Bond Length Alternation Research Articles

Anharmonic Motion in the Crystal Structure of 2-Mercaptopyridone

With the present study, we revise earlier results about the title compound 2-mercaptopyridone in which the deformation density was determined from an X–N study in 1982 (X-ray, neutron diffraction). In the current X–X study (X-ray, X-ray), anharmonic motion parameters for the atoms were included and it resulted in a very clean deformation density map without the unexplainable features of the literature results. The presence of anharmonic effects is supported by a study of the thermal expansion in the temperature range 100–260 K. A topological study of the electron density confirms a bond length alternation in the six-membered ring. The calculation of the electrostatic potential indicates that the N–H⋯S hydrogen bond is an electrostatic interaction, and that other attractive intermolecular contacts are probably dispersive.

Bond Length Alternation and Internal Dynamics in Model Aromatic Substituents of Lignin.

Broadband microwave spectra were recorded over the 2-18 GHz frequency range for a series of four model aromatic components of lignin; namely, guaiacol (ortho-methoxy phenol, G), syringol (2,6-dimethoxy phenol, S), 4-methyl guaiacol (MG), and 4-vinyl guaiacol (VG), under jet-cooled conditions in the gas phase. Using a combination of 13 C isotopic data and electronic structure calculations, distortions of the phenyl ring by the substituents on the ring are identified. In all four molecules, the rC(1)-C(6) bond between the two substituted C-atoms lengthens, leading to clear bond alternation that reflects an increase in the phenyl ring resonance structure with double bonds at rC(1)-C(2) , rC(3)-C(4) and rC(5)-C(6) . Syringol, with its symmetric methoxy substituents, possesses a microwave spectrum with tunneling doublets in the a-type transitions associated with H-atom tunneling. These splittings were fit to determine a barrier to hindered rotation of the OH group of 1975 cm-1 , a value nearly 50 % greater than that in phenol, due to the presence of the intramolecular OH⋅⋅⋅OCH3 H-bonds at the two equivalent planar geometries. In 4-methyl guaiacol, methyl rotor splittings are observed and used to confirm and refine an earlier measurement of the three-fold barrier V3 =67 cm-1 . Finally, 4-vinyl guaiacol shows transitions due to two conformers differing in the relative orientations of the vinyl and OH groups.

Bond length alternation- and data mining-assisted exploration of molecular adsorbates with π-conjugation and amines for two-dimensional halide perovskite surface

Bond length alternation- and data mining-assisted exploration of molecular adsorbates with π-conjugation and amines for two-dimensional halide perovskite surface

The structure of a pentachromium(II) extended metal atom chain at 3 K: Cotton's conjecture proven.

We provide definitive experimental proof that the archetypal string-like compound [Cr5(tpda)4(NCS)2] has alternating long and short Cr-Cr separations in the solid state, as conjectured by F. A. Cotton, rather than essentially equally spaced Cr atoms, as initially claimed (H2tpda = N2,N6-di(pyridin-2-yl)pyridine-2,6-diamine). Single-crystal X-ray data collected from 292 to 3 K revealed that the misinterpretation is caused by pseudo-merohedral twinning and that bond length alternation is enhanced at low temperature.

Para-Azaquinodimethane based quinoidal polymers for opto-electronic applications: impact of donor units on the opto-electronic properties

para-Azaquinodimethane (p-AQM) based quinoidal–donor (Q–D) polymers have been synthesized following a strategy for enhancing the backbone planarity and control the bond length alternation (BLA).

Helical versus linear Jahn-Teller distortions in allene and spiropentadiene radical cations.

The allene radical cation can be stabilized both by Jahn-Teller distortion of the bond lengths and by torsion of the end-groups. However, only the latter happens and the allene radical cation relaxes into a twisted D2 symmetry structure with equal double-bond lengths. Here we revisit the Jahn-Teller distortion of allene and spiropentadiene by assessing the possible implications of their helical π-systems in the radical cations. We describe a general relation between the structure and the number of π-electrons in spiroconjugated and linearly conjugated systems. Through constrained optimizations we compare the stabilization achieved by bond-length alternation and axial torsion in the radical cations, which we explain with a simple frontier molecular orbital (MO) picture. While structurally different, allene and spiropentadiene have similar helical frontier MOs. Both cations relax through torsion because the stabilization of their helical frontier MOs is bigger than that which can be achieved by linear π-conjugation. Electrohelicity thus manifests in molecular systems with partial occupation as a helical π-conjugation effect, which evidently provides more stabilization than its linear counterpart in terms of the Jahn-Teller distortion. This mechanism may be a driving factor for the relaxation in a range of spiroconjugated and linearly conjugated cationic systems.

Chemisorption-Induced Formation of Biphenylene Dimer on Ag(111).

We report an example that demonstrates the clear interdependence between surface-supported reactions and molecular-adsorption configurations. Two biphenyl-based molecules with two and four bromine substituents, i.e., 2,2'-dibromobiphenyl (DBBP) and 2,2',6,6'-tetrabromo-1,1'-biphenyl (TBBP), show completely different reaction pathways on a Ag(111) surface, leading to the selective formation of dibenzo[e,l]pyrene and biphenylene dimer, respectively. By combining low-temperature scanning tunneling microscopy, synchrotron radiation photoemission spectroscopy, and density functional theory calculations, we unravel the underlying reaction mechanism. After debromination, a biradical biphenyl can be stabilized by surface Ag adatoms, while a four-radical biphenyl undergoes spontaneous intramolecular annulation due to its extreme instability on Ag(111). Such different chemisorption-induced precursor states between DBBP and TBBP consequently lead to different reaction pathways after further annealing. In addition, using bond-resolving scanning tunneling microscopy and scanning tunneling spectroscopy, we determine with atomic precision the bond-length alternation of the biphenylene dimer product, which contains 4-, 6-, and 8-membered rings. The 4-membered ring units turn out to be radialene structures.

A Peierls Transition in Long Polymethine Molecular Wires: Evolution of Molecular Geometry and Single-Molecule Conductance

Molecules capable of mediating charge transport over several nanometers with minimal decay in conductance have fundamental and technological implications. Polymethine cyanine dyes are fascinating molecular wires because up to a critical length, they have no bond-length alternation (BLA) and their electronic structure resembles a one-dimensional free-electron gas. Beyond this threshold, they undergo a symmetry-breaking Peierls transition, which increases the HOMO-LUMO gap. We have investigated cationic cyanines with central polymethine chains of 5-13 carbon atoms (Cy3+-Cy11+). The absorption spectra and crystal structures show that symmetry breaking is sensitive to the polarity of the medium and the size of the counterion. X-ray crystallography reveals that Cy9·PF6 and Cy11·B(C6F5)4 are Peierls distorted, with high BLA at one end of the π-system, away from the partially delocalized positive charge. This pattern of BLA distribution resembles that of solitons in polyacetylene. The single-molecule conductance is essentially independent of molecular length for the polymethine salts of Cy3+-Cy11+ with the large B(C6F5)4- counterion, but with the PF6- counterion, the conductance decreases for the longer molecules, Cy7+-Cy11+, because this smaller anion polarizes the π-system, inducing a symmetry-breaking transition. At higher bias (0.9 V), the conductance of the shorter chains, Cy3+-Cy7+, increases with length (negative attenuation factor, β = -1.6 nm-1), but the conductance still drops in Cy9+ and Cy11+ with the small polarizing PF6- counteranion.

Tuning the Quantum Chemical Properties of Flavins via Modification at C8.

Flavins are central to countless enzymes but display different reactivities depending on their environments. This is understood to reflect modulation of the flavin electronic structure. To understand changes in orbital natures, energies, and correlation over the ring system, we begin by comparing seven flavin variants differing at C8, exploiting their different electronic spectra to validate quantum chemical calculations. Ground state calculations replicate a Hammett trend and reveal the significance of the flavin π-system. Comparison of higher-level theories establishes CC2 and ACD(2) as methods of choice for characterization of electronic transitions. Charge transfer character and electron correlation prove responsive to the identity of the substituent at C8. Indeed, bond length alternation analysis demonstrates extensive conjugation and delocalization from the C8 position throughout the ring system. Moreover, we succeed in replicating a particularly challenging UV/Vis spectrum by implementing hybrid QM/MM in explicit solvents. Our calculations reveal that the presence of nonbonding lone pairs correlates with the change in the UV/Vis spectrum observed when the 8-methyl is replaced by NH2, OH, or SH. Thus, our computations offer routes to understanding the spectra of flavins with different modifications. This is a first step toward understanding how the same is accomplished by different binding environments.

Tuning the Quantum Chemical Properties of Flavins via Modification at C8.

Flavins are central to countless enzymes but display different reactivities depending on their environments. This is understood to reflect modulation of the flavin electronic structure. To understand changes in orbital natures, energies, and correlation over the ring system, we begin by comparing seven flavin variants differing at C8, exploiting their different electronic spectra to validate quantum chemical calculations. Ground state calculations replicate a Hammett trend and reveal the significance of the flavin π-system. Comparison of higher-level theories establishes CC2 and ACD(2) as methods of choice for characterization of electronic transitions. Charge transfer character and electron correlation prove responsive to the identity of the substituent at C8. Indeed, bond length alternation analysis demonstrates extensive conjugation and delocalization from the C8 position throughout the ring system. Moreover, we succeed in replicating a particularly challenging UV/Vis spectrum by implementing hybrid QM/MM in explicit solvents. Our calculations reveal that the presence of nonbonding lone pairs correlates with the change in the UV/Vis spectrum observed when the 8-methyl is replaced by NH2, OH, or SH. Thus, our computations offer routes to understanding the spectra of flavins with different modifications. This is a first step toward understanding how the same is accomplished by different binding environments.

Cover Feature: Quinoid‐Aromatic Resonance for Very Small Optical Energy Gaps in Small‐Molecule Organic Semiconductors: A Naphthodithiophenedione‐oligothiophene Triad System (Chem. Eur. J. 63/2021)

Near-infrared absorbing properties are of great interest in organic semiconducting materials for near-infrared-active optoelectronic applications. A series of thienoquinoid-containing molecules are presented that show very small optical energy gaps of down to 0.72 eV, corresponding to a wavelength of 1700 nm. The key to the very small optical energy gaps is an efficient quinoid-aromatic resonance along the conjugated backbones that significantly reduces the bond length alternation. More information can be found in the Full Paper by K. Kawabata and K. Takimiya (DOI: 10.1002/chem.202102663).

Dominant Role of Quantum Anharmonicity in the Stability and Optical Properties of Infinite Linear Acetylenic Carbon Chains.

Carbyne, an infinite-length straight chain of carbon atoms, is supposed to undergo a second order phase transition from the metallic bond-symmetric cumulene (═C═C═)∞ toward the distorted insulating polyyne chain (-C≡C-)∞ displaying bond-length alternation. However, recent synthesis of ultra long carbon chains (∼6000 atoms, [Nat. Mater., 2016, 15, 634]) did not show any phase transition and detected only the polyyne phase, in agreement with previous experiments on capped finite carbon chains. Here, by performing first-principles calculations, we show that quantum-anharmonicity reduces the energy gain of the polyyne phase with respect to the cumulene one by 71%. The magnitude of the bond-length alternation increases by increasing temperature, in stark contrast with a second order phase transition, confining the cumulene-to-polyyne transition to extremely high and unphysical temperatures. Finally, we predict that a high temperature insulator-to-metal transition occurs in the polyyne phase confined in insulating nanotubes with sufficiently large dielectric constant due to a giant quantum-anharmonic bandgap renormalization.

Quinoid-Aromatic Resonance for Very Small Optical Energy Gaps in Small-Molecule Organic Semiconductors: A Naphthodithiophenedione-oligothiophene Triad System.

Organic semiconductors with very small optical energy gaps have attracted a lot of attention for near-infrared-active optoelectronic applications. Herein, we present a series of donor-acceptor-donor (D-A-D) organic semiconductors consisting of a highly electron-deficient naphtho[1,2-b:5,6-b']dithiophene-2,7-dione quinoidal acceptor and oligothiophene donors that show very small optical energy gaps of down to 0.72 eV in the solid state. Investigation of the physicochemical properties of the D-A-D molecules as well as theoretical calculations of their electronic structures revealed an efficient intramolecular interaction between the quinoidal acceptor and the aromatic oligothiophene donors in the D-A-D molecules; this significantly enhances the backbone resonance and thus reduces the bond length alternation along the π-conjugated backbones. Despite the very small optical energy gaps, the D-A-D molecules have low-lying frontier orbital energy levels that give rise to air-stable ambipolar carrier transport properties with hole and electron mobilities of up to 0.026 and 0.043 cm2 V-1 s-1 , respectively, in field-effect transistors.

Quinoidal Small Molecule Containing Ring-Extended Termini for Organic Field-Effect Transistors.

In this work, we synthesized and characterized two quinoidal small molecules based on benzothiophene modified and original isatin terminal units, benzothiophene quinoidal thiophene (BzTQuT) and quinoidal thiophene (QuT), respectively, to investigate the effect of introducing a fused ring into the termini of quinoidal molecules. Extending the terminal unit of the quinoidal molecule affected the extension of π-electron delocalization and decreased the bond length alternation, which led to the downshifting of the collective Raman band and dramatically lowering the band gap. Organic field-effect transistor (OFET) devices in neat BzTQuT films showed p-type transport behavior with low hole mobility, which was ascribed to the unsuitable film morphology for charge transport. By blending with an amorphous insulating polymer, polystyrene, and poly(2-vinylnaphthalene), an OFET based on a BzTQuT film annealed at 150 °C exhibited improved mobility up to 0.09 cm2 V–1 s–1. This work successfully demonstrated that the extension of terminal groups into the quinoidal structure should be an effective strategy for constructing narrow band gap and high charge transporting organic semiconductors.

Internal Conversion between Bright (11Bu+) and Dark (21Ag-) States in s-trans-Butadiene and s-trans-Hexatriene.

Internal conversion (IC) between the two lowest singlet excited states, 11Bu+ and 21Ag-, of s-trans-butadiene and s-trans-hexatriene is investigated using a series of single- and multi- reference wave function and density functional theory (DFT) methodologies. Three independent types of the equation-of-motion coupled-cluster (EOMCC) theory capable of providing an accurate and balanced description of one- as well as two-electron transitions, abbreviated as δ-CR-EOMCC(2,3), DIP-EOMCC(4h2p){No}, and DEA-EOMCC(4p2h){Nu} or DEA-EOMCC(3p1h,4p2h){Nu}, consistently predict that the 11Bu+/21Ag- crossing in both molecules occurs along the bond length alternation coordinate. However, the analogous 11Bu+ and 21Ag- potentials obtained with some multireference approaches, such as CASSCF and MRCIS(D), as well as with the linear-response formulation of time-dependent DFT (TDDFT), do not cross. Hence, caution needs to be exercised when studying the low-lying singlet excited states of polyenes with conventional multiconfigurational methods and TDDFT. The multistate many-body perturbation theory methods, such as XMCQDPT2, do correctly reproduce the curve crossing. Among the simplest and least expensive computational methodologies, the DFT approaches that incorporate the contributions of doubly excited configurations, abbreviated as MRSF (mixed reference spin-flip) TDDFT and SSR(4,4), accurately reproduce our best EOMCC results. This is highly promising for nonadiabatic molecular dynamics simulations in larger systems.

Spin-Spin Interactions in One-Dimensional Assemblies of a Cumulene-Based Singlet Biradical.

The synthesis of phenalenyl-endcapped [5]cumulene as a cumulene-based singlet biradical and the spin correlation changes of one-dimensional aggregates are described. The high propensity for self-aggregation of phenalenyl rings and the introduction of bulky substituents into the appropriate positions led to the formation of a one-dimensional chain assembly. Single-crystal X-ray structural analysis indicated that the bond length alternation of the cumulene chain increased with decreasing temperature, along with improved overlapping of the phenalenyl rings. Variable-temperature Raman spectroscopy and magnetic susceptibility measurements revealed that a localized spin pair within the molecule decouples at low temperatures, and a continuum spin system involving intra- and intermolecular spin-spin interactions emerges in the one-dimensional chain.

Spin–Spin Interactions in One‐Dimensional Assemblies of a Cumulene‐Based Singlet Biradical

AbstractThe synthesis of phenalenyl‐endcapped [5]cumulene as a cumulene‐based singlet biradical and the spin correlation changes of one‐dimensional aggregates are described. The high propensity for self‐aggregation of phenalenyl rings and the introduction of bulky substituents into the appropriate positions led to the formation of a one‐dimensional chain assembly. Single‐crystal X‐ray structural analysis indicated that the bond length alternation of the cumulene chain increased with decreasing temperature, along with improved overlapping of the phenalenyl rings. Variable‐temperature Raman spectroscopy and magnetic susceptibility measurements revealed that a localized spin pair within the molecule decouples at low temperatures, and a continuum spin system involving intra‐ and intermolecular spin–spin interactions emerges in the one‐dimensional chain.

How to Predict Excited State Geometry by Using Empirical Parameters Obtained from Franck-Condon Analysis of Optical Spectrum.

Excited state geometries of molecules can be calculated with highly reliable wavefunction schemes. Most of such schemes, however, are applicable to small molecules and can hardly be viewed as error-free for excited state geometries. In this study, a theoretical approach is presented in which the excited state geometries of molecules can be predicted by using vibrationally resolved experimental absorption spectrum in combination with the theoretical modelling of vibrational pattern based on Franck-Condon approximation. Huang-Rhys factors have been empirically determined and used as input for revealing the structural changes occurring between the ground and the excited state geometries upon photoexcitation. Naphthalene molecule has been chosen as a test case to show the robustness of the proposed theoretical approach. Predicted 1B2u excited state geometry of the naphthalene has similar but slightly different bond length alternation pattern when compared with the geometries calculated with CIS, B3LYP, and CC2 methods. Excited state geometries of perylene and pyrene molecules are also determined with the presented theoretical approach. This powerful method can be applied to other molecules and specifically to relatively large molecules rather easily as long as vibrationally resolved experimental spectra are available to use.

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.

Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2.

Channelrhodopsins are photosensitive proteins that trigger flagella motion in single-cell algae and have been successfully utilized in optogenetic applications. In optogenetics, light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using quantum mechanical/molecular mechanical molecular dynamics and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified time-dependent density functional theory. In contrast to previous reports, we found that different hydrogen-bonding networks-involving the retinal protonated Schiff base, the putative counterions E162 and D292, and water molecules-had only a small impact on the absorption spectrum. However, in the case of deprotonated E162, increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factors were found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 and 82%, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.