked to pimTE-catalyzed 26-m-r lactonization. Compared to non-hemiketal TEs, pimTE is characterized by an aspartic acid residue (D179) accessible to the U-turn motif in the acyl-enzyme intermediate. Both the covalent docking and molecular dynamics simulations demonstrate that the reactive conformations for macrocyclic lactonization are drastically promoted by the 6-m-r hemiketal. Moreover, the small-model quantum mechanistic calculations suggest that protic residues can significantly accelerate the 6-m-r hemiketal cyclization. In addition, the post-hemiketal molecular dynamic simulations demonstrate that hydrogen-bonding networks surrounding the substrate U-turn of the hairpin-shaped conformation changes significantly when the 6-m-r hemiketal is formed. In particular, the R-hemiketal intermediate is not only catalyzed by the D179 residue, but also twists the hairpin structure to the 26-m-r lactonizing pre-reaction state. By contrast, the S-hemiketal formation is unlikely catalyzed by D179, which twists the hairpin in an opposite direction. Our results propose that pimTE could be a bi-functional enzyme, which can synergistically catalyze tandem 6-m-r and 26-m-r formations during the main-chain release of pimaricin biosynthesis.

Machine Learning of First-Principles Force-Fields for Alkane and Polyene Hydrocarbons.

Machine learning (ML) interatomic potentials (ML-IAPs) are generated for alkane and polyene hydrocarbons using on-the-fly adaptive sampling and a sparse Gaussian process regression (SGPR) algorithm. The ML model is generated based on the PBE+D3 level of density functional theory (DFT) with molecular dynamics (MD) for small alkane and polyene molecules. Intermolecular interactions are also trained with clusters and condensed phases of small molecules. It shows excellent transferability to long alkanes and closely describes the ab inito potential energy surface for polyenes. Simulation of liquid ethane also shows reasonable agreement with experimental reports. This is a promising initiative toward a universal ab initio quality force-field for hydrocarbons and organic molecules.

Understanding the impact of correlation on bond length alternation in polyenes

This article analyzes the electronic factors governing bond length alternation (BLA) in linear polyenes. The impact of the various effects is illustrated on small all-trans polyenes, namely butadiene, hexatriene and octatetraene prototype molecules. It is well known that self-consistent-field single determinant treatments overestimate the bond length alternation and the paper aims to identify physical effects of correlation which correct this defect. The question is addressed using an orthogonal valence bond-type formalism in which the wave function is expressed in terms of strongly localized bonding and antibonding molecular orbitals. This paper shows that dynamic polarization effects of π orbitals accounted for in the full-π complete active space wave function significantly reduce bond alternation. These effects are brought by single excitations applied on the inter-bond charge transfer determinants. The dynamic polarization of σ bonds, of either CC or CH character, is analyzed afterward by either enlarging the active space or by adding the 1hole-1particle excitations. It is shown that these effects also decrease the BLA and increase the coefficients of the charge transfer determinants. Moreover, the relation with dynamic polarization of ligand-to-metal and metal-to-ligand charge transfer (LMCT and MLCT, respectively) components in magnetic transition-metal compounds is discussed.

Biotechnological production and application of the antibiotic pimaricin: biosynthesis and its regulation.

Pimaricin (natamycin) is a small polyene macrolide antibiotic used worldwide. This efficient antimycotic and antiprotozoal agent, produced by several soil bacterial species of the genus Streptomyces, has found application in human therapy, in the food and beverage industries and as pesticide. It displays a broad spectrum of activity, targeting ergosterol but bearing a particular mode of action different to other polyene macrolides. The biosynthesis of this only antifungal agent with a GRAS status has been thoroughly studied, which has permitted the manipulation of producers to engineer the biosynthetic gene clusters in order to generate several analogues. Regulation of its production has been largely unveiled, constituting a model for other polyenes and setting the leads for optimizing the production of these valuable compounds. This review describes and discusses the molecular genetics, uses, mode of action, analogue generation, regulation and strategies for increasing pimaricin production yields.

The nature of singlet exciton fission in carotenoid aggregates.

Singlet exciton fission allows the fast and efficient generation of two spin triplet states from one photoexcited singlet. It has the potential to improve organic photovoltaics, enabling efficient coupling to the blue to ultraviolet region of the solar spectrum to capture the energy generally lost as waste heat. However, many questions remain about the underlying fission mechanism. The relation between intermolecular geometry and singlet fission rate and yield is poorly understood and remains one of the most significant barriers to the design of new singlet fission sensitizers. Here we explore the structure–property relationship and examine the mechanism of singlet fission in aggregates of astaxanthin, a small polyene. We isolate five distinct supramolecular structures of astaxanthin generated through self-assembly in solution. Each is capable of undergoing intermolecular singlet fission, with rates of triplet generation and annihilation that can be correlated with intermolecular coupling strength. In contrast with the conventional model of singlet fission in linear molecules, we demonstrate that no intermediate states are involved in the triplet formation: instead, singlet fission occurs directly from the initial 1Bu photoexcited state on ultrafast time scales. This result demands a re-evaluation of current theories of polyene photophysics and highlights the robustness of carotenoid singlet fission.

Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems

Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

Cyclization Strategies to Polyenes Using Pd(II)-Catalyzed Couplings of Pinacol Vinylboronates

As a complement to Pd(0)-catalyzed cyclizations, seven Pd(II)-catalyzed cyclization strategies are reported. α,ω-Diynes are selectively hydroborated to bis(boronate esters), which cyclize under Pd(II)-catalysis producing a diverse array of small, medium, and macrocyclic polyenes with controlled E,E, Z,Z, or E,Z stereochemistry. Various functional groups are tolerated including aryl bromides, and applications are illustrated.

Conjugated Molecules Described by a One-Dimensional Dirac Equation.

Starting from the Hückel Hamiltonian of conjugated hydrocarbon chains (ethylene, allyl radical, butadiene, pentadienyl radical, hexatriene, etc.), we perform a simple unitary transformation and obtain a Dirac matrix Hamiltonian. Thus already small molecules are described exactly in terms of a discrete Dirac equation, the continuum limit of which yields a one-dimensional Dirac Hamiltonian. Augmenting this Hamiltonian with specially adapted boundary conditions, we find that all the orbitals of the unsaturated hydrocarbon chains are reproduced by the continuous Dirac equation. However, only orbital energies close to the highest occupied molecular orbital/lowest unoccupied molecular orbital energy are accurately predicted by the Dirac equation. Since it is known that a continuous Dirac equation describes the electronic structure of graphene around the Fermi energy, our findings answer the question to what extent this peculiar electronic structure is already developed in small molecules containing a delocalized π-electron system. We illustrate how the electronic structure of small polyenes carries over to a certain class of rectangular graphene sheets and eventually to graphene itself. Thus the peculiar electronic structure of graphene extends to a large degree to the smallest unsaturated molecule (ethylene).

Theoretical Investigation of Excited States of Large Polyene Cations as Model Systems for Lightly Doped Polyacetylene.

Electronic excitations of polyene cations with chain lengths of up to 101 CH units were investigated as model systems for lightly doped polyacetylene (PA). Since high level ab initio calculations such as complete active space perturbation theory (CASPT2) are limited to systems with about 14 CH units, the performances of time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) were evaluated. It turned out that TDDFT excitations energies are much more accurate for polyene cations than for neutral polyenes. The difference between TDHF and TDDFT excitation energies for the first allowed excited state of C49H51(+) is only 0.30 eV with pure DFT and 0.21 eV with a hybrid functional. For open-shell systems, pure DFT is found to be superior to DFT-hybrid functionals because it does not suffer from spin-contamination. Pure TDDFT excitation energies and oscillator strengths for small open-shell polyene cations compare well with high level ab initio results. Excitation energies are found to be almost independent of the geometry, i.e., the size of the defect. Localization of the defect, however, shifts oscillator strengths from the HOMO-LUMO transition to higher lying excited states of the same symmetry. Lightly doped PA is predicted to exhibit several strong absorptions below 1 eV.

Olefin metathesis for metal incorporation: Preparation of conjugated ruthenium-containing complexes and polymers

Olefin Metathesis for Metal Incorporation (OMMI) was used for the stoichiometric attachment of ruthenium to both small and large polyenes. The dinuclear complexes (PCy 3) 2C1 2Ru CH(CH CH) n CH Ru(PCy 3) 2Cl 2 ( n = 1, 2), were prepared by reacting 2 equiv. of the Grubbs first-generation catalyst (PCy 3) 2C1 2Ru (CHPh)) with 1 equiv. of the appropriate polyene (1,3,5-hexatriene for n = 1 and 1,3,5,7-octatetraene for n = 2). Use of excess hexatriene led to the formation of the monoruthenium complex (PCy 3) 2C1 2Ru CHCH CHCH CH 2. The mono- and di-ruthenium complexes exhibited marked differences in their spectroscopic and electrochemical properties, in addition to their Z– E isomerization rates. Nucleophilic attack of PCy 3 on the end CH 2 of the mono complex was observed, leading to both isomerization and phosphonium products. Extending the OMMI strategy to the second-generation catalyst was also done, despite the reduced initiation rate. The more reactive catalyst (H 2IMes)RuCl 2( CHPh)(3-bromopyridine) 2 allowed for ruthenium incorporation into polyacetylene, leading to the formation of polymers and oligomers with high ruthenium content.

Analysis of long-range NMR spin–spin coupling in polyenes and the π-mechanism

The J-OC-PSP (decomposition of J into Orbital Contributions using Orbital Currents and Partial Spin Polarization) method is applied to analyze NMR spin-spin coupling constants in polyenes, which were calculated using coupled perturbed density functional theory in connection with the B3LYP hybrid functional and a [7s,6p,2d/4s,2p] basis set. The analysis revealed that the pi-mechanism for Fermi contact (FC) spin coupling is based on passive pi-orbital contributions. The pi-orbitals transfer spin information between sigma orbitals (spin-transport mechanism) or increase the spin information of a sigma orbital by an echo effect. The calculated FC(pi) values are rather constant for small polyenes ranging between 3.5-5.5 Hz for a double bond. They decay more slowly with the distance between perturbing and responding nucleus than the sigma contributions to the FC term. The sign of the passive FC(pi) contribution can be assessed from a Dirac vector model. The limits for long-range coupling in a polyene were determined and their practical implications discussed.

Local orbitals for the study of the ???* excitation in polyenes

Localized orbitals have recently been employed in large ab initio calculations, but their use has generally been restricted to ground-state problems. In this work, we analyze the molecular orbitals of the excited states, optimized with a recently proposed local procedure. This method produces local orbitals of the CAS–SCF type, which permits its application to the study of excited states. In particular, we focus on the π→π* triplet excited state in polyenes, calculated using a 2/2 CAS space which includes two electrons in one π and one π* orbitals. In small polyenes, these two singly occupied active orbitals are delocalized all along the molecule. The extent of the delocalization is analyzed by studying polyenes of increasing size. Different polyenes have been studied, going from C14H16 to the C70H72 polyene. The relation of the π→π* excitation with the cation and anion systems is also discussed. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Investigation of the frequency‐dispersion effects on the Raman spectra of small polyenes

AbstractThe time‐dependent Hartree–Fock scheme is applied for determining the frequency‐dependent Raman intensities of C2nH2n+2 molecules with n = 1–3. This analytic scheme, recently developed and implemented in the GAMESS program (Quinet, O.; Champagne, B. J Chem Phys 2001, 115, 6293), takes advantage of the 2n + 1 rule to express the polarizability derivatives in terms of first‐order derivatives. It is found that including frequency dispersion strongly modifies the intensity activy coefficients of many vibrational normal modes and therefore changes the aspect of the spectra. On the other hand, the depolarization ratio is much less frequency dependent. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Electrical response in chemical potential equalization schemes

In this paper we compare the polarization response given by two different chemical potential equalization schemes to be applied to molecular dynamics simulations: the standard fluctuating point charge model (FQ) and the atom–atom charge transfer model (AACT). We have tested the transferability of FQ and AACT parameters, fitted to the polarizability of small size alkanes and polyenes, to large size homologues. We show that the FQ scheme is not adequate for the n-alkanes as it strongly overestimates the polarizability tensor components as the number of carbon atoms increases. The FQ approach has been found more predictive for highly conjugated systems like polyenes, although still unsatisfactory. The AACT parameters tuned on ethane are instead perfectly transferable to alkanes of any length and conformation. The AACT scheme satisfactorily reproduces the polarization response also for highly conjugated systems.

Transition Dipole Orientation of Linear Polyenes: Semiempirical Models and Extrapolation to the Infinite Chain Limit

Linear conjugated polyenes have an electronic transition dipole moment for the strongly allowed 1Ag to 1Bu electronic excitation that is not oriented along the major axis of the polyene chain. In this paper, the experimental values of this off-axis angle are compared to semiempirical and ab initio theoretical predictions. The semiempirical computations are shown to be reliable and are extended to long chains (n = 20). The results are then extrapolated to the infinite chain limit. A nonzero value of 6°−11° for the infinite polyene is suggested by this extrapolation but state of the art ab initio results for a series of small polyenes yield a zero asymptotic value.

Ab Initio Design of Two-Photon Absorbing Materials

AbstractTwo-photon absorbing materials such as conjugated polyenes show promise as nonlinear optical materials. Prediction of two-photon absorption frequencies and cross-sections has been limited by the high level of ab initio calculations that must be carried out in order to accurately calculate excited state energies and transition dipole moments, by the size of many of the compounds of interest, and by the difficulty of handling condensed phase effects in the calculations. We have carried out geometry optimizations at the multi-configurational selfconsistent field level on a small polyene, hexatriene, both in the gas-phase and in solution, with the solvent effects being modeled by the effective fragment potential. The excited-state energies have been calculated by the multiconfigurational quasidegenerate perturbation theory. Transition dipole moment calculations have also been carried out, from which the two-photon absorption cross-section can be estimated. The results indicate that just one or two solvent molecules can have a large effect on the nonlinear optical properties of two-photon absorbing materials.

Pathway approach to ultrafast photochemistry: potential surfaces, conical intersections and isomerizations of small polyenes

The dynamics of molecules, attention to which is being stimulated by modern ultrafast spectroscopy, as well as progress in quantum chemistry are giving new impetus to the approach which follows the detailed pathway of the molecules along the potential energy surfaces from the excited to the ground state. Local properties such as slopes, saddle points, barriers and funnels with conical intersections as exits are taken into account. We show the fruitfulness of this approach by means of new and published experimental results on photochemical pericyclic reactions. The experimental data support the importance of conical intersections and, in some cases, yield a very detailed picture of the dynamics on the potential energy surfaces. We emphasize the relation of the pericyclic potential surfaces to those of cis–trans isomerization and show that, in this case, the geometries of the conical intersections are interrelated and can be intuitively understood. The conical intersections of stilbene and polyenes can be deduced from the prototype of ethylene, and their geometries are supported by photochemical evidence.